Biology subjects

Williams, A. J.

Publications and source records attributed to Williams, A. J..

14 recordsLinked to original sources

bioRxiv2026

Developmental Cerebellar Pathology in Mouse Models of SCN2A Premature Termination Codon Variants

Autism spectrum disorder is a neurodevelopmental disorder with both genetic and environmental contributors. SCN2A, the gene which encodes the alpha subunit of the voltage-gated sodium channel Nav1.2, is a known monogenetic risk factor for autism spectrum disorder. The cerebellum is frequently implicated in autism spectrum disorder and other neurodevelopmental disorders but has largely been unexplored in relation to SCN2A variants, especially from a developmental perspective. Nav1.2 is highly expressed within the cerebellum, specifically within cerebellar granule neurons, where it helps to drive action potential generation and propagation. Cerebellar granule neuron activity and maturation is crucial for shaping the development and morphology of the rest of the cerebellar cortex. Here we investigated early-postnatal cerebellar development in two mouse models carrying patient-derived SCN2A premature termination codon variants, Scn2a-p.Y84X and -p.R1627X. Overall, both Scn2a premature termination codon variant mouse lines displayed largely normal physical development and unaffected non-cerebellar developmental milestones. Scn2aY84X/+ mice, but not Scn2aR1627X/+ mice, demonstrated alterations in cerebellar-driven motor behaviors, specifically faster performance in the surface righting reflex and cliff avoidance compared to wildtype littermates. Coinciding with the behavioral findings, Scn2a variants had divergent and age-dependent effects on cerebellar glutamatergic presynaptic marker expression, indicating that some, but not all, Scn2a premature termination codons impair glutamatergic synapse development. Both Scn2a variants exhibited changes to cerebellar cytoarchitecture, such as reductions in Purkinje cell density and soma size, which was more prominent in Scn2aY84X/+ mice, and faster migration of cerebellar granule neurons from the external granule layer to the internal, indicating a possible shift in the timing of cerebellar maturation. Our results situate the cerebellum as an early site for SCN2A pathophysiology and establish that cerebellar consequences of SCN2A premature termination codon variants may be position- and age-dependent, suggesting that influences beyond simple heterozygous loss of Nav1.2 drive phenotypes. Our characterization of how Scn2a premature termination codon variants differentially impair cerebellar development may help explain the heterogeneity of clinical presentations of SCN2A loss of function variants and potentially inform upon the timing of therapeutic intervention.

neuroscience↗

bioRxiv2025

Position-dependent effects of SCN2A premature stop codons on neuronal excitability and behavior

SCN2A encodes the voltage-gated sodium channel NaV1.2, a key determinant of spike initiation and propagation in glutamatergic neurons. Premature termination codons are often assumed to produce uniform haploinsufficiency via nonsense-mediated decay, yet whether distinct SCN2A premature stop codons yield equivalent molecular, cellular, and behavioral outcomes remains unknown. We generated two mouse lines carrying patient mutations--Scn2aY84X/+ (p.Tyr84UAA; early coding sequence) and Scn2aR1627X/+(p.Arg1627UGA; terminal coding exon)--on a C57BL/6J background. Allele-specific expression was quantified by targeted next-generation sequencing of whole-brain reverse transcribed cDNA. NaV1.2 protein was measured in half-brain lysates by automated western blot and ex vivo whole-cell recordings were obtained from layer 5b pyramidal-tract neurons in medial prefrontal cortex. A panel of behavioral assays assessed locomotion/exploration, motor learning, anxiety-like behavior, sociability, sensorimotor gating, and seizure susceptibility. Allele-specific RNA handling diverged by position: mRNA carrying Y84X engaged partial nonsense-mediated decay, whereas R1627X transcripts were at allelic balance. Despite this difference in RNA fate, NaV1.2 protein was comparably reduced in both lines. Electrophysiologically, both premature termination codon mutations slowed the action-potential upstroke, with a larger decrement in Scn2aY84X/+than in Scn2aR1627X/+. Spike threshold was depolarized only in Scn2aY84X/+, whereas Scn2aR1627X/+ remained similar to wild type. Frequency-current relations showed reduced firing at near-rheobase inputs in both mutants, with responses approaching wild type at stronger currents. Behaviorally, locomotion, sociability, and sensorimotor gating were preserved. Both lines exhibited increased grooming--consistent with restrictive, repetitive behavior; Scn2aY84X/+alone showed greater exploration in the elevated-risk context and a male-predominant deficit in rotarod learning. In maximal electroshock testing, mortality was lower in both lines without differences in seizure threshold or severity. Our results show that distinct SCN2A premature termination codons are not equivalent to one another, nor to a uniform haploinsufficient state. An early, nonsense-mediated decay-competent premature stop codon (Y84X) and a terminal-exon one (R1627X) produce partially overlapping yet allele-specific effects on neuronal excitability and behavior. These findings establish premature termination codon position as a determinant of phenotype, supporting allele-tailored mechanistic studies and therapeutic strategies.

neuroscience↗

bioRxiv2025

Comparison of AAV9-driven motor neuron transduction following different CNS-directed delivery methods in mice

AbstractO_ST_ABSBackgroundC_ST_ABSGene therapies are promising for diseases previously considered incurable. Adeno-associated virus serotype 9 (AAV9) demonstrates remarkable tropism for motor neurons (MNs) and represents an exciting candidate to target genetic causes of motor neuron diseases like amyotrophic lateral sclerosis (ALS). However, systemic delivery risks immunogenicity and off-target effects, therefore localised delivery to the CNS is advantageous. New methodWe assessed MN transduction in wild-type mice using AAV9-controlled, cytomegalovirus-promoter driven, enhanced GFP expression. Intra-cisterna magna (ICM) and intra-cerebroventricular (ICV) methods were compared. Four weeks post-delivery, GFP positivity in MN and astrocytes were quantified via immunohistochemical approaches and viral genome copy number determined by qPCR. ResultsAll delivery methods achieved high MN transduction in lumbar spinal cord (>68%). Unilateral ICV delivery provided the highest and most consistent levels (89 {+/-} 3%), and minimal peripheral viral copies. ICV delivery resulted in higher astrocytic transduction, most notably in the cortex. Brainstem MN transduction was high with all methods (>55%). We failed to find evidence of neuronal transduction in motor cortex. Viral genome copies trended higher in spinal cord and brainstem with ICV approaches, however further work is required to understand how bilateral delivery leads to such profound increases. Comparison to existing methodsWhilst several routes of administration into cerebrospinal fluid exist, direct comparisons for targeting MNs in vivo remain limited. ConclusionsOverall, consideration of gene therapy delivery methods is critical to ensure that the most appropriate administration route is chosen to reach MNs effectively, selectively, and at high levels to exact biological effects. HighlightsO_LICSF delivery of AAV9 targets >68% of lumbar spinal cord (SC) motor neurons C_LIO_LIUnilateral ICV yields high and consistent lumbar SC motor neuron transduction (>88%) C_LIO_LIUnilateral ICV results in the lowest number of peripheral viral copies C_LIO_LIICV targets significantly more astrocytes, particularly in cortex C_LIO_LIBilateral ICV leads to significantly higher viral copies in the liver C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/662642v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@bd83a5org.highwire.dtl.DTLVardef@df63aorg.highwire.dtl.DTLVardef@a09142org.highwire.dtl.DTLVardef@1a0887a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Deletion of the voltage-gated calcium channel gene, CaV1.3, reduces Purkinje cell dendritic complexity without altering cerebellar-mediated eyeblink conditioning

Genetic variation in CACNA1D, the gene that encodes the pore-forming subunit of the L-type calcium channel CaV1.3, has been associated with increased risk for neuropsychiatric disorders that display abnormalities in cerebellar structures. We sought to clarify if deletion of CaV1.3 in mice would induce abnormalities in cerebellar cortex cytoarchitecture or synapse morphology. Since CaV1.3 is highly expressed in cerebellar molecular layer interneurons (MLIs) and L-type channels appear to regulate GABA release from MLIs, we hypothesized that loss of CaV1.3 would alter GABAergic synapses between MLIs and Purkinje cells (PCs) without altering MLI numbers or PC structure. As expected, we did not observe changes in the numbers of MLIs or PCs. Surprisingly, CaV1.3 KO mice do have decreased complexity of PC dendritic arbors without differences in the number or structure of GABAergic synapses onto PCs. Loss of CaV1.3 was not associated with impaired acquisition of delay eyeblink conditioning. Therefore, our data suggest that CaV1.3 expression is important for PC structure but does not affect other measures of cerebellar cortex morphology or cerebellar function as assessed by delay eyeblink conditioning.

neuroscience↗

bioRxiv2025

Reference Library for Suspect Non-targeted Screening of Environmental Toxicants Using Ion Mobility Spectrometry-Mass Spectrometry

As our health is affected by the xenobiotic chemicals we are exposed to, it is important to rapidly assess these molecules both in the environment and our bodies. Targeted analytical methods coupling either gas or liquid chromatography with mass spectrometry (GC-MS or LC-MS) are commonly utilized in current exposure assessments. While these methods are accepted as the gold standard for exposure analyses, they often require multiple sample preparation steps and more than 30 minutes per sample. This throughput limitation is a critical gap for exposure assessments and has resulted in an evolving interest in using ion mobility spectrometry and MS (IMS-MS) for non-targeted studies. IMS-MS is a unique technique due to its rapid analytical capabilities (millisecond scanning) and detection of a wide range of chemicals based on unique collision cross section (CCS) and mass-to-charge (m/z) values. To increase the availability of IMS-MS information for exposure studies, here we utilized drift tube IMS-MS to evaluate 4,685 xenobiotic chemical standards from the Environmental Protection Agency Toxicity Forecaster (ToxCast) program including pesticides, industrial chemicals, pharmaceuticals, consumer products, and per- and polyfluoroalkyl substances (PFAS). In the analyses, 3,993 [M+H]+, [M+Na]+, [M-H]- and [M+]+ ion types were observed with high confidence and reproducibility ([≤]1% error intra-laboratory and [≤]2% inter-laboratory) from 2,140 unique chemicals. These values were then assembled into an openly available multidimensional database and uploaded to PubChem to enable rapid IMS-MS suspect screening for a wide range of environmental contaminants, faster response time in environmental exposure assessments, and assessments of xenobiotic-disease connections.

ecology↗

bioRxiv2024

The GPR4 antagonist NE-52-QQ57 increases survival, mitigates the hyperinflammatory response and reduces viral load in SARS-CoV-2-infected K18-hACE2 transgenic mice

COVID-19 (Coronavirus disease 19) is caused by infection with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the respiratory system and other organ systems. Tissue injuries resulting from viral infection and host hyperinflammatory responses may lead to moderate to severe pneumonia, systemic complications, and even death. While anti-inflammatory agents have been used to treat patients with severe COVID-19, their therapeutic effects are limited. GPR4 (G protein-coupled receptor 4) is a pro-inflammatory receptor expressed on vascular endothelial cells, regulating leukocyte infiltration and inflammatory responses. In this study, we evaluated the effects of a GPR4 antagonist, NE-52-QQ57, in the SARS-CoV-2-infected K18-hACE2 transgenic mouse model. Our results demonstrated that GPR4 antagonist treatment increased the survival rate in this severe COVID-19 mouse model. The inflammatory response, characterized by proinflammatory cytokines and chemokines, was reduced in the GPR4 antagonist group compared with the vehicle group. Additionally, both SARS-CoV-2 RNA copy numbers and infectious viral titers in the mouse lung were decreased in the GPR4 antagonist group. The percentage of SARS-CoV-2 antigen-positive mouse brains was also decreased in the GPR4 antagonist group compared to the vehicle group. Furthermore, the GPR4 antagonist inhibited SARS-CoV-2 propagation in Vero E6 cells. Together, these results suggest that GPR4 antagonism may be explored as a novel approach for the treatment of COVID-19 and other similar viral diseases.

pharmacology and toxicology↗

bioRxiv2024

Predicting purification process fit of monoclonal antibodies using machine learning

0In early stage development of therapeutic monoclonal antibodies, assessment of ease of purification process development typically requires extensive experimentation. However, upstream protein expression and downstream purification experiments are often in conflict with timeline pressures and material constraints, limiting the number of molecules and process conditions that can reasonably be assessed. Recently, high-throughput batch-binding screen data along with improved molecular descriptors have enabled development of robust quantitative structure-property relationship (QSPR) models which predict monoclonal antibody chromatographic binding behavior from the amino acid sequence. This work describes a QSPR strategy for in silico monoclonal antibody purification process fit assessment. Principal Component Analysis is applied to extract a one-dimensional basis for comparison of molecular chromatographic binding behavior from multi-dimensional high-throughput batch-binding screen data. Kernel Ridge Regression is employed to predict the first principal component for new molecular sequences. This workflow is demonstrated with a set of 97 monoclonal antibodies for five chromatography resins in two salt types across a range of pH and salt concentrations. Model development benchmarks four descriptor sets from biophysical structural models and protein language models. The investigation illustrates the value QSPR models can provide to purification process fit assessment, and selection of resins and operating conditions from sequence alone.

bioinformatics↗

bioRxiv2024

Introducing identification probability for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.

biochemistry↗

bioRxiv2023

16p11.2 Microduplication is Associated with Lobule-Specific Abnormalities in Cerebellar Structure and Function

The 16p11.2 microduplication (16p11.2dp/+) is associated with several neuropsychiatric disorders including schizophrenia, autism spectrum disorder, bipolar disorder, intellectual disability, and attention deficit/hyperactivity disorder (ADHD). Cerebellar abnormalities have been increasingly implicated in these neuropsychiatric disorders, including those conferred by 16p11.2 microduplication. In 16p11.2dp/+ mouse models, the cerebellum is a site of transcriptional dysregulation, and cerebellar microcephaly has been reported in humans with 16p11.2 microduplication. Despite mounting evidence indicating a role for the cerebellum in neuropsychiatric disorders associated with this CNV, cerebellar cellular structure and cerebellar-dependent behavior in mice with 16p11.2 microduplication remain uncharacterized. To address this, we histologically labeled Purkinje cells (PCs) and molecular layer interneurons (MLIs) in a mouse model of 16p11.2 microduplication. We did not find any structural differences in cerebellar lobule IV/V, nor did we observe impairments in gait or motor coordination, behaviors that are associated with lobule IV/V. In contrast, we discovered a significant increase in calbindin/parvalbumin-positive PCs mislocalized to the granule layer of cerebellar lobule VI in 16p11.2dp/+ mice compared to wild-type (WT) littermates. Additionally, we found a significant decrease in parvalbumin-positive MLIs without a decrease in total DAPI-positive cell counts in lobule VI of 16p11.2dp/+ mice compared to WT littermates. Cerebellar lobule VI is associated with delay eyeblink conditioning, and 16p11.2dp/+ mice are impaired in cerebellum-dependent associative learning on this task. Specifically, 16p11.2dp/+ mice showed deficits in both conditioned response (CR) percentage and CR onset latency relative to WT mice. These results suggest that lobule VI-specific alterations to PC localization and MLI parvalbumin expression in 16p11.2dp/+ mice impair both cerebellar learning and adaptive timing of cerebellar-driven, conditioned responses. Thus, we have identified novel structural and functional alterations in the cerebellum that are associated with 16p11.2 microduplication. Importantly, individuals with schizophrenia and ADHD also show CR acquisition deficits in delay eyeblink conditioning. Together, these data suggest that the behavioral impairments in 16p11.2dp/+ mice resemble impairments seen in neuropsychiatric disorders linked to 16p11.2 microduplication in humans. Further investigation of cerebellar cortex neurons in 16p11.2dp/+ mice may provide insights into the pathogenesis of neuropsychiatric disorders linked to this copy number variant.

neuroscience↗

bioRxiv2023

Cerebellar Morphological Differences in Bipolar Disorder Type I

BackgroundThe neural underpinnings of bipolar disorder (BD) remain poorly understood. The cerebellum is ideally positioned to modulate emotional regulation circuitry yet has been understudied in BD. Previous studies have suggested differences in cerebellar activity and metabolism in BD, however findings on cerebellar structural differences remain contradictory. MethodsWe collected 3T anatomical MRI scans from participants with (N = 131) and without (N = 81) BD type I. Differences in cerebellar volumes were assessed along with factors that influence the results. ResultsThe cerebellar cortex was smaller bilaterally in participants with BD. Polygenic propensity score (bipolar N = 103, control N = 64) did not predict any cerebellar volumes, suggesting that non-genetic factors may have greater influence on the cerebellar volume difference we observed in BD. Cerebellar white matter volumes increased with more adverse childhood events, but we did not observe any associations with parental psychiatric illness. We also evaluated time from onset and symptom burden and found no associations with cerebellar volumes, suggesting neurodevelopment may differ prior to onset. Finally, we found taking sedatives was associated with larger cerebellar white matter and non-significantly larger cortical volume. LimitationsThis study was cross-sectional, limiting interpretation of possible mechanisms. Most of our participants were White, which could limit the generalizability. Additionally, we did not account for potential polypharmacy interactions. ConclusionsThese findings suggest that external influences, such as medications, may influence cerebellum structure in BD and may mask underlying differences. Accounting for medication may be critical for consistent findings in future studies.

neuroscience↗

bioRxiv2023

Functional Connectivity of the Cerebellar Vermis in Bipolar Disorder and Associations with Mood

PurposeStudies of the neural underpinnings of bipolar type I disorder have focused on the emotional control network. However, there is also growing evidence for cerebellar involvement, including abnormal structure, function, and metabolism. Here, we sought to assess functional connectivity of the cerebellum with the cerebrum in bipolar disorder and to assess whether any effects might depend on mood. MethodsThis cross-sectional study enrolled 128 participants with bipolar type I disorder and 83 control comparison participants who completed a 3T MRI scan, which included anatomical imaging as well as resting state BOLD imaging. Functional connectivity of the cerebellar vermis to all other brain regions was assessed. Based on quality control metrics of the fMRI data, 109 participants with bipolar disorder and 79 controls were used to in the statistical analysis comparing connectivity of the vermis as well as associations with mood. Potential impacts of medications were also explored. ResultsFunctional connectivity of the cerebellar vermis in bipolar disorder was found to differ significantly between brain regions known to be involved in the control of emotion, motor function, and language. While connections with emotion and motor control areas were significantly stronger in bipolar disorder, connection to a region associated language production was significantly weaker. In the participants with bipolar disorder, ratings of depression and mania were inversely associated with vermis functional connectivity. No effect of medications on these connections were observed. ConclusionTogether the findings suggest cerebellum may play a compensatory role in bipolar disorder and when it can no longer fulfill this role, depression and mania develop. The proximity of the cerebellar vermis to the skull may make this region a potential target for treatment with transcranial magnetic stimulation.

neuroscience↗

bioRxiv2022

A low-cost recombinant glycoconjugate vaccine confers immunogenicity and protection against enterotoxigenic Escherichia coli infections in mice

Enterotoxigenic Escherichia coli (ETEC) is the primary etiologic agent of travelers diarrhea and a major cause of diarrheal disease and death worldwide, especially in infants and young children. Despite significant efforts over the past several decades, an affordable vaccine that significantly reduces mortality and morbidity associated with moderate to severe diarrhea among children under the age of 5 years remains an unmet aspirational goal. Here, we describe robust, cost-effective biosynthetic routes that leverage glycoengineered strains of non-pathogenic Escherichia coli or their cell-free extracts for producing conjugate vaccine candidates against two of the most prevalent O serogroups of ETEC, O148 and O78. Specifically, we demonstrate site-specific installation of O-antigen polysaccharides (O-PS) corresponding to these serogroups onto licensed carrier proteins using the oligosaccharyltransferase PglB from Campylobacter jejuni. The resulting conjugates stimulate strong O-PS-specific humoral responses in mice and elicit IgG antibodies that possess bactericidal activity against the cognate pathogens. We also show that one of the prototype conjugates decorated with serogroup O148 O-PS confers protection against ETEC infection in mice. We anticipate that our bacterial cell-based and cell-free platforms will enable creation of multivalent formulations with the potential for broad ETEC serogroup protection and increased access through low-cost biomanufacturing.

synthetic biology↗

bioRxiv2020

Deletion of the voltage-gated calcium channel, CaV1.3, causes deficits in motor performance and associative learning

L-type voltage-gated calcium channels are important regulators of neuronal activity and are widely expressed throughout the brain. One of the major L-type voltage-gated calcium channel isoforms in the brain is CaV1.3. Mice lacking CaV1.3 are reported to have impairments in fear conditioning and depressive-like behaviors, which have been linked to CaV1.3 function in the hippocampus and amygdala. Genetic variation in CaV1.3 has been linked to a variety of psychiatric disorders, including autism and schizophrenia, which are associated with altered motor learning, associative learning, and social function. Here, we explored whether CaV1.3 plays a role in these behaviors. We found that CaV1.3 knockout mice have deficits in rotarod learning despite normal locomotor function. Deletion of CaV1.3 is also associated with impaired gait adaptation and associative learning on the Erasmus Ladder. We did not observe any impairments in CaV1.3 knockout mice on assays of anxiety-like, depression-like, or social preference behaviors. Our results suggest an important role for CaV1.3 in neural circuits involved in motor learning and concur with previous data showing its involvement in associative learning.

neuroscience↗

bioRxiv2017

Exposing the Exposome with Global Metabolomics andCognitive Computing

Concurrent exposure to a wide variety of xenobiotics and their combined toxic effects can play a pivotal role in health and disease, yet are largely unexplored. Investigating the totality of these exposures, i.e. the exposome, and their specific biological effects constitutes a new paradigm for environmental health but still lacks high-throughput, user-friendly technology. We demonstrate the utility of mass spectrometry-based global exposure metabolomics combined with tailored database queries and cognitive computing for comprehensive exposure assessment and the straightforward elucidation of biological effects. The METLIN Exposome database has been redesigned to help identify environmental toxicants, food contaminants and supplements, drugs, and antibiotics as well as their biotransformation products, through its expansion with over 700,000 chemical structures to now include more than 950,000 unique small molecules. More importantly, we demonstrate how the XCMS/METLIN platform now allows for the readout of the biological effect of a toxicant through metabolomic-derived pathway analysis and further, cognitive computing provides a means of assessing the role of a potential toxicant. The presented workflow addresses many of the outstanding methodological challenges current exposome research is facing and will serve to gain a deeper understanding of the impact of environmental exposures and combinatory toxic effects on human health.

epidemiology↗