Biology subjects

Cao, T.

Publications and source records attributed to Cao, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Conservation of gene co-expression networks and neuropsychiatric-neurological disease gene programs between mouse and human frontal cortex at single-cell resolution

Mouse models are widely used in translational neuroscience, but whether a gene has the same partners in mouse and human prefrontal cortex (PFC) is unknown. The genes whose expression rises and falls with a given gene across samples (its co-expression partners) indicate the molecular program to which it belongs. We compared the co-expression of 13,214 genes between mouse medial PFC and human dorsolateral PFC in 246,211 single-nucleus RNA-sequencing profiles. These two regions are not homologous, so part of any measured difference may reflect region and not species. The study has five main findings. First, the similarity of partners for single genes was modest (median 0.169; 0, unrelated; 1, identical). This median was below that of every comparison among human datasets but within the range of comparisons among mouse datasets, and correction for measurement noise raised it to 0.349 at most. Second, groups of co-expressed genes (modules) were strongly preserved. Third, neuropsychiatric disease genes were modestly more conserved than other genes, but no more than control genes matched for mutational constraint and expression, consistent with general gene properties and with how these genes are discovered. Fourth, no disease gene was shown to have different partners in the two species. Fifth, four of five human modules recurred in an independent human dataset. We also identified two sources of error: analyzing only the most variable genes excludes most disease genes, and networks built from few samples, as for glial cells, underestimate the similarity between species. Scores and code are released for cross-species studies.

genomics↗

bioRxiv2026

Restoring multiple TDP-43 cryptic targets, but not solely Unc13a, rescues motor neuron disease

Dysfunction of TAR DNA-binding protein 43kDa (TDP-43) underlies amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder with limited therapeutic options. While current therapeutic approaches are designed to individually target unique cryptic exons of TDP-43 such as UNC13A, the sufficiency of such a strategy to mitigate motor neuron disease remains unclear. Using a mouse model lacking TDP-43 in spinal motor neurons which mimics early stages of ALS, we show that the exclusion of Unc13a cryptic exon fails to mitigate motor neuron disease. In contrast, the restoration of multiple TDP-43 cryptic targets, including Unc13a, attenuated motor neuron loss, and rescued motor neuron disease. Additionally, compared to brain neurons, spinal motor neurons accumulate markedly lower amounts of Unc13a cryptic exons in mice and humans, suggesting that the contribution of this TDP-43 cryptic target to spinal motor neuron loss may be limited. Together, these results strongly support ALS therapeutic strategies designed to simultaneously restore multiple TDP-43 cryptic targets to attenuate spinal motor neuron loss.

neuroscience↗

bioRxiv2026

Prevention of Unc13a cryptic splicing is sufficient to preserve memory

TDP-43 dysfunction is thought to underlie frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, neurodegenerative dementias currently without effective therapy. Therapeutic strategies are designed to correct individual cryptic targets of TDP-43, such as UNC13A, whereby its cryptic splicing compromises synaptic function, yet the sufficiency of such an approach to prevent memory deficits is unclear. Using a forebrain neuron-specific TDP-43 knockout mouse model that recapitulates TDP-43 dysfunction occurring during early stages of human disorders, we found here that prevention of cryptic splicing to include that of Unc13a attenuated memory deficits. We show that genetic ablation of Unc13a cryptic exon solely in such TDP-43 knockout mice is sufficient to preserve cognition, supporting the clinical value of targeting UNC13A to mitigate memory deficits. Prevention of cryptic splicing of multiple targets of TDP-43 additionally attenuate neuron loss. For optimal outcomes in TDP-43 related dementias, these findings thus strongly support strategies designed to repress cryptic splicing of multiple targets of TDP-43, including UNC13A.

pathology↗

bioRxiv2026

A sensitive bioassay for detecting Plasmodiophora brassicae in canola field soils

We describe a biodegradable-cup bioassay for detecting viable Plasmodiophora brassicae in soil samples. Soil samples either artificially inoculated with P. brassicae resting spores or collected from canola fields were aliquoted into biodegradable cups containing 20 g of soil per cup. Two cups representing the same soil sample or inoculum concentration were placed in each pot filled with Sunshine Mix. Six seeds of the canola cultivar Westar were sown into each cup and thinned to four seedlings per cup ten days after planting. After four weeks, roots were examined for the presence of clubroot galls. Across three independent inoculated-soil experiments, galls were observed in samples containing as few as 1 resting spore g-1 soil. In contrast, under a qPCR assay evaluated in parallel, consistent amplification across three technical replicates was obtained only at 100 resting spores g-1 soil or greater. In field samples, the bioassay produced galls from 11 qPCR-positive samples and seven of ten qPCR-negative samples. Although the bioassay is not intended for rapid diagnosis or direct quantification, it provides a practical tool for annual clubroot surveys and for studies requiring recovery, propagation, or characterization of viable P. brassicae from soil samples collected across diverse geographic regions.

microbiology↗

bioRxiv2026

A cargo receptor entrapment complex is a therapeutic node for genetically and clinically distinct proteinopathies

Severe proteinopathies--such as retinitis pigmentosa, a form of inherited blindness--are driven by genetic mutations that overwhelm the quality control of the post-endoplasmic reticulum (post-ER) secretory pathway, causing toxic protein accumulation. Here, we identify a therapeutic node defined by a hetero-oligomeric cargo receptor complex consisting of TMED7, 2, 9, and 10. This "entrapment complex" anchors structurally and functionally diverse mutant clients within the early secretory pathway via TMED7 binding to the integral Golgi protein GRASP55. Disruption of the entrapment complex results in the clearance of accumulated protein cargoes. In vivo ablation of the entrapment node via inducible genetic deletion or via the small molecule BRD7635 reverses histopathological hallmarks and rescues functional deficits in clinically distinct proteinopathies of the kidney and the eye, including mitigating vision loss in a mouse model of retinitis pigmentosa.

cell biology↗

bioRxiv2026

NKG2C+CD27- Defines Human CD8+ Regulatory T Cells

Here we identify NKG2C+CD27- as a novel surface marker unifying multiple previously reported CD8+ regulatory T cell (Treg) populations. This population displays high clonality and divides into CD226- (Treg1) and CD226+ (Treg2) subsets, with Treg2 exhibiting stronger suppressive activities. Up to 35% of CD8+ TEMRA cells are Tregs, whereas approximately 85% of CD8+ Tregs are TEMRA cells, which increase with aging. These findings establish a unified and novel cell surface marker for CD8+ Tregs and their subsets, which resolves prior heterogeneity in the field, and show that CD8+ TEMRA cells are a heterogeneous population that includes T cells with regulatory function. Our findings provide a critical framework for the isolation and in-depth functional characterization of CD8+ Tregs in health, aging, and disease.

immunology↗

bioRxiv2026

A Multidimensional Framework for Behavioral Persistence: Dissociable Dimensions of Effort, Endurance, and Sequence Stability in Mice

Behavioral persistence, the maintenance of goal-directed action despite obstacles, is a fundamental adaptive process, yet its scientific study remains fragmented across disciplines with disparate operational definitions. Here, we introduce the Persistence Spectrum (PERCS) framework, a five-dimensional model deconstructing persistence into Perseverance of Effort (P), Strategic Endurance (E), Resistance to Extinction (R), Temporal Consistency (C), and Repetitive Sequence Stability (S). Using programmable operant schedules via the FED3 system, we induced a continuum of persistent food-seeking in mice across four paradigms: Fixed Ratio (FR), Alternating 2x2 and 5x5, and Random Progressive Ratio (RPR). To objectively identify persistence periods, we developed a session-specific Gaussian mixture model, providing a data-driven alternative to arbitrary frequency thresholds. We found that persistence bouts were fundamentally driven by unrewarded effort, not reward delivery: instantaneous frequency for incorrect pokes significantly exceeded that for correct pokes in FR, 2x2, and 5x5 (all p < 0.05). This pattern was most pronounced in the high-demand RPR schedule, where high-rate poking continued unabated even after successes, directly challenging reinforcement-centric models and providing strong empirical support for frustration theory. Linear mixed-effects modeling revealed that frequency increased with consecutive unrewarded pokes across all paradigms, with a quadratic (inverted-U) relationship specific to FR and 2x2 (p < 0.001), suggesting effort invigoration followed by strategic disengagement in simpler tasks, whereas high-demand schedules maintained linear increases. Notably, the collapse of Sequence Stability (S) in RPR is partly constrained by the tasks environmental contingency: random reward rules mathematically restrict stable sequence learning. Aggregate analysis showed total poke counts and unrewarded effort scaled with task difficulty (all p < 2e-16), yet pellet retrieval rates remained stable, indicating goal achievement despite increased challenge. Crucially, PERCS profiles were robust across independent and continuous training histories, demonstrating they reflect stable phenotypes shaped by current contingencies rather than training artifacts. Application of PERCS revealed distinct fingerprints: FR produced near-zero P, E, R, and C but maximal S, characteristic of an efficient habit; 2x2 and 5x5 elevated P, E, and R while reducing S; and RPR generated highest P and R, lowest S, and marked inter-individual variability. These findings demonstrate that operant schedules dissociably shape distinct persistence dimensions, with unrewarded effort acting as a key motivational trigger, positioning frustrative nonreward as a primary engine of persistent behavior. The PERCS framework provides a unified, quantitative language for characterizing persistent behavior across species and paradigms, offering a powerful tool for linking dimensions to neural circuits and understanding their breakdown in neuropsychiatric disorders.

animal behavior and cognition↗

bioRxiv2026

On the sensitivity of qPCR diagnostics for the canola clubroot pathogen Plasmodiophora brassicae

Clubroot, caused by Plasmodiophora brassicae, is an important disease of canola and other Brassica crops. Polymerase chain reaction (PCR), particularly probe-based quantitative PCR (qPCR), is widely used for the detection of P. brassicae in soil samples. To improve consistency in clubroot detection while maintaining efficiency, diagnostic laboratories would benefit from adopting a single, highly efficient qPCR system for routine testing. In this study, we analyzed the primer and probe sequences of all published PCR and qPCR systems for P. brassicae detection. Based on these analyses, three independently developed probe-based qPCR systems were selected and their performance was evaluated using synthesized target DNA (gBlock). One probe-based qPCR system exhibiting superior sensitivity on gBlock was subsequently evaluated on P. brassicae genomic DNA. This system consistently detected DNA equivalent to four resting spores per reaction, corresponding to a soil sample containing 1,000 spores per g soil when the DNA extraction protocol was considered as a component of the qPCR system. The sensitivity of the system was further validated using DNA extracted from soil samples collected from multiple locations across Alberta, where P. brassicae was detected at levels below those associated with visible clubroot symptoms. Based on these results, we recommend this qPCR system for routine clubroot diagnostics in laboratories across Canada.

microbiology↗

bioRxiv2026

Regional heterogeneity shapes macroscopic wave dynamics of the human and non-human primate cortex

Growing evidence indicates that macroscopic cortical activity is dominated by propagating waves of excitation. However, many computational models of such wave dynamics assume that the cortex is a spatially homogeneous medium, ignoring the rich regional variations in cellular, molecular, and physiological properties that are known to shape how brain activity evolves through both space and time. Here, we develop a general framework grounded in neural field theory to model how regional heterogeneities in diverse cortical properties shape spatiotemporal brain activity evolving on cortical surface meshes. This enables high resolution, vertex-level simulations without requiring predefined parcellations. The model requires only a standard mesh model of the cortical manifold and a spatial heterogeneity map, providing a biologically grounded and computationally efficient framework that can be generalised to human and non-human species. Using multiple cellular, molecular, and physiological maps in humans--and analogous maps in macaques and marmosets--we show that our model can consistently recapitulate known relationships between regional heterogeneities and variations in cortical wave speed. In particular, we find that models parameterised by heterogeneities in intracortical myelin and excitation-inhibition balance yield the largest performance improvements relative to spatially homogeneous models. Our results identify a key role for regional variations in myelin, receptor, and genetic architecture in shaping the spatial patterning of macroscale cortex-wide activity that is conserved across primate species with diverse cortical geometries.

neuroscience↗

bioRxiv2025

Sensory Circuit Dynamics in a Mouse Model of Epileptic Encephalopathy

Epileptic encephalopathies (EEs) are severe developmental disorders with abnormal EEG activity that worsens neurodevelopmental deficits, yet underlying sensory and cognitive impairment mechanisms are unclear. We studied cortical circuit dynamics in Ank3-1b-/- mice, an EE model with parvalbumin interneuron dysfunction, using laminar electrophysiology, spike-field coherence (SFC), single-unit analyses, and behavioral assays. Ank3-1b-/- mice showed disrupted excitatory-inhibitory (E-I) balance, with reduced sink/source ratios (p = 0.0279) and elevated net currents (AVREC; p < 0.01), indicating hyperexcitability. In awake states, sensory-evoked intra-columnar connectivity was impaired, with lower Pearson correlations (p < 0.001) and increased low-frequency (3-30 Hz) SFC (p < 0.001), but intact gamma-band coherence, suggesting aberrant synchronization. Inhibitory neuron latencies were delayed in infragranular layers under anesthesia (p < 0.001) and supragranular layers when awake (p = 0.005), implying thalamocortical deficits. Despite preserved sensory adaptation and recognition memory, Ank3-1b-/- mice exhibited heightened anxiety (p < 0.05) and variable circadian rhythms, indicating selective affective and regulatory deficits. These results show that Ank3-1b loss disrupts cortical E-I balance and synchrony, delaying sensory processing, while compensatory mechanisms maintain critical sensory functions. This study links ANK3 mutations to layer-specific circuit dysfunction, offering insights into EE pathophysiology and sensory deficits.

neuroscience↗

bioRxiv2025

Geometric constraints on the architecture of mammalian cortical connectomes

The intricate network of axonal fibres that forms the mammalian cortical connectome has a complex topology, being organized in a way that is neither completely regular nor random, as well as a characteristic topography, in which specific anatomical locations are imbued with distinctive connectivity profiles. The mechanisms that give rise to such properties remain a mystery. Here, we formulate a simple analytic model derived from neural field theory that prioritizes physical constraints on connectome architecture by assuming that connectivity is preferentially concentrated between pairs of cortical locations that facilitate the excitation of resonant geometric modes of the cortex. We show that the model outperforms existing approaches in reproducing multiple topological and topographical properties of cortical connectomes mapped at spatial scales spanning orders of magnitude in humans, chimpanzees, macaques, marmosets, and mice, as mapped with either non-invasive diffusion magnetic resonance imaging or invasive viral tract-tracing. Our findings thus point to a fundamental role of geometry in shaping the multiscale architecture of cortical connectomes that has been conserved across 90 million years of evolution.

neuroscience↗

bioRxiv2025

CSRefiner: A lightweight framework for fine-tuning cell segmentation models with small datasets

AO_SCPLOWBSTRACTC_SCPLOWRecent advances in spatial omics technologies have enabled transcriptome profiling at subcellular resolution. By performing cell segmentation on nuclear or membrane staining images, researchers can acquire single cell level spatial gene expression data, which in turn enables subsequent biological interpretation. Although deep learning-based segmentation models achieve high overall accuracy, their performance remains suboptimal for whole-tissue analysis, particularly in ensuring consistent segmentation accuracy across diverse cell populations. Existing fine-tuning approaches often require extensive retraining or are tailored to specific model architectures, limiting their adaptability and scalability in practical settings. To address these challenges, we present CSRefiner, a lightweight and efficient fine-tuning framework for precise whole-tissue single-cell spatial expression analysis. Our approach incorporates support for fine-tuning widely uaed segmentation models in the field of spatial omics, including recent published model Cellpose-SAM, while achieving high accuracy with very limited annotated data. This study demonstrates CSRefiners superior performance across various staining types and its compatibility with multiple mainstream models. Combining operational simplicity with robust accuracy, our framework offers a practical solution for real-world spatial transcriptomics applications.

bioinformatics↗

bioRxiv2025

TDP-43 loss of function drives aberrant splicing in Parkinson's disease

Introductory paragraphWhile mRNA splicing dysregulation is a well-established contributor to neurodegeneration in disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), its role in Parkinsons disease (PD) remains underexplored. Here, we analyse transcriptomic data from >500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.

neuroscience↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Cryo-EM structure of DNA-unbound human MCM2-7 complex reveals new disease-relevant regulation

Chromatin loading of the hexameric replicative helicase MCM2-7 complex requires coordinated interactions with the origin recognition complex (ORC), CDC6, and CDT1. MCM2-7 not bound to DNA forms a single hexamer (SH) with an open DNA entry gate. Two MCM2-7 SHs are loaded sequentially to form the double hexamer (DH) that encircles the DNA duplex. Activated MCM2-7 then unwinds DNA and initiates DNA replication. Our cryo-electron microscopy analyses show that a fraction of human MCM2-7 without DNA exists as DH. Unexpectedly, we find that the MCM3 winged helix domain (WHD) docks on MCM2 in both DNA-free DH and SH, creating a safety latch across the DNA entry gate to block DNA entry into the central channel. The safety latch can be opened by ORC-CDC6 binding. Disrupting this latch by designed or human disease-related mutations of MCM3 causes replication defects and DNA damage checkpoint activation. Our findings uncover a new regulated step in MCM2-7 loading with implications for human diseases.

biophysics↗

bioRxiv2025

Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits

Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease processes, we integrated 31 human and mouse spatial datasets from 8 organs with genes that are genetically implicated in 32 human diseases. Applying our novel approach STEAM, we identified both known and novel roles of tissue structures in human diseases and identified spatially clustered disease gene subsets. For example, in the brain we observed enrichment of neuropsychiatric disease in cortical layers, and immune and barrier dysfunction in Alzheimers disease, with integration with single-cell data highlighting the complementary insights from the two data types. Spatial coexpression of drug target genes with genetically implicated genes in enriched tissue structures showed potential for spatially informed drug repurposing. Altogether, we show vast potential for integration of genetic discoveries with growing spatial datasets to understand human disease biology.

genetics↗

bioRxiv2025

Resolution of in situ inflammation in human lupus nephritis into principal immune cell trajectories

In human lupus nephritis (LuN), tubulointerstitial inflammation (TII) is prognostically more important than glomerular inflammation. However, a comprehensive understanding of both TII complexity and heterogeneity is lacking. Herein, we used high-dimensional confocal microscopy and specialized computer vision techniques to quantify immune cell populations and localize these within normal and diseased renal cortex structures. With these tools, we compared LuN to renal allograft rejection (RAR) and normal kidney. In both LuN and RAR, the 33 characterized immune cell populations formed discrete subgroups whose constituents co-varied in prevalence across biopsies. In both diseases, these co-variant immune cell subgroups organized into the same unique niches. Therefore, inflammation could be resolved into trajectories representing the relative prevalence and density of cardinal immune cell members of each co-variant subgroup. Indeed, in any one biopsy, the inflammatory state could be characterized by quantifying constituent immune cell trajectories. Remarkably, LuN heterogeneity could be captured by quantifying a few myeloid immune cell trajectories while RAR was more complex with additional T cell trajectories. Our studies identify rules governing renal inflammation and thus provide an approach for resolving LuN into discrete mechanistic categories. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/638655v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@109dd33org.highwire.dtl.DTLVardef@995037org.highwire.dtl.DTLVardef@161525dorg.highwire.dtl.DTLVardef@6692d8_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

immunology↗

bioRxiv2024

Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding

Allosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzymes kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this sites function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2s biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2s role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.

biochemistry↗