Biology subjects

Guo, C.

Publications and source records attributed to Guo, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

High Purity Differential Expression of Genes across Spatial Domains

Spatial transcriptomics maps gene expression within tissue architecture, offering deep insights into cellular function. A key yet overlooked phenomenon is the systematic imbalance in gene regulation within spatial domains, contrasting with traditional analyses. We define and validate this as a prevalent hallmark--High-Purity Differential Expression (HiP-DEP)--where genes in a domain shift predominantly in one direction (i.e., predominantly up- or downregulated). We introduce a Spatial Purity index to quantify it. Analysis of 190 diverse datasets across diverse tissues, diseases, and technologies revealed that spatial domains possess significantly higher purity than conventional bulk (p = 5.4 x 10-11) or single-cell data (p = 6.9 x 10-14), establishing HiP- DEP as a core hallmark of spatial biology. Using our HiP-DEP framework, we show its utility in: decoding core oncogenic regulation and its spatial gradient in breast cancer; uncovering hidden phenotypic divergence between morphologically similar Alzheimers plaques; and identifying active cellular communication niches in normal brain tissue. By shifting focus from individual genes to coordinated transcriptional programs, HiP-DEP provides a new paradigm for precision spatial omics analysis.

bioinformatics↗

bioRxiv2026

Layer-5 Pyramidal Cell tLTD Requires Astrocytic Ca2+ and CB1 Receptor Signaling

Timing-dependent long-term depression (tLTD) is a form of spike timing-dependent plasticity (STDP) that has been attributed to presynaptic NMDA and CB1 receptors at synapses between layer 5 (L5) pyramidal cells (PCs) in visual cortex. Here, we asked whether astrocytes, known for gliotransmission and tripartite synapse formation, are also required. Using quadruple whole-cell recordings in acute slices from C57BL/6 mice, we found that L5 PC [->] PC tLTD was abolished by the glial metabolic inhibitor sodium fluoroacetate. Disrupting astrocyte Ca2+ signaling through loss-of-function approaches such as AAV-mediated expression of CalEx and BAPTA loading of astrocyte networks consistently prevented tLTD. Optogenetic activation of astrocyte Gq signaling during tLTD induction abolished tLTD and led to potentiation. Since tLTD relies on endocannabinoid (eCB) signaling and astrocytes express CB1 receptors, we conditionally deleted CB1 receptors from astrocytes and found that this manipulation abolished tLTD. Taken together, our results show that L5 PC [->] PC tLTD requires astrocyte Ca2+ signaling and CB1 receptor activation. These findings suggest that astrocyte-dependent control of STDP may represent a general principle across circuit and synapse types. Significance StatementSpike timing-dependent plasticity (STDP) enables neural circuits to adapt based on the precise timing of activity, with timing-dependent long-term depression (tLTD) promoting competition and stabilization. While tLTD is often considered a two-factor process involving pre- and postsynaptic neurons, we show that astrocytes form a key third element. Using targeted loss-of-function approaches, we demonstrate that tLTD at layer-5 pyramidal cell synapses in visual cortex requires astrocyte Ca2+ signaling and CB1 receptors. Unexpectedly, optogenetic stimulation of astrocyte Gq signaling during induction blocked depression and instead triggered potentiation. These findings call for a revision of existing models of STDP and suggest that astrocyte-dependent plasticity may reflect a general regulatory principle across cortical circuits.

neuroscience↗

bioRxiv2026

A SIRT5-induced metabolic switch underlies chemoresistance and ATR checkpoint dependence in triple-negative breast cancer

Chemoresistance is the leading cause of poor prognosis in triple-negative breast cancer (TNBC), yet the underlying mechanisms remain unknown. To reveal metabolic drivers of de novo chemoresistance in TNBC, we analyzed pretreatment primary tumor biopsies, employing quantitative proteomics and metabolomics. Chemoresistant TNBCs exhibit hallmarks of oxidative phosphorylation (OXPHOS) and altered nucleotide metabolism linked to overexpression of the mitochondrial sirtuin, SIRT5. Through gain- and loss-of-function studies and stable isotope tracing, we demonstrate that SIRT5 induces a coordinated metabolic switch that redirects glycolysis to the pentose phosphate pathway, thereby augmenting nucleotide pools, while enhancing glutaminolysis to support OXPHOS. Mechanistically, SIRT5 enhances conversion of 6-phospho-D-gluconate to ribulose-5-phosphate through demalonylation of 6-phosphogluconate dehydrogenase (6-PGD), and coordinately activates oncogenic c-MYC to promote glutamine utilization and dependence. Concurrently, SIRT5-induced nucleotide deregulation induces replication stress and hypersensitivity to ATR checkpoint activation, and ATR inhibition synergistically reverses chemoresistance in TNBC. Thus, elevated SIRT5 orchestrates a coordinated metabolic switch to expand nucleotide pools and drive chemoresistance, while producing ATR checkpoint dependence that represents a metabolic vulnerability of SIRT5-overexpressing TNBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/716852v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1c7a27corg.highwire.dtl.DTLVardef@17cb22borg.highwire.dtl.DTLVardef@1956670org.highwire.dtl.DTLVardef@1786dee_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Gene III Ergothioneine ameliorates alcoholic fatty liver disease: A dual strategy of accelerated ethanol elimination and reducing oxidative stress

BackgroundAlcoholic fatty liver disease (AFLD) is a progressive hepatic pathology triggered by chronic ethanol consumption, serving as the initial stage of severe liver injury. Currently, there are no FDA-approved pharmacological interventions that specifically target alcohol-induced hepatic steatosis or prevent disease progression, highlighting an urgent need for effective preventive strategies. This study evaluated the preventive efficacy and underlying mechanisms of Gene III Ergothioneine (EGT) in a clinically relevant preclinical model. MethodsC57BL/6 mice were randomized into five groups: a Control group, an alcoholic fatty liver Model group, a Positive control group treated with Silybin (100 mg/kg), and three EGT treatment groups (10, 30, and 50 mg/kg). The NIAAA mouse model was utilized to induce alcoholic fatty liver. Various biochemical, histological, and molecular markers were assessed to evaluate liver damage, alcohol metabolism, lipid profiles, oxidative stress, and inflammation. ResultsGene III EGT treatment significantly ameliorated hepatic steatosis and necrosis, as confirmed by H&E and Oil Red O staining. Notably, EGT accelerated alcohol clearance, reducing serum ethanol levels by up to 54.4% in a dose-dependent manner. Furthermore, EGT restored liver function markers (ALT, AST, GGT) and corrected dyslipidemia by lowering TG, TC, and LDL-C while elevating HDL-C. Mechanistically, EGT suppressed pro-inflammatory cytokines (IL-6, IL-1 {beta}) and mitigated oxidative stress by reducing malondialdehyde (MDA) accumulation and restoring superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities. ConclusionGene III Ergothioneine prevents alcoholic liver injury through a dual mechanism: accelerating ethanol metabolism and enhancing hepatocyte antioxidative and anti-inflammatory defenses. These findings position EGT as a promising therapeutic candidate for AFLD management.

pharmacology and toxicology↗

bioRxiv2026

Gene III Ergothioneine Ameliorates Exercise-Induced Fatigue by Attenuating Oxidative Stress, Inflammation, and Modulating the AMPK/PGC-1α Signaling Pathway

BackgroundExercise-induced fatigue is a complex physiological phenomenon involving oxidative stress, inflammation, and metabolic disturbances. Ergothioneine (EGT), a naturally occurring amino acid with potent antioxidant properties, has garnered interest for its potential health benefits. This study aimed to evaluate the anti-fatigue effects of Gene III(R) EGT in a mouse model of exhaustive exercise and to elucidate its underlying mechanisms. MethodsMale C57BL/6 mice were randomly divided into five groups: a control group (CTL), low-dose EGT (EGT-L, 10 mg/kg), medium-dose EGT (EGT-M, 30 mg/kg), high-dose EGT (EGT-H, 50 mg/kg), and a positive control group (Coenzyme Q10, 50 mg/kg). Mice were subjected to a 4-week treadmill training protocol, followed by an exhaustive running test. We measured exercise performance and collected blood and skeletal muscle samples at multiple time points to assess biochemical markers, inflammatory cytokines, antioxidant status, and key signaling proteins. ResultsGene III(R) EGT supplementation, particularly at medium and high doses, significantly extended the time to exhaustion and running distance. Compared to the control group, EGT treatment significantly reduced post-exercise levels of lactic acid (LA), lactate dehydrogenase (LDH), and blood urea nitrogen (BUN). Furthermore, Gene III(R) EGT suppressed the exercise-induced increase in pro-inflammatory cytokines, including IL-1{beta}, IL-6, and TNF-. The anti-fatigue effect of EGT was also associated with a reduction in malondialdehyde (MDA) and an increase in the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). Mechanistically, EGT promoted the phosphorylation of AMP-activated protein kinase (AMPK) and the expression of peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1) in skeletal muscle, while also increasing the Bcl-2/Bax ratio, suggesting enhanced mitochondrial biogenesis and reduced apoptosis. ConclusionsOur findings demonstrate that Gene III(R) EGT effectively enhances exercise performance and alleviates fatigue. The underlying mechanisms involve the mitigation of oxidative stress and inflammation, as well as the activation of the AMPK/PGC-1 signaling pathway to promote mitochondrial function and cellular protection. These results highlight the potential of Gene III(R) EGT as a nutritional supplement for combating exercise-induced fatigue.

pharmacology and toxicology↗

bioRxiv2026

A Pan-Cancer Single-Cell Atlas to Evaluate Tumor Identity, Cell Line Concordance, and Dependency Mapping

Bulk RNA sequencing enables pan-cancer transcriptional analyses, but obscures cancer cell-specific programs due to admixture with nonmalignant cells, thereby limiting direct comparison between experimental models and primary tumors. Single-cell RNA sequencing (scRNA-seq) overcomes these limitations; however, the biological interpretability of public datasets is often compromised by variable data quality, inconsistent annotation, and atlas-scale aggregation strategies that prioritize data volume over biological coherence. We therefore developed a stringent integration framework that prioritizes representative malignant transcriptional states. Using Mahalanobis distance-based selection within batch-corrected latent space, we constructed a pan-cancer atlas comprising 135,424 high-quality malignant cells from 499 samples across 36 adult and pediatric cancers. Atlas-derived cancer signatures were used to determine tumor-cell line concordance and project ElasticNet models trained on DepMap CRISPR screens to infer cancer-specific gene dependencies. The scTumor Atlas establishes a scalable framework for tumor identity inference, cancer cell line benchmarking, and systematic identification of genetic vulnerabilities.

cancer biology↗

bioRxiv2026

TCR signal strength determines Treg instability and discrimination of self versus non-self antigens

Regulatory T cells (Tregs) expressing autoreactive T-cell receptors (TCRs) maintain immune self-tolerance, yet their fate upon antigen encounter remains unclear. Although selected in the thymus for high-affinity self-recognition, the cross-reactive nature of the TCR repertoire allows some Tregs to also recognize foreign antigens with high affinity. Here, we identify cross-reactive destabilization, a process in which high-affinity recognition of foreign antigens erodes Treg stability and redirects lineage fate. Using a thymic-derived Treg (tTreg) TCR capable of recognizing both self and foreign antigens distinct from the self-ligand that mediated its thymic selection, we show that stimulation with high-affinity non-self agonists induces Foxp3 loss and conversion into effector-like ex-Tregs, whereas self-antigen stimulation preserves lineage stability. Treg instability also increases with age and correlates with activation, suggesting that cumulative foreign-antigen exposure drives this process. These findings reveal a signal-strength-dependent model in which strong TCR engagement induces cross-reactive destabilization to balance immune responsiveness and self-tolerance. One Sentence SummaryForeign antigen-driven destabilization of Treg cells balances immunity and tolerance

immunology↗

bioRxiv2026

Deletion of NLRP3 gene blocks traumatic brain injury induced abnormal immune response in 3xTg AD mice

Traumatic brain injury (TBI) is a significant risk factor for the development of Alzheimers disease (AD) and related dementia. In both TBI and AD, inflammation plays a pivotal role. It is known that NLRP3 inflammasome plays an important role in pathogenesis of AD while TBI triggers activation of NLRP3 inflammasome in the brain. To evaluate the importance of NLRP3 inflammasome in mediating TBI-induced immune response in the context of predisposition of AD, we have examined the immune profiles in the brain using a novel transgenic AD mouse line with the NLRP3 gene deleted. Briefly, a group of 4 months old male and female 3xTg and 3xTg/NLRP3-/- mice received a moderate lateral fluid percussive injury or sham. Immune cell phenotypes and cytokine gene expression were assessed at 3- and 7-days post injury (dpi). We found that NLRP3 gene deletion counteracted injury-induced alteration of immune response in AD mice with a significant sex-related difference. Specifically, TBI induced a significant brain infiltration of neutrophils, macrophages and {gamma}{delta} T-cells in 3xTg mice in both sexes at 3dpi, and NLRP3 gene deletion blocked this injury effect only in males not in females. NLRP3 gene deletion also blocked injury-enhanced IL-1{beta}, TNF- gene expression in male AD mice, but not in female mice. In conclusion, our study has confirmed that TBI significantly alters the immune response in 3xTg-AD mice and NLRP3 inflammasome is important in mediating these TBI-induced changes with significant sex-related differences.

immunology↗

bioRxiv2026

Lmna deficiency promotes EPHX2 nuclear translocation to ameliorate cardiac dysfunction in mice

BackgroundCardiovascular diseases are often associated with altered protein subcellular localization. As a major cause of inherited cardiomyopathy, LMNA deficiency could trigger nuclear envelope rupture and broadly impair the localization of nuclear and cytoplasmic proteins. Systemic approaches to identify, dissect and manipulate the localization of endogenous proteins are important for mechanistic and therapeutic investigation. MethodProximity proteomics of the nuclear lamina was performed specifically in cardiomyocytes in Lmna-deficient murine models. AAV-mediated Cas9-based gene silencing and subcellular gene upregulation were conducted via the nuclear localization signal (NLS) and nuclear export signal (NES). Cas9-based somatic mutagenesis was supplemented with the single-strand DNA templates of AAV to achieve robust homology-directed repair (HDR) and targeted NLS knock-in, which translocated cytoplasmic proteins into nuclei. ResultIn vivo proximity proteomics detected increased epoxide hydrolase 2 (EPHX2) in cardiomyocyte nuclei in mice carrying germline or cardiac-specific Lmna truncating variants. This phenotype was associated with ruptured nuclear envelope. Cas9-mediated Ephx2 knockout in cardiomyocytes ameliorated cardiac dysfunction in Lmna-deficient mice. Strikingly, overexpression of NLS-EPHX2, but not NES-EPHX2, also mitigated cardiac dysfunction. The cardiac protective EPHX2 substrates, epoxyeicosatrienoic acids (EETs), did not alter upon NLS-EPHX2 overexpression. By contrast, the Lmna-related DNA damage marker {gamma}-H2AX was reduced. The EPHX-D333A mutant lacking hydrolase activity recapitulated the effects of wildtype EPHX2 in nuclei. AAV-Cas9-based HDR achieved efficient NLS knock-in and EPHX2 nuclear translocation in more than 60% cardiomyocytes, which improved cardiac function. ConclusionLmna deficiency leads to the nuclear translocation of EPHX2, which ameliorated cardiac dysfunction in a hydrolase-independent manner. AAV-HDR-mediated somatic gene editing provides an efficient approach to manipulate the subcellular localization of endogenous proteins in cardiomyocytes in vivo. What is Known?O_LICardiovascular diseases are regulated by the changes in protein subcellular localization. In particular, LMNA-related cardiomyopathy is associated with nuclear rupture and impaired separation between nuclear and cytoplasmic proteins. C_LIO_LIEpoxide hydrolase 2 (EPHX2) is a cytoplasmic hydrolase that catalyzes the hydrolysis of cardioprotective epoxyeicosatrienoic acids (EETs) and aggravates an array of heart diseases including myocardial infarction and heart failure. C_LIO_LICRISPR/Cas9-mediated homology-directed repair (HDR) exhibits uniquely high gene editing efficiency in cardiomyocytes with an AAV-based DNA donor, which is suitable for somatic genetic knock-in of small DNA fragments in vivo. C_LI What New Information Does This Article Contribute?O_LILamin-targeted proximity proteomics specifically in cardiomyocytes uncovers novel proteins undergoing subcellular localization changes upon Lmna deficiency. C_LIO_LILmna deficiency leads to EPHX2 nuclear translocation that ameliorates cardiac dysfunction by both mechanisms of cytoplasmic reduction and nuclear induction. C_LIO_LIAAV-HDR-mediated knock-in provides a robust platform to manipulate subcellular localization of endogenous proteins specifically in cardiomyocytes in vivo. C_LI Cardiovascular diseases are often associated with altered protein subcellular localization, but systemic approaches to identify, study and manipulate subcellular localization remain incomplete. This study established an in vivo proximity proteomics approach to identify novel proteins undergoing localization changes relative to the nuclear lamina. In murine models of LMNA-related cardiomyopathy, this approach uncovered EPHX2, a classic cytoplasmic hydrolase that aggravates cardiovascular diseases, as a new protein that translocated into cell nucleus and exerted a cardiac protective effect. CRISPR/Cas9-based cardiomyocyte gene editing with an AAV-based DNA donor efficiently achieved NLS knock-in into the Ephx2 gene, promoted EPHX2 protein nuclear translocation and mitigated cardiac dysfunction with Lmna deficiency. These findings indicated a novel avenue to identify and manipulate the subcellular localization changes of endogenous proteins for basic and translational cardiology.

pathology↗

bioRxiv2026

Fibroblast-specific Deletion of Yap/Taz Impairs Mouse Postnatal Dermal Development by Suppressing Collagen Production and Deposition

The Hippo pathway effectors YAP and TAZ are key regulators of cell proliferation, apoptosis, and differentiation, thereby maintaining tissue homeostasis and controlling organ size. While their roles in epithelial tissues and cancer are well established, their role in dermal fibroblast extracellular matrix (ECM) regulation is less understood. Here, we investigated the role of Yap/Taz during postnatal skin dermis development. During postnatal growth, mouse skin steadily grows and undergoes significant surface expansion. Postnatal deletion of Yap/Taz in dermal fibroblasts, the primary cells responsible for dermal ECM homeostasis, significantly impaired dermal maturation, as evidenced by marked deficiencies in collagen synthesis and deposition. Isolated fibroblasts from Yap/Taz knockout mice showed reduced proliferation and diminished expression of Yap/Taz target genes (Ccn2, Col1a1), which were rescued by reintroduction of active Yap/Taz. RNA-seq, and spatial transcriptomics and proteomics of Yap/Taz knockout skin revealed substantial downregulation of matrisome genes, including type I (Col1a1, Col1a2) and type III (Col1a3) collagens, which together constitute more than 90% of the skins collagen content. These findings demonstrate that Yap/Taz are essential for dermal ECM homeostasis, highlighting their therapeutic potential in skin regeneration, fibrosis, and aging-related ECM decline.

cell biology↗

bioRxiv2025

Ergothioneine: Evaluation of a Novel Antioxidant for Targeting Ocular Oxidative Stress

PurposeTo evaluate L-Ergothioneine (EGT), a naturally occurring amino acid and endogenous antioxidant, as a novel therapeutic agent for oxidative stress-related ocular diseases. This evaluation specifically aimed to address the challenge of targeted ocular delivery by assessing EGT s antioxidant potency, stability, ocular tolerance, and crucially, its ability to reach the posterior segment (fundus) via topical administration. MethodsThis study evaluated EGT as a novel ocular antioxidant by examining its radical scavenging capacity (DPPH assay compared to glutathione, astaxanthin, and coenzyme Q10), stability (at 40{degrees}C/75% relative humidity for six months using HPLC), ocular tolerance (using a New Zealand rabbit model), and fundus delivery efficiency (topical D9-EGT eye drops quantified by LC-MS/MS). ResultsEGT demonstrated significantly superior radical scavenging activity, exhibiting 6.4-fold and 46-fold higher rates than glutathione and coenzyme Q10, respectively, at 50 ppm. It also showed excellent stability, retaining over 97% of its initial concentration after six months, and caused no ocular irritation at any tested concentration (score 0). Importantly, topical administration of EGT resulted in effective fundus delivery, with peak concentrations reached at 0.5 hours post-application (1181 {+/-} 56 ng/g), confirming successful penetration through corneal and scleral barriers. These findings establish EGT as a potent, multi-mechanistic antioxidant characterized by high stability, ocular safety, and exceptional posterior segment penetrance via non-invasive eye drops. ConclusionThese findings establish EGT as a potent, multi-mechanistic antioxidant characterized by high stability, ocular safety, and exceptional posterior segment penetrance via non-invasive eye drops. By overcoming key delivery limitations, EGT presents a promising therapeutic strategy for oxidative stress-related ocular diseases such as age-related macular degeneration and diabetic retinopathy. Further studies are warranted to evaluate its long-term efficacy and clinical translation potential.

pharmacology and toxicology↗

bioRxiv2025

Longitudinal Identification of Zebrafish Individuals by Deep Learning

The zebrafish (Danio rerio) is a critical vertebrate model organism in biomedical research. Accurate identification and longitudinal tracking of individual fish within cohorts enable linking genotype to complex phenotypes, essential for elucidating the molecular mechanisms underlying disease pathogenesis and trait formation. Nevertheless, the establishment of reliable long-term individual identification remains a significant challenge, primarily due to their diminutive size and minimal interindividual morphological variations. We developed ESC-IDNet, a dual-stage deep learning cascade architecture deployed on the FishIndivID platform (http://bioinfo.ihb.ac.cn/fishindivid), enabling high-precision identification. Trained and tested on [~]300,000 images from 450 zebrafish (31-122 dpf), our lateral body-based identification maintained >95% accuracy with updates only every 20 days, significantly outperforming dorsal head identification (requiring [~]13-day updates). Both views achieved 100% accuracy in 1-2 day tasks. ESC-IDNet surpassed alternatives in segmentation, alignment, feature extraction, and feature matching. This framework provides a robust, transferable paradigm for individual identification in fish species.

bioinformatics↗

bioRxiv2025

General features of cognition gene polymorphism patterns in marine fish

A growing body of evidence suggests that the cognitive abilities of fish are far more advanced than traditionally believed. They are not mere "automata" driven by instinct, but complex organisms capable of learning, remembering, solving simple problems, engaging in social interactions, and even deception. This situation has prompted us to explore genes related to cognitive functions in the fish genome, examining the pattern status of a set of SNVs (single nucleotide variations) in their cognitive genes relative to the human genome sequence. This study investigates the locus status of 1,824 SNVs from 33 human cognitive genes across the whole genomes of 90 fish species. Based on this, preliminary findings indicate that fish exhibit approximately four patterns of cognitive gene polymorphism. One of these patterns includes at least two coelacanth/lungfish samples, which directly point to the evolutionary direction of the ancient human sd1 sample (an ancient human hair sample from Sudan, Africa).

molecular biology↗

bioRxiv2025

TDP-43 suppression of ATP8A2 cryptic splicing implicates phosphatidylserine-driven neuroinflammation in ALS/FTD

Inappropriate externalization of phosphatidylserine (PS) is a candidate mechanism of pathogenic neuroinflammation, a critical driver of neurodegenerative disease. ATP8A2, a flippase that maintains PS on the plasma membrane inner leaflet, is mutated in both Wabbler-lethal mice and patients with the ataxia syndrome CAMRQ4. Here, we identify ATP8A2 as a target of TDP-43 cryptic exon suppression, and demonstrate that ATP8A2 loss leads to immune-mediated neurodegeneration. ATP8A2 splicing is significantly dysregulated following TDP-43 depletion in human neurons and in brains of patients with Amyotrophic Lateral Sclerosis-Frontotemporal Dementia (ALS-FTD). In mice, Atp8a2 loss increases PS exposure and promotes neuroinflammation. Depletion of peripheral macrophages rescues motor axon degeneration and doubles Atp8a2 knockout mouse lifespan, while depletion of both peripheral macrophages and central microglia quadruples lifespan and improves coordination. Hence, ATP8A2 is a pathologically relevant TDP-43 target and inhibition of phagocytic immune cell attack against neurons is a potential treatment for patients with CAMRQ4 and ALS-FTD.

neuroscience↗

bioRxiv2025

Multidimensional Single-Cell Transcriptomic Profiling of Uterine Leiomyosarcomas Identifies Molecular Subtypes with Distinct Therapeutic Vulnerabilities

Uterine leiomyosarcoma (ULMS) is an orphan disease that frequently recurs and metastasizes, with patients undergoing multiple lines of chemotherapy due to lack of effective therapeutic targets. To address this gap, we used single-cell RNA sequencing and spatial transcriptomic analysis to comprehensively profile ULMS. We uncovered multiple states of tumor cells, including tumor cells with mesenchyme-like features, ischemic tumor cells defined by a MYC program, inflammatory tumor cells with active interferon signaling, and stem cell-like hormone receptor-positive cells. The inferred spatial correlates of these tumor cell states demonstrated unique localization patterns. By correlating these signatures to bulk RNA sequencing data, we demonstrate the relevance of these findings to clinical outcomes. Finally, using the single-cell integration and drug response prediction algorithm (scIDUC), we propose drug predictions that may target specific tumor states. Our findings suggest new avenues for further exploration of individualized and multifaceted therapeutic strategies to treat ULMS.

cancer biology↗

bioRxiv2025

High-Fidelity Neural Speech Reconstruction through an Efficient Acoustic-Linguistic Dual-Pathway Framework

Reconstructing speech from neural recordings is crucial for understanding speech coding and developing brain-computer interfaces (BCIs). However, existing methods trade off acoustic richness (pitch, prosody) for linguistic intelligibility (words, phonemes). To overcome this limitation, we propose a dual-path framework to concurrently decode acoustic and linguistic representations. The acoustic pathway uses a long-short term memory (LSTM) decoder and a high-fidelity generative adversarial network (HiFi-GAN) to reconstruct spectrotemporal features. The linguistic pathway employs a transformer adaptor and text-to-speech (TTS) generator for word tokens. These two pathways merge via voice cloning to combine both acoustic and linguistic validity. Using only 20 minutes of electrocorticography (ECoG) data per subject, our approach achieves highly intelligible synthesized speech (mean opinion score = 4.0/5.0, word error rate = 18.9%). Our dual-path framework reconstructs natural and intelligible speech from ECoG, resolving the acoustic-linguistic trade-off.

neuroscience↗

bioRxiv2025

A paradigm shift of SERPINA3N in neurobehavioral development and brain injury

Murine serine protease inhibitor clade A member 3N (SERPINA3N) and its human ortholog SERPINA3 are dysregulated in neurological disorders. SERPINA3N has been proposed as a protective factor, enhancing neurobehavioral development under homeostasis and mitigating neuronal/glial and vascular damage under neurological conditions. Here, we employed powerful, non-invasive genetic tools to revisit the concept of SERPINA3N in brain development and injury. Brain-specific SERPINA3N overexpression neither alters neuronal or glial development nor improves cognitive ability under homeostasis. In stark contrast, SERPINA3N drives a pro-inflammatory response to brain injury and exacerbates blood-brain barrier dysfunction. Its overexpression promotes neurodegeneration through apoptosis-mediated neuronal loss and disrupts oligodendroglial differentiation and myelination following neonatal brain injury. Collectively, our findings challenge the prevailing paradigm of SERPINA3N in neurodevelopment and injury, revealing that while SERPINA3N is dispensable for neurobehavioral development, it aggravates neural injury and vascular damage under pathological conditions.

neuroscience↗

bioRxiv2025

Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction

TDP-43 pathology is a defining pathological hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major feature of TDP-43 pathology is its nuclear depletion, leading to the aberrant inclusion of cryptic exons during RNA splicing. STMN2 and UNC13A have emerged as prominent TDP-43 splicing targets, but the broader impact of TDP-43-dependent cryptic splicing on neuronal function remains unclear. Here, we report new TDP-43 splicing targets critical for membrane excitability and synaptic function, including KALRN, RAP1GAP, SYT7 and KCNQ2. Using human stem cell-derived neurons, we show that TDP-43 reduction induces cryptic splicing and downregulation of these genes, resulting in impaired excitability and synaptic transmission. In postmortem brains from patients with FTD, these cryptic splicing events occur selectively in neurons with TDP-43 pathology. Importantly, suppressing individual cryptic splicing events using antisense oligonucleotides partially restores neuronal function, and combined targeting almost fully rescues the synaptic deficit caused by TDP-43 loss. Together, our findings provide evidence that cryptic splicing in these synaptic and membrane excitability genes is not only a downstream marker but instead a direct driver of neuronal dysfunction, establishing a mechanistic link between TDP-43 pathology and neurodegeneration in ALS and FTD.

neuroscience↗