Biology subjects

Thompson, D.

Publications and source records attributed to Thompson, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Inference and validation of causal genetic interactions in aging human fibroblasts

In the past hundred years, the fraction of fatalities due to age-related disease has risen from an envied minority of cases to the leading cause of death and economic morbidity in the developed world. Despite notable advances in understanding aging, its intrinsic complexity has prevented major therapeutic breakthroughs. This complexity extends across all systems and scales in an organism, leaving a "fingerprint of aging" across every aspect of cell and tissue behavior whose interrelationships are difficult to untangle. Compounding this problem, human aging is observed largely through cross-sectional rather than longitudinal data. Whether such data retain sufficient dynamical information to reveal causal interactions is unclear. Here we show that they can. Using convergent cross mapping (CCM), a method for identifying causal interactions in nonlinear dynamical systems, we reconstruct directed genetic interactions from age-ordered, cross-sectional transcriptomic data - recovering dynamics from populations rather than individuals. Applied to dermal fibroblasts from 490 GTEx donors, CCM identifies a genome-scale causal network whose topology, together with age-dependent changes in gene expression, predicts candidate drivers of aging. We tested these predictions experimentally by single-gene overexpression in fibroblasts from 55-year-old donors. Single-cell RNA sequencing confirmed 53.8% of testable CCM-predicted causal interactions, showing that dynamics reconstructed from cross-sectional populations contain experimentally recoverable information about gene-gene interactions. This 53.8% additionally exceeded that produced by multiple comparanda methods and a random null. We then asked whether this information could identify interventions that reverse cellular aging. Independent transcriptomic and high-dimensional morphological assays show that CCM-selected perturbations shift old fibroblasts toward states characteristic of young cells. These two measures of rejuvenation are strongly correlated, and the strongest interventions cause a majority of 55-year-old cells to resemble cells from 25-year-old donors. Thus, causal dynamics can be recovered from cross-sectional population data and used to identify interventions in aging. More generally, the results suggest a way to distinguish genes that change with age from genes that drive those changes, providing experimentally testable targets for altering the aging phenotype.

systems biology↗

bioRxiv2026

Genetic susceptibility to obesity-related asthma and its modulation by sequelae of obesity

RationaleAsthma is a multifactorial disease with a role of genetic susceptibility and environmental exposures. These aspects are poorly understood for pediatric obesity-related asthma, a phenotype of non-allergic asthma. ObjectiveTo quantify gene by environment interactions in obesity-related asthma MethodsUsing expression quantitative trait loci (eQTLs) as measure of genetic susceptibility, and obesity-mediated effects on anthropometrics, metabolic measures, and T helper cell proportions as biological sequelae of obesogenic environment, we quantified the association of eQTLs with asthma burden, and its modulation by obesity-mediated effects, in primary cohort of 144 children, and validation cohort of 101 children. Measurements and Main ResultsOf the 3,904 eQTLs associated with gene expression, up to 30% were associated with pulmonary function indices, including FVC, FEV1, TLC, FRC and IC, and were enriched for African ancestry. These eQTLs encoded for antigen presentation, cell mobility, autophagy, small GTPase signal transduction, fatty acid metabolism, and chromosome segregation pathways. Neck and waist circumference, insulin resistance, leptin and adiponectin levels, and T helper 1 and 17 cell proportions attenuated association of up to 51% eQTLs with pulmonary function, which encoded for all but fatty acid metabolism and chromosome segregation pathways. eQTLs associated with ATF6 and MEI1 retained significance. eQTLs for RNASET2, FBLN5, STX2, HEATR3 and SERPINB6 genes were associated with pulmonary function in the validation cohort. ConclusionsWe report novel genetic susceptibility markers of asthma burden in pediatric obesity-related asthma that are enriched for African ancestry and are partly attenuated by truncal fat load and obesity-mediated inflammation and metabolic dysregulation.

immunology↗

bioRxiv2026

Epidemiology and phylodynamic analysis of canine distemper virus circulating in Michigan, USA

Canine distemper virus (CDV) is a highly contagious generalist pathogen that can cause significant mortality in domestic dogs and wild mammals. Due to the fast-evolving nature of CDV and its global spread, epizootic events and the emergence of new strains have been frequently reported. In Michigan, CDV surveillance from 2008 to 2018 was previously reported. Here, we combine and extend these data through 2023 to bring together 16 years of CDV surveillance in wild mammals in Michigan. We also sequenced CDV strains originating from both wildlife and domestic dogs to examine viral evolution across host populations. To facilitate interpretation of these data in both local and global contexts, we developed a Nextstrain workflow for CDV, enabling interactive visualization of viral evolution over time and geographic space. Our data show persistence of CDV in Michigan mammals during the study period and point to temporal, geographic, and host factors associated with CDV occurrence. Phylogenetic analysis using the newly built Nextstrain workflow showed that three CDV lineages--America-3, America-5, and Canada-1--are currently circulating in both wild and domestic animals in Michigan. The Nextstrain workflow enables reproducible, scalable integration of genomic sequencing into local surveillance and provides an updateable platform for ongoing and future surveillance efforts. This study demonstrates the value of coupling wildlife surveillance and diagnostic testing with genomic sequencing to identify lineage turnover and anticipate changes in viral behavior.

microbiology↗

bioRxiv2026

The NMR Exchange Format (NEF): Specification and Applications

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of structural restraints, and related metadata, thus allowing for data exchange across software platforms. By enabling direct, lossless transfer of information, NEF simplifies multi-software workflows, improves reproducibility, and supports FAIR (Findable, Accessible, Interoperable, Reusable) data principles. We describe the NEF specification, its current implementation across commonly used NMR software packages, and its application in areas including biomolecular structure determination, metabolomics, and ligand screening. Testing demonstrates that NEF can be used to exchange complete datasets between programs without loss of information or functionality. We also outline recent developments and future directions, such as inclusion of NMR relaxation data and support for non-standard residue topologies. NEFs growing adoption highlights its potential as a unifying standard for NMR data, enabling more efficient, transparent and collaborative research.

biochemistry↗

bioRxiv2026

New paradigm of CRISPR spacerome for classification of global Escherichia coli lineages

Our research team has recently identified a proof-of-concept for a previously unrecognized spacerome signature in a subset of globally distributed E. coli. Motivated by our initial observation, we pursued a more in-depth CRISPR spacerome analysis, which revealed a novel insight in discrimination of global E. coli sequence type (ST) lineages. We systematically retrieved publicly available E. coli complete genomes, analyzed and compared CRISPR spacerome of globally distributed strains. We found that global strains harbored spacerome that has remained conserved spaceromes for decades across multiple continents. Strains with the conserved spacerome belong to specific ST lineages of clinical importance. In addition, most protospacers were assigned to Gammaproteobacteria and Caudoviricetes. Our findings reveal unexpected long-term conservation of CRISPR spaceromes and their potential as high-resolution markers for E. coli epidemiological tracking.

microbiology↗

bioRxiv2025

A Mechanism-Aware Dual Attention Deep Model for Molecular-Protein Binding Affinity Prediction with Enhanced Generalizability and Interpretability

Accurate prediction of molecular-protein binding affinity (MPBA) is paramount in drug discovery, yet current computational models often lack generalizability, interpretability, and explicit mechanistic understanding. To address these limitations, we introduce BindMecNet (Binding Mechanism Network), a novel mechanism-aware, multi-scale deep model. BindMec-Nets core innovation lies in its Interfacial Interaction Prediction Module, which explicitly predicts an atom-residue level interaction map, serving as a crucial mechanistic inductive bias. This map guides a Mechanism-Aware Dual Attention Interaction Module, ensuring that information exchange between protein and ligand representations is focused on genuinely interacting regions, fostering a deeper understanding of binding mechanisms. We employ a robust two-stage training strategy: initial pre-training on PDBBind with a multi-task loss (affinity and interaction prediction), followed by fine-tuning on challenging generalization datasets using predicted protein and ligand structures. Our comprehensive evaluations on unseen protein families using predicted binding conformations demonstrate BindMecNets superior performance, significantly outperforming state-of-the-art deep learning baselines. Ablation studies confirm that both the PDBBind pre-training and the explicit mechanistic inductive bias are critical for achieving this enhanced generalizability and accuracy. Furthermore, BindMecNets predicted interaction maps offer valuable, interpretable insights into binding hotspots, paving the way for more rational and mechanism-driven drug design.

bioinformatics↗

bioRxiv2025

Metabolic alterations in the absence of a detectable neuromuscular phenotype in novel genomically humanised SOD1A4V mice.

Amyotrophic lateral sclerosis (ALS) caused by mutation in superoxide dismutase 1 (SOD1) accounts for 15-30% of familial ALS and is typically autosomal dominant. How single base pair/amino acid changes in this small protein cause neurodegeneration is unknown. In North America, SOD1A4V is the most common familial ALS SOD1 mutation and results in an aggressive form of ALS. Here, we present a novel genomically humanised mouse model of SOD1A4V, in which the mouse Sod1 locus has been replaced by the human SOD1 gene, with intact genomic architecture of exons and introns, but bearing an A4V mutation. In agreement with previously reported human genomic knock-in mice, the phenotype is mild; however, transcriptomic and metabolomic profiling reveal significant dysregulation of glycolysis, the tricarboxylic acid (TCA) cycle, and lipid metabolism. These changes suggest an early bioenergetic imbalance that precedes neuromuscular impairment. Our findings support metabolic dysfunction as an early event in ALS pathogenesis. This freely available SOD1A4V model provides a valuable tool for studying ALS progression and identifying therapeutic targets for pre-symptomatic treatment. SUMMARY STATEMENTThis study describes the generation and analysis of novel genomically humanised SOD1A4V mice, revealing metabolic dysfunction through integrated multi-omic analyses, characterising a freely available potential pre-symptomatic ALS model for future research.

neuroscience↗

bioRxiv2025

Plant host identity drives Andropogon gerardii rhizobiome assembly strategies under increasing abiotic stress

Predicted changes in precipitation threaten tallgrass prairies by altering the soil microbial communities that are essential for plant resilience. Andropogon gerardii, a dominant grass in tallgrass prairies, spans the contiguous North American precipitation gradient. However, it remains unclear to what extent the rhizosphere microbiomes (rhizobiomes) are influenced by the plant-host environmental interaction. To assess how environmental and host factors shape the rhizobiome, we surveyed A. gerardii populations across 25 remnant prairie sites (June-August 2023) within its native range in the United States, characterizing the microbiomes in the rhizosphere and soils using 16S amplicon sequencing. We demonstrated that while geographic location largely structured both rhizosphere and soil communities, regional precipitation (60-day rainfall) emerged as a primary driver of the microbial community assembly. We observed distinct microbial divides across the dry and wet regions of the North American "arid-humid divide." Importantly, we found the first compelling large-scale evidence that regional precipitation has a profound influence on rhizobiome assembly. In the most arid regions, rhizosphere microbial communities exhibited significantly more predicted stochasticity than those in the local soil and contained taxa related to host-benefiting functions. Our study suggests that intensified host-driven selection for specific microbial variants occurs under heightened abiotic stress, highlighting the hosts pivotal role in shaping its rhizobiome composition in challenging environments.

microbiology↗

bioRxiv2025

Generation of C9orf72 repeat knock-in iPSC lines for modelling ALS and FTD

Induced pluripotent stem cell (iPSC) models are powerful tools for neurodegenerative disease modelling, as they allow mechanistic studies in a human genetic environment and they can be differentiated into a range of neuronal and non-neuronal cells. However, these models come with inherent challenges due to line-to-line and clonal variability. To combat this issue, the iPSC Neurodegenerative Disease Initiative (iNDI) has generated an iPSC repository using a single clonal reference line, KOLF2.1J, into which disease-causing mutations and revertants are introduced via gene editing. Here we describe the generation and validation of lines carrying the most common causative mutation for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a repeat expansion in the C9orf72 gene, for the iNDI collection of neurodegenerative iPSC models. We demonstrate that these C9orf72 knock-in lines differentiate efficiently into neurons and display characteristic C9orf72-associated pathologies, including reduced C9orf72 levels and the presence of dipeptide repeat proteins (DPRs) and RNA foci, which increase in abundance over time in culture. These pathologies are not present in revertant cells lacking the repeat expansion. These repeat expansion and revertant cell lines are now available to academic and for-profit institutions through the JAX iPS cell repository and will help to facilitate and standardise iPSC-based ALS/FTD research.

neuroscience↗

bioRxiv2025

Generation of C9orf72h370 mice, an intron 1 humanised C9orf72 repeat-expansion knock-in model

An autosomal dominant GGGGCC repeat expansion in intron 1 of the C9orf72 gene is the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we set out to engineer a gene targeted mouse model harbouring a pathogenic length humanised C9orf72 repeat expansion allele, in order to model pathological mechanisms in a physiological context. In human disease, pathogenic repeats typically range from the hundreds to thousands of units in length, representing a considerable challenge for cellular and in vivo model generation given the instability of GC rich and repetitive DNA sequences during molecular cloning. To overcome this challenge, we developed new methodology to synthetically and iteratively build pure GGGGCC repeats within a linear vector system, which we then seamlessly and scarlessly embedded within the native human genomic sequence. This created a gene targeting DNA vector for homologous recombination of the human sequence in mouse embryonic stem cells. We used this novel targeting vector to generate a new gene targeted mouse allele, C9orf72h370, that for the first time has mouse C9orf72 intron 1 scarlessly replaced with human intron 1 including a pure (GGGGCC)370 hexanucleotide repeat expansion. We confirm that the mouse model expresses human intron 1-derived RNA and produces dipeptide repeat proteins derived from the GGGGCC repeat expansion. We now provide this model as a new freely available resource for the field. In addition, we demonstrate the utility of our cloning method for engineering diverse repeat expansion sequences for modelling other disorders, such as Fragile X Syndrome.

molecular biology↗

bioRxiv2024

On Levodopa interactions with brain disease proteins at the nanoscale

The cerebral accumulation of -Synuclein (-Syn) and amyloid {beta}-1-42 (A{beta}-42) proteins are known to play a crucial role in the pathology of neurocognitive disorders such as Parkinsons disease (PD). Currently, Levodopa (L-dopa) is the dopamine replacement therapy for treating bradykinetic symptoms visible in PD patients. Here, we use atomic force microscopy to evidence at nanometer length scales the effects of L-dopa on the morphology of -Syn and A{beta}-42 protein fibrils. L-dopa treatment reduces the length and diameter of both types of protein fibrils, with a stark reduction observed for A{beta}-42 both in physiological buffer and human spinal fluid. The insights gained on A{beta}-42 fibril disassembly from the nanoscale imaging experiments are substantiated using atomic-scale molecular dynamics simulations. Our results reveal the mechanism governing L-dopa-driven reversal of protein aggregation, which may be useful in drug design of small molecule drugs for potentially treating neurocognitive disorders and provide leads for designing chemical effector-mediated disassembly of protein architectures.

neuroscience↗

bioRxiv2024

Substrate-specific regulation of mTORC1 activity by G protein-coupled receptors

The mammalian/mechanistic Target of Rapamycin Complex 1 (mTORC1) orchestrates cell growth and metabolism in response to diverse external cues. mTORC1 has a myriad of phosphorylation substrates, each playing important physiological roles. Emerging evidence suggests that mTORC1 can respond to upstream signals in a nuanced manner, enabling differential regulation of individual substrates and downstream biological processes. However, the nature of signals that determine the signaling selectivity of mTORC1 remains incompletely understood. Here, we studied mTORC1 regulation by G protein-coupled receptors (GPCRs). We found that phosphorylation of the Transcription Factor EB (TFEB), a non-canonical mTORC1 substrate that controls lysosome biogenesis, responds to GPCRs differently, compared to canonical mTORC1 substrates controlling protein synthesis such as S6K1 and 4EBP1. In particular, the muscarinic acetylcholine receptor M5 (M5R) promoted phosphorylation of S6K1 and 4EBP1, while triggering TFEB dephosphorylation. Consequently, M5R stimulated protein synthesis without inhibiting lysosome biogenesis. The regulations of an anabolic process and a catabolic process, albeit both governed by mTORC1, are thus decoupled downstream of M5R. This study highlights the importance of reassessing the effects of GPCRs on mTORC1 by concurrently monitoring individual substrates, a critical consideration to be made when evaluating GPCR ligands as therapeutic agents targeting the mTORC1 pathway.

cell biology↗

bioRxiv2024

Single-cell analysis identifies distinct CD4+ T cells associated with the pathobiology of pediatric obesity-related asthma

Pediatric obesity-related asthma is characterized by non-atopic T helper 1 (Th1) inflammation and steroid resistance. CDC42 upregulation in CD4+T cells underliesTh1 inflammation but the CD4+T cell subtype(s) with CDC42 upregulation and their contribution to steroid resistance are not known. Compared to healthy-weight asthma, obesity-alone and healthy-weight controls, single-cell transcriptomics of obese asthma CD4+T cells revealed CDC42 upregulation in 3 clusters comprised of naive and central memory T cells, which differed from the cluster enriched for Th1 responses that was comprised of effector T cells. NR3C1, coding for glucocorticoid receptor, was downregulated, while genes coding for NLRP3 inflammasome were upregulated, in clusters with CDC42 upregulation and Th1 responses. Conserved genes in these clusters correlated with pulmonary function deficits in obese asthma. These findings suggest that several distinct CD4+T cell subtypes are programmed in obese asthma for CDC42 upregulation, Th1 inflammation, and steroid resistance, and together contribute to obese asthma phenotype. SummaryCD4+T cells from obese children with asthma are distinctly programmed for non-allergic immune responses, steroid resistance and inflammasome activation, that underlie the obese asthma phenotype.

immunology↗

bioRxiv2024

Global overview of sea turtle fibropapillomatosis tumors: a survey of expert opinions and trends.

Marine environments offer a wealth of opportunities to improve understanding and treatment options for cancers, through insights into a range of fields from drug discovery to mechanistic insights. By applying One Health principles the knowledge obtained can benefit both human and animal populations, including marine species suffering from cancer. One such species is green sea turtles (Chelonia mydas), which are under threat from fibropapillomatosis (FP), an epizootic tumor disease (animal epidemic) that continues to spread and increase in prevalence globally. In order to effectively address this epizootic, a more thorough understanding is required of the prevalence of the disease and the approaches to treating afflicted turtles. To identify knowledge gaps and assess future needs, we conducted a survey of sea turtle FP experts. The survey consisted of 47 questions designed to assess general perceptions of FP, the areas where more information is needed, local FP trends, the disease status, and mitigation needs, and was voluntarily completed by 44 experts across a broad geographic range. The survey responses provided a valuable overview of the current FP status in sea turtles, FP research, and insight into the approaches currently taken by turtle rehabilitation facilities around the world. Over 70% of respondents both recognized FP as a cancerous panzootic disease, and reported that FP is increasing in prevalence. They report several factors contributing to this increase. Nearly all of the respondents reported that FP research, patient treatment and rehabilitation required more funding in their area, and reported inadequate facilities and capacity for dealing with FP patients. Treatment approaches varied: just over 70% of the medical experts that responded surgically remove FP tumors, either using laser or scalpel. Just under half of respondents use anti-cancer drugs in their treatment of FP. Internal tumors were reported as justification for euthanasia by 61.5% of respondents, and 30.8% reported severe external tumors to be sufficient grounds for euthanasia. Most medical respondents (93.3%) routinely perform necropsy on deceased or euthanized FP-afflicted turtles. Over 80% of respondents considered large-scale multidisciplinary collaboration extremely important for advancing the field of FP research. The survey responses provide a valuable insight into the current state of FP treatment, rehabilitation and research, and help to identify critical FP-related research and rehabilitation areas most in need of attention.

cancer biology↗

bioRxiv2024

An ascending vagal sensory-central noradrenergic pathway modulates retrieval of passive avoidance memory

BackgroundVisceral feedback from the body is often subconscious, but plays an important role in guiding motivated behaviors. Vagal sensory neurons relay "gut feelings" to noradrenergic (NA) neurons in the caudal nucleus of the solitary tract (cNTS), which in turn project to the anterior ventrolateral bed nucleus of the stria terminalis (vlBNST) and other hypothalamic-limbic forebrain regions. Prior work supports a role for these circuits in modulating memory consolidation and extinction, but a potential role in retrieval of conditioned avoidance remains untested. ResultsTo examine this, adult male rats underwent passive avoidance conditioning. We then lesioned gut-sensing vagal afferents by injecting cholecystokinin-conjugated saporin toxin (CSAP) into the vagal nodose ganglia (Experiment 1), or lesioned NA inputs to the vlBNST by injecting saporin toxin conjugated to an antibody against dopamine-beta hydroxylase (DSAP) into the vlBNST (Experiment 2). When avoidance behavior was later assessed, rats with vagal CSAP lesions or NA DSAP lesions displayed significantly increased conditioned passive avoidance. ConclusionsThese new findings support the view that a gut vagal afferent-to-cNTSNA-to-vlBNST circuit plays a role in modulating the expression/retrieval of learned passive avoidance. Overall, our data suggest a dynamic modulatory role of vagal sensory feedback to the limbic forebrain in integrating interoceptive signals with contextual cues that elicit conditioned avoidance behavior.

neuroscience↗

bioRxiv2024

Hydroxysteroid 17-beta dehydrogenase 13 (Hsd17b13) knockdown attenuates liver steatosis in high-fat diet obese mice

Hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) loss-of-function gene variants are associated with decreased risk of metabolic dysfunction-associated steatotic liver disease (MASLD). Our RNA-seq analysis of steatotic liver from obese mice -/+ Fenretinide treatment identified major beneficial effects of Fenretinide on hepatic gene expression including Hsd17b13. We sought to determine the relationship between Hsd17b13 expression and MASLD and to validate it as a therapeutic target by liver-specific knockdown. Hsd17b13 expression, which is unique to hepatocytes and associated with the lipid-droplet, was elevated in multiple models of MASLD and normalised with prevention of obesity and steatotic liver. Direct, liver- specific, shRNA-mediated knockdown of Hsd17b13 (shHsd17b13) in high-fat diet (HFD)-obese mice, markedly improved hepatic steatosis with no effect on body weight, adiposity or glycaemia. shHsd17b13 decreased elevated serum ALT, serum FGF21 levels and markers of liver fibrosis e.g. Timp2. shHsd17b13 knockdown in HFD-obese mice and Hsd17b13 overexpression in cells reciprocally regulated expression of lipid metabolism genes e.g. Cd36. Global lipidomic analysis of liver tissue revealed a major decrease in diacylglycerols (e.g. DAG 34:3) with shHsd17b13 and an increase in phosphatidylcholines containing polyunsaturated fatty acids (PUFA) e.g. PC 34:3 and PC 42:10. Expression of key genes involved in phospholipid and PUFA metabolism e.g. Cept1, were also reciprocally regulated suggesting a potential mechanism of Hsd17b13 biological function and role in MASLD. In conclusion, Hsd17b13 knockdown in HFD-obese adult mice was able to alleviate MASLD via regulation of fatty acid and phospholipid metabolism, thereby confirming HSD17B13 as a genuine therapeutic target for MASLD and development of liver fibrosis. KEY POINTSO_LIHSD17B13 loss-of-function gene variants are associated with decreased risk of metabolic dysfunction-associated (MA) steatotic liver disease and steatohepatitis (MASLD and MASH). C_LIO_LIRNA-seq analysis of steatotic liver identified beneficial effects of Fenretinide on hepatic gene expression including downregulation of Hsd17b13. C_LIO_LILiver-specific shRNA knockdown of Hsd17b13 in obese mice markedly improved hepatic steatosis and markers of liver health e.g. serum ALT, serum Fgf21 levels. C_LIO_LIHsd17b13 influenced expression of lipid/phospholipid metabolism genes e.g. Cd36 and Cept1 and phosphatidylcholines PC 34:3 and PC 42:10. C_LIO_LIOur study suggests a mechanism of HSD17B13s biological function and the strong rationale behind targeting HSD17B13 for MASLD/MASH. C_LI

physiology↗

bioRxiv2023

Creation of de novo cryptic splicing for ALS/FTD precision medicine

A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe "TDP-REG", a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOF in vitro and in vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate the UNC13A cryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals. One-Sentence SummaryWe engineer TDP-43-regulated cryptic exons, enabling exceptionally precise activation of gene therapies in diseased neurons.

molecular biology↗

bioRxiv2023

Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022

This article describes the first detections of disease due to natural infection with highly pathogenic avian influenza virus (HPAIv) H5N1 of the Eurasian lineage goose/Guangdong clade 2.3.4.4b in wild terrestrial mammals throughout the United States during 2021-2022. Affected mammalian species include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.

pathology↗