Biology subjects

Pedersen, M. G.

Publications and source records attributed to Pedersen, M. G..

9 recordsLinked to original sources

bioRxiv2025

FLIM-FRET Imaging of AMPA Receptors: New Principle for Subtype-Specific Elucidation

-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) mediate fast excitatory neurotransmission, and their subunit composition (GluA1-4) critically shapes synaptic strength and plasticity. Discriminating AMPAR subtypes at the molecular level remains challenging with conventional techniques. Here, we applied Forster resonance energy transfer (FRET) combined with fluorescence-lifetime imaging microscopy (FLIM) to resolve subtype-specific AMPAR assemblies. Cyan fluorescent protein (CFP) and HALO domain were genetically introduced into GluA1-3 subunits to make intrareceptor FRET pairs. Self-labeling protein (SLP) domains such as SNAP and HALO were used with cell-impermeable substrates to selectively label surface-expressed receptors. This approach identified di-heterotetrameric GluA1/2 and GluA2/3 assemblies at the HEK293T cell membrane, whereas GluA1/3 failed to form di-heteromers. These findings demonstrate the FLIM-FRET method as a tool for differentiating AMPAR subtypes in living cells, providing a foundation for studying subtype-specific receptor organization in excitatory synapses.

neuroscience↗

bioRxiv2025

On the role of L-type Ca2+ and BK channels in a biophysical model of cartwheel interneurons

Cartwheel interneurons (CWCs) in the auditory system exhibit a range of activity patterns relevant to auditory function and pathologies. Although experiments have shown how these patterns can vary across individual neurons and can change under pharmacological manipulations, the field has lacked a computational framework in which to explore the contributions of particular currents to these observations and to generate new predictions about the effects of manipulations on CWCs. In this work, we address this deficiency by presenting a conductance-based CWC computational model. This model captures the diversity of CWC activity patterns observed experimentally and suggests parameter changes that may underlie differences across cells. Bifurcation analysis of this model provides an explanation of how distinct dynamic mechanisms contribute to these differences, while direct simulations suggest how cells with different baseline dynamics will respond to variations in certain experimentally-accessible potassium and calcium channel conductances. In addition to the full model that we introduce, we present a reduced model that preserves CWC dynamic regimes. We classify the reduced model variables in terms of distinct dynamic timescales and show that the key transitions in dynamic patterns can be explained based on equilibria of the averaged dynamics of the slowest model variables, in a regime where the faster model variables exhibit oscillations. Overall, this study predicts how changes in parameters will influence CWC behavior, suggests how bifurcations contribute to changes in CWC dynamics, and provides a theoretical foundation that supports our simulation findings. Author summaryCartwheel interneurons (CWCs) are the most common class of inhibitory interneurons in an auditory brainstem region involved in sound localization and are believed to be important for auditory processing and pathologies. Distinct patterns of CWC activity have been observed experimentally in a variety of conditions. In this work, we present two novel computational models that simulate the factors contributing to CWC dynamics. By harnessing this framework, we are able to reveal the contributions of key ion currents to modulating CWC activity. Indeed, we find that the factors present in CWC neurons can produce a complicated dynamic landscape, with a wide range of output patterns possible as the relative strengths of these factors are varied. Overall, our models represent useful tools for understanding experimental results and generating new predictions about CWC behavior. In particular, in the more reduced of the two models, we can perform mathematical analysis to make more detailed predictions about the effects of current modulation on whether CWC neurons will exhibit regular spiking or more complex forms of outputs.

neuroscience↗

bioRxiv2024

Structural Determinants for Activity of the Antidepressant Vortioxetine at Human and Rodent 5-HT3 receptors

Vortioxetine (VTX) is a recent antidepressant that targets a variety of serotonin receptors. We investigate the drugs molecular mechanism of operation at serotonin 5-HT3 receptors (5-HT3R), which features two mysterious properties: VTX acts differently on rodent and human 5-HT3R; VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT3R and an agonist bound-like state of the human 5-HT3R, in line with the functional profile of the drug. We report four human 5-HT3R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.

biochemistry↗

bioRxiv2023

Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels

Cyclic AMP controls neuronal ion channel activity. For example hyperpolarizationactivated cyclic nucleotide-gated (HCN) and M-type K+ channels are activated by cAMP. These effects have been suggested to be involved in astrocyte control of neuronal activity, for example, by controlling the action potential firing frequency. In cortical neurons, cAMP can induce mixed-mode oscillations (MMOs) consisting of small-amplitude, subthreshold oscillations separating complete action potentials, which lowers the firing frequency greatly. We extend a model of neuronal activity by including HCN and M channels, and show that it can reproduce a series of experimental results under various conditions involving and inferring with cAMP-induced activation of HCN and M channels. In particular, we find that the model can exhibit MMOs as found experimentally, and argue that both HCN and M channels are crucial for reproducing these patterns. To understand how M and HCN channels contribute to produce MMOs, we exploit the fact that the model is a multiple-time scale dynamical system. We show that the MMO mechanism does not rely on the very slow dynamics of HCN and M channel gating variables, since the model is able to produce MMOs even when HCN and M channel activity is kept constant. In other words, the cAMP-induced increase in the average activity of HCN and M channels allows MMOs to be produced by the fast subsystem alone. We show that the fast-subsystem MMOs are due to a folded node singularity, a geometrical structure well known to be involved in the generation of MMOs in slow-fast systems. Besides raising new mathematical questions for multiple-timescale systems, our work is a starting point for future research on how cAMP signalling, for example resulting from interactions between neurons and glial cells, affects neuronal activity via HCN and M channels. Author summaryNeurons use the frequency of electrical signals called action potentials to encode information, and various messenger systems interact with ion channels to control this so-called firing frequency. Recent experimental recordings show that the intracellular messenger cAMP can induce mixed-mode oscillations (MMOs) consisting of small-amplitude, subthreshold oscillations separating action potentials, which lowers the firing frequency greatly. We extend a recent mathematical model of neuronal electrical activity to investigate how MMOs occur from interactions between ion channels regulated by cAMP. Our simulations reproduce a range of experimental results, including cAMP-induced MMOs. We explain the model dynamics using modern geometrical methods that exploit the different timescales in the model. Our analyses show that the slow dynamics of cAMP-regulated HCN and M ion channels is not crucial for creating MMOs, but rather that the cAMP-induced increase in their average activity is important. Our analyses suggest that both HCN and M channels are crucial for MMOs and controlling the firing frequency, which has implications for our understanding of how astrocytes control neuronal information processing. Moreover, our study raises new mathematical questions related to how slow dynamical variables modify MMOs.

neuroscience↗

bioRxiv2018

Genome-wide Association Study of Anxiety and Stress-related Disorders in the iPSYCH Cohort

Anxiety and stress-related disorders (ASRD) are among the most common mental disorders with the majority of patients suffering from additional disorders. Family and twin studies indicate that genetic and environmental factors are underlying their etiology. As ASRD are likely to configure various expressions of abnormalities in the basic stress-response system, we conducted a genome-wide association study including 12,655 cases with various anxiety and stress-related diagnoses and 19,225 controls. Standard association analyses were performed supplemented by a framework of sensitivity analyses. Variants in PDE4B showed consistent association with ASRD across a wide range of our analyses. In mice models, alternations in PDE4B expression were observed in those mice displaying anxious behavior after exposure to chronic stress. We also showed that 28% of the variance in ASRD was accounted for by common variants and that the genetic signature of ASRD overlapped with psychiatric traits, educational outcomes, obesity-related phenotypes, smoking, and reproductive success.

genetics↗

bioRxiv2017

A genome-wide association study for shared risk across major psychiatric disorders in a nation-wide birth cohort implicates fetal neurodevelopment as a key mediator

There is mounting evidence that seemingly diverse psychiatric disorders share genetic etiology, but the biological substrates mediating this overlap are not well characterized. Here, we leverage the unique iPSYCH study, a nationally representative cohort ascertained through clinical psychiatric diagnoses indicated in Danish national health registers. We confirm previous reports of individual and cross-disorder SNP-heritability for major psychiatric disorders and perform a cross-disorder genome-wide association study. We identify four novel genome-wide significant loci encompassing variants predicted to regulate genes expressed in radial glia and interneurons in the developing neocortex during midgestation. This epoch is supported by partitioning cross-disorder SNP-heritability which is enriched at regulatory chromatin active during fetal neurodevelopment. These findings indicate that dysregulation of genes that direct neurodevelopment by common genetic variants results in general liability for many later psychiatric outcomes.

genetics↗

bioRxiv2017

Elevated polygenic burden for autism is associated with differential DNA methylation at birth.

BackgroundAutism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis.\n\nMethodsWe quantified neonatal methylomic variation in 1,263 infants - of whom ~50% went on to subsequently develop ASD - using DNA isolated from a unique collection of archived blood spots taken shortly after birth. We used matched genetic data from the same individuals to examine the molecular consequences of ASD genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings.\n\nResultsAlthough we did not identify specific loci showing consistent changes in neonatal DNA methylation associated with later ASD, we found a significant association between increased polygenic burden for autism and methylomic variation at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8.\n\nConclusionsThis study is the largest analysis of DNA methylation in ASD yet undertaken and the first to integrate both genetic and epigenetic variation at birth in ASD. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.

genetics↗

bioRxiv2017

The iPSYCH2012 case-cohort sample: New directions for unravelling genetic and environmental architectures of severe mental disorders

The iPSYCH consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born 1981-2005 including 1,472,762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3,540), autism (N=16,146), ADHD (N=18,726), and affective disorder (N=26,380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30,000). Within the sample of 86,189 individuals, a total of 57,377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.

genetics↗

bioRxiv2017

Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

Attention-Deficit/Hyperactivity Disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of school-age children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no individual variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, revealing new and important information on the underlying biology of ADHD. Associations are enriched in evolutionarily constrained genomic regions and loss-of-function intolerant genes, as well as around brain-expressed regulatory marks. These findings, based on clinical interviews and/or medical records are supported by additional analyses of a self-reported ADHD sample and a study of quantitative measures of ADHD symptoms in the population. Meta-analyzing these data with our primary scan yielded a total of 16 genome-wide significant loci. The results support the hypothesis that clinical diagnosis of ADHD is an extreme expression of one or more continuous heritable traits.

genetics↗