Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Revealing the antibiotic resistome in the global hadal trenches by large-scale cultivation and metagenomics

The global hadal trenches that reside more than 6000 meters below the sea level, represent one of Earths most remote ecosystems, potentially harboring a microbial reservoir for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the global hadal environments remain the least investigated ecosystem for ARB/ARG compositions and distribution. This study took three-fold approaches to investigate the ARB/ARGs in the global hadal trench sediments, i.e., large-scale cultivation to isolate and verify ARB/ARGs from Challenger Deep sediments, metagenomic analysis of sediment samples from Challenger Deep over a six-year period, and comparative study of resistomes across six hadal trenches through metagenomic analysis. The Challenger Deep sediments had a consistent average ARG abundance of 0.02 copy/cell over a six-year period, whereas some ARG subtypes fluctuated and showed distinct temporal dynamics. Large-scale screening of ARB via microbial cultivation using 13 classes of antibiotics led to enriching distinct ARB, for which eleven genera were identified by metagenomic sequencing as major host for ARGs. The global hadal trench sediments showed a variable ARG abundance, which was significantly lower than those from environments in proximity to human activities, representing a relatively pristine reservoir. Phylogenetic analysis suggested the hadal ARGs underwent niche-specific selections and formed hadal trench-specific clusters that diverged from human-associated lineages, which can be outward transported when disturbed. The study established the hadal trench sediments, as a relatively pristine reservoir of natural ARGs, providing a crucial environmental baseline for assessing their impacts on the ecosystems and public health risks.

microbiology↗

bioRxiv2025

In vitro study of the growth, reproduction and pathogenicity responses of Fusarium oxysporum f. sp. zingiberi to autotoxins from ginger

Long-term monoculture of ginger triggers Fusarium wilt, a disease caused by Fusarium oxysporum f. sp. niveum (Foz). However, the role of autotoxins in promoting pathogen growth remains unclear. Four representative autotoxins, syringic acid, coumarin, ferulic acid and 7-Hydrooxycoumarin were selected to investigate their allelopathic effects on the growth, reproduction, and virulence-associated traits of Foz. The responses of Foz to these compounds exhibited notable variations, which may be attributed to the structural differences among the autotoxins. The autotoxic compounds differentially enhanced the key pathogenic traits of Foz. Syringic acid was the most effective stimulant of mycelial growth and cell wall-degrading enzymes activity, concurrently boosting mycotoxin production via upregulating FUB3 gene expression. Ferulic acid was the most potent promoter of sporulation and biomass accumulation, whereas 7-Hydroxycoumarin most effectively stimulated conidial germination. Notably, coumarin suppressed mycelial growth but strongly induced mycotoxin synthesis in Foz. These results provide mechanistic insights into how autotoxins in ginger monoculture systems promote Fusarium wilt.

microbiology↗

bioRxiv2025

Engineering the citrus phyllosphere microbiome for enhanced disease resistance to bacterial canker

Engineering phyllosphere microbiomes toward plant protection against pathogens on crops has shown promising effects. Here we tested the effect of application of beneficial bacteria individually and as a synthetic community (SynCom) on the phyllosphere microbiome and management of bacterial canker caused by Xanthomonas citri subsp. citri (Xcc). Foliar spray of a SynCom consisting of three citrus endophytic bacterial strains (Paenibacillus sp. ATY16, Bacillus megaterium PT6, and Bacillus subtilis PT26A, SynCom1) with mechanistically complemented plant-beneficial properties exerted a more profound effect on the leaf microbiota and suppression of citrus canker than single strains. Cultivation-dependent and bacterial 16S rRNA gene-sequence profiling analyses revealed that leaf endophytic Bradyrhizobium, Brevibacillus, Cellvibrio, Flavobacterium, and Pseudomonas were significantly enriched in the SynCom treated plants, in addition to Bacillus and Paenibacillus. The enriched Brevibacillus and Pseudomonas spp. were isolated, whole-genome sequenced, and confirmed to possess multiple beneficial traits including antimicrobial activity against Xcc, Moreover, the expression of citrus defense genes was induced by the SynCom1 inoculation. Foliar application of SynCom1 and a newly assembled SynCom (SynCom2; SynCom1 with representative Brevibacillus and Pseudomonas isolates) prior to Xcc inoculation significantly reduced the citrus canker disease severity in greenhouse assays, and SynCom2 had a better efficacy, comparable to a copper bactericide. Three-year field tests showed that both SynCom1 and SynCom2 effectively controlled citrus canker, with a 50% reduction of foliar and fruit canker incidence. Collectively, these findings provide novel insights and valuable clues for microbiome engineering to serve as a sustainable strategy for the control of phyllosphere pathogens on crops.

plant biology↗

bioRxiv2025

Creating an energy efficient central metabolism for boosting biosynthesis without compromising cell growth of yeast

Long-term natural evolution selects glycolysis as the major metabolic mode for rapid cell growth, which however lacks sufficient NADPH supply to dive the biosynthesis of reduced chemicals such as free fatty acids (FFAs). Engineering energy economical pathway for chemical overproduction always compromises cellular fitness due to the rigidity of cellular metabolism. Here, we successfully replaced glycolysis metabolism with an optimized pentose phosphate pathway (PPP) in an industrial yeast Ogataea polymorpha, for the first time, which enabled a higher energy generation efficiency than glycolysis and a balanced supply of ATP and NADPH. More importantly, we discovered a global carbon metabolism regulator CMR that drives metabolic flux toward glycolysis for energy generation, and its disruption relieved the tight regulation of metabolic flux distribution and significantly enhanced the efficiency of cellular energy generation, which significantly boosted the FFA production by 63% in a FFA overproducing chassis. The final engineered yeast produced FFAs at a titer of 41.7 g/L, the highest titer reported by microbial fermentation. Our work provides valuable insights into the metabolic regulation mechanisms and a feasible approach for constructing energy efficient metabolism for chemical overproduction.

synthetic biology↗

bioRxiv2025

Reconstructing the emergence of the human chorion via HIPPO-mediated trophoblast induction

The first lineage decision in the mammalian blastocyst commits outer cells to the trophectoderm and initiates the trajectory that gives rise to the placental chorion. The molecular sequence that unfolds downstream of HIPPO pathway inactivation, linking human trophectoderm specification to the early organization of the chorion, has remained unknown. Here, we establish a developmentally informed model that leverages HIPPO pathway modulation to induce the native trophectoderm trajectory in the absence of exogenous BMP or WNT signaling. We first transiently reset primed human pluripotent stem cells into a trophectoderm-competent ground state, followed by LATS kinase inhibition to set the trajectory in motion. To benchmark fidelity, we built an embryo-chorion single-cell reference integrating published early human and placental transcriptomes and applied a computational stage-matching tool to align our cultures to natural development. Stage matching revealed an ordered progression along the trophectoderm trajectory from early TE to post-implantation trophoblast. With extended culture, all major cell types of the nascent chorion emerged, encompassing both trophoblast and chorionic mesoderm lineages. Within the trophoblast, we identified proliferative and non-cycling villous cytotrophoblast, a columnar population connecting villous and extravillous domains, as well as syncytia and extravillous subtypes. When cultured in suspension, these lineages self-organized into three-dimensional organoids that recapitulated the stromal-epithelial architecture and proliferative-syncytial polarity of the emergent chorion. We identified CLDN6 as a defining surface marker of columnar trophoblast, the population that bridges villous and extravillous compartments. Prospective isolation of living CLDN6+ trophoblast revealed their capacity to reacquire a proliferative villous state and, under directed cues, generate both syncytial and extravillous fates, confirming their proposed dual developmental potential within the chorion. Together, these findings establish a developmentally informed framework that connects human trophectoderm specification to the emergent chorion and provides a dynamic platform for investigating the earliest steps of placental specification and the origins of implantation disorders.

cell biology↗

bioRxiv2025

Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases

Colorectal cancer (CRC) brain metastases have a poor prognosis and limited treatment options, including resistance to radiation therapy. Little is known about the molecular and cellular mechanisms that enable CRC tumor cells to adapt to the brain and establish a supportive tumor microenvironment. To address this gap we used spatial transcriptomics to analyze 51 CRC brain metastases. A subset had matched primary colon tumors and longitudinally paired metastatic resections before and after radiation treatment. We identified the critical spatial cellular features of the tumor epithelium and the surrounding tumor microenvironment that support metastatic growth in the brain. CRC brain metastases developed a stromal microenvironment with abundant fibroblasts and tumor-associated macrophages. A fibroblast-macrophage cellular neighborhood promoted angiogenesis, extracellular matrix remodeling, and immune suppression. Tumor cells showed local adaptations. In endothelial-rich regions, they were proliferative whereas in macrophage-rich regions, they were more differentiated and immune evasive. Compared with paired primary tumors, CRC brain metastases showed increased chromosomal instability, with activation of RNA-processing, stress response, and junctional remodeling pathways. After radiation treatment, resistant clones had increased epithelial-mesenchymal transition, while the immunosuppressive stroma remained intact. We identified tumor-derived MIF, GDF15, PRSS3 and SEMA3C ligands and macrophage-derived SPP1 that have the potential to affect multiple cell types in the metastatic niche. These ligand-receptor interactions drive angiogenesis, stromal activation and immune suppression. In a macrophage-tumor-fibroblast co-culture model, knockout of SPP1 in macrophages led to reduced expression of lipid-metabolism related genes and disrupted tumor-promoting interactions. Together, these results indicate that CRC growth in the brain is sustained by a specific cellular organization with immunosuppressive multicellular interactions.

cancer biology↗

bioRxiv2025

Deep learning reveals a microprotein atlas in maize and uncovers novel regulators of seed amino acid metabolism

Microproteins represent a vast and functionally important class of genes that remain largely unexplored in plant genomes. Here, we developed DeepMp, a deep learning framework that integrated multi-omics evidence and built the most comprehensive plant microprotein atlas to date, identifying 18,338 high-confidence candidates in maize. The majority of these appear to have originated de novo from regions previously annotated as noncoding, and they show hallmarks of rapid, lineage-specific evolution and pronounced tissue specificity. These novel microproteins were found integrated into core regulatory networks, particularly in organ development and nutrient storage. Focusing on the maize kernel, population-scale analyses linked microprotein expression to natural variation in amino acid content. We functionally validated three grain-filling-specific candidates originating from noncoding regions by CRISPR-Cas9 knockouts, which confirmed their roles as precise modulators of arginine, aspartate, and methionine levels, without pleiotropic effects on kernel morphology. Our study provides a foundational resource and analytical framework, establishes microproteins as a new and functionally important coding layer in maize, and uncovers a previously untapped source of targets for crop improvement.

genomics↗

bioRxiv2025

mRNA isoform switching plays a crucial role in mural cumulus differentiation

During gonadotropin-induced ovarian follicle development, an antral cavity forms within the layers of granulosa cells (GCs). Gonadotropin stimulation also differentiates the GCs into two distinct lineages: mural GCs (mGCs), which surround the antral cavity, and cumulus GCs (cGCs), which stay in contact with the oocyte. We examined the transcriptomes of mouse mural and cumulus cells to understand the mechanism of differentiation. In addition to analyzing a single transcript expression per gene, we also considered multiple isoform expressions to explore differential transcriptomics. GC-specific core transcription factors Foxl2, Nr5a1, Nr5a2, Runx1, and Runx2 were expressed at high levels in mGCs but downregulated in cGCs, indicating that cGCs acquire a more differentiated state. Both single-transcript and multiple-isoform analyses revealed differential expression of about 70% of transcripts between mGCs and cGCs. Although the counts were similar, the differentially expressed genes (DEGs) at the single transcript level did not correlate well with the respective differentially expressed transcript isoforms (DETI). We identified DETIs originating from key epigenetic and transcriptional regulator genes, such as Chd1, Ezh2, Kdm5a, Kdm5b, Gata4, Esr2, Fos, Myc, and Ybx1, that were not differentially expressed at the single-transcript analysis. Further analysis revealed a transcript switch in one-third of the DETIs. Most of the transcript isoforms were protein-coding, followed by non-coding regulatory RNAs. A total of 1,302 transcript isoforms were silenced in cGCs, including those of Adar, Cebpa, Dnmt3a, Foxo4, Pgr, Rest, Runx1, Satb2, Sirt1, Sirt2, and Tead1. Conversely, 529 transcript isoforms were activated in cGCs, including transcripts for Brd7, Crem, Chd1, Med21, Med27, Nfkbia, Rbm39, Rbmx, Suv39h2, Tcf12, Xist, and Ybx3. Additionally, 57 genes exhibited DETIs, with at least one isoform turned off and another turned on in cGCs, including Csde1, Dab2, Ezh2, Gata4, Gnas, Gtf2i, Macf1, Klf10, Setdb1, and Sp3. Finally, we explored the mechanisms underlying transcript switching during the differentiation of mGCs and cGCs. Our findings suggest that gonadotropin-induced transcript switching in GCs is crucial for mural and cumulus granulosa differentiation, a key insight that would be missed without mRNA isoform analysis.

cell biology↗

bioRxiv2025

The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize

Heterosis, or hybrid vigor, is a key phenomenon in genetics research and agricultural production, and has been primarily attributed to non-additive genetic effects such as dominance -- a prevailing consensus shaped by decades of empirical research and theoretical debate. Although dominance may arguably arise from distal modifiers, their selective advantage is debated due to presumably small individual effects. To address this long-standing question, particularly how genetic dominance manifests at the transcriptomic level and contributes to phenotypic heterosis, we integrated transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We found that [~] 30% of the expressed seedling genes in a significant proportion of hybrids exhibited expression patterns deviating from the average of the two parents, indicative of non-additivity. Further analysis suggests that while hybrid gene expression per se is primarily regulated by cis-eQTLs, expression dominance (or non-additivity) is disproportionately controlled by trans-eQTLs. These trans-eQTLs cluster into hotspots that regulate the non-additivity of hundreds of target genes, mostly within co-expression networks, and are notably enriched for transcription factors (TFs). Focusing on one such hotspot, we functionally validated a classical maize gene ZmR1, a basic helix-loop-helix (bHLH) TF associated with multiple seedling trait heterosis, as a candidate regulator of expression dominance across hundreds of genes. Overexpression of ZmR1 enhances expression dominance of downstream genes and increases phenotypic heterosis in both seedling and adult traits. Further experiments confirmed its direct regulatory role in modulating genes involved in anthocyanin biosynthesis and lignin metabolism, driving transcriptome-level dominance. These results provide empirical support for the modifier hypothesis under an omnigenic model, suggesting that heterosis arises not from the modification of a single genes inheritance but through the coordinated regulation of hundreds of phenotype-associated genes, thereby helping to reconcile the long-standing debate over the genetic basis of dominance in heterosis.

genetics↗

bioRxiv2025

StrainOptimizer empowers rational cell factory design through multi-scale metabolic models with expression and proteome constraints

The rational design of microbial cell factories for high bioproduction remains a key challenge in metabolic engineering. While advanced modelling frameworks incorporating protein resource allocation, such as enzyme-constrained models (ecGEMs) and Expression and Thermodynamic Flux (ETFL), provide superior predictive power, their application is limited by a lack of user-friendly computational tools. Here, we present strainOptimizer, a comprehensive computational platform for rational strain design that systematically evaluates key resource allocation principles: the coupling of gene expression with metabolism, subcellular compartmentalization, and enzyme capacity limitations. Our benchmark analyses demonstrate that each principle offers distinct advantages: models coupling metabolism and expression (like ETFL) enable the identification of non-metabolic targets, organelle-level proteomic constraints improve precision for high-protein-cost products, and protein-usage-based objectives consistently outperformed traditional flux-based approaches. To demonstrate its practical utility, we applied strainOptimizer to an engineered sclareol-overproducing Saccharomyces cerevisiae strain. The platform identified novel targets, and experimental validation confirmed a 67% success rate, increasing the final sclareol titer by 14-26% and productivity by up to 45%. StrainOptimizer bridges the gap between resource allocation theory and applied engineering, providing a powerful, validated tool to accelerate the development of high-performance cell factories.

bioengineering↗

bioRxiv2025

High-throughput functional characterization of enhancers in totipotent-like cells

Zygotic genome activation (ZGA) marks the initial transcription event in embryogenesis, yet the cis-regulatory mechanism remains unclear. Here, utilizing massively parallel reporter assays, we functionally dissect enhancers across mouse genome in DUX-induced 2C-like cells (2CLCs). Integrated analysis with epigenomic and transcriptomic data from 2CLCs and 2-cell (2C) embryos, active enhancers in totipotent cells are depicted. Among them, a notable proportion of promoters exhibit enhancer activities, showing elevated active chromatin features and correlating with enhanced gene expression during ZGA. Furthermore, only half of the MT2_Mm exhibit enhancer activities in 2CLCs. In addition, 2CLC enhancers augment transcription in 2C embryos. Finally, deleting enhancer regions in both 2CLCs and 2C embryos highlighted their crucial role in facilitating transcription of ZGA genes. These findings advance our comprehension of the cis-regulatory mechanism governing ZGA process.

developmental biology↗

bioRxiv2025

Disruption of ADAMTSL4 Causes Ectopia Pupillae in Zebrafish via COL8A1-Driven Cell Migration

Congenital ectopia lentis (EL) poses a significant threat to visual outcomes in children. Although emerging causative genes have been identified, their biological functions remain poorly understood. In this study, we investigated the contribution of ADAMTSL4 variants to congenital EL in a cohort of 702 pedigrees. Pathogenic variants in ADAMTSL4 were identified in 23 probands (3.28%), comprising 29 distinct variants, with 14 being novel, making ADAMTSL4 the second most frequently mutated gene in the cohort. All affected individuals exhibited EL, and 26.09% also presented with ectopia pupillae (EP), also referred to as ectopia lentis et pupillae. To explore the functional consequences of ADAMTSL4 deficiency, we generated a CRISPR/Cas9-mediated adamtsl4-knockout zebrafish model, that faithfully recapitulated cardinal human disease features with an incidence comparable to that observed in affected patients. Histological and ultrastructural analysis revealed disrupted zonular fiber anchorage at the lens capsule, even in mutated eyes without overt EL or EP. Transgenic overexpression of adamtsl4 successfully reversed the ocular phenotypes, confirming the genes essential role in ocular development. Single-cell RNA-sequencing and fluorescence in situ hybridization demonstrated enriched ADAMTSL4/adamtsl4 expression in the equatorial lens epithelium, retinal pigment epithelium (RPE), iris anterior pigmented epithelium, and choroid fibroblast. Functional assays using zebrafish and human RPEs revealed that ADAMTSL4 deficiency compromised cell adhesion and promoted cell migration. Transcriptomic profiling revealed significant enrichment of extracellular matrix organization and cell adhesion pathways, with cross-species validation identifying consistent upregulation of COL8A1/col8a1b. Notably, COL8A1 knockdown in ADAMTSL4-deficient RPEs partially reversed the aberrant migratory phenotype, suggesting a functional interaction. Together, these findings establish ADAMTSL4 as a major causative gene in ectopia lentis et pupillae, highlight its role in orchestrating ocular integrity via regulation of extracellular matrix and cell behavior.

genetics↗

bioRxiv2025

PCSK9 and High-Fat Diet Synergistically Induce Neurovascular Dysfunction and Neuroinflammation

Cerebral small vessel disease (CSVD) is strongly linked to metabolic risk factors and represents a major cause of vascular cognitive impairment and dementia. The interactions of genetic and environmental risk factors driving cerebrovascular pathology in metabolic syndrome are poorly understood. Here, we characterize neuroinflammatory and neurodegenerative phenotypes in a mouse model of metabolic syndrome with atherosclerosis induced by hepatic proprotein convertase subtilisin/kexin type 9 (PCSK9) overexpression combined with high-fat diet (HFD). PCSK9+HFD mice exhibit hallmark features of CSVD including vascular rarefaction, impaired neurovascular coupling, blood-brain barrier disruption, white matter injury, neuronal loss, and cognitive deficits. Notably, we identify lipid-droplet accumulating microglia (LDAM) as a distinct cellular phenotype that emerges in response to metabolic stress and correlates with cerebrovascular dysfunction. Three-dimensional light sheet microscopy reveals widespread vascular network disruption. Immunophenotyping demonstrates that microglia in PCSK9+HFD group exhibit enhanced phagocytic activation and ramification complexity yet accumulate perivascular amyloid-{beta}, suggesting impaired clearance capacity. Importantly, we observed vascular amyloid-{beta} deposition in wild-type mice without genetic Alzheimers disease mutations, suggesting that metabolic stress contributes to cerebrovascular amyloid pathology. PCSK9+HFD mice displayed recognition memory deficits and increased anxiety-like behavior. Our findings establish that severe hypercholesterolemia accelerates CSVD pathogenesis, and identify LDAM as a distinct pathological feature linking systemic metabolic syndrome to cerebrovascular dysfunction and cognitive impairment.

neuroscience↗

bioRxiv2025

Diverse ways of holding verbal information in mind revealed with functional Magnetic Resonance Imaging and Transcranial Magnetic Stimulation: Individual differences in left anterior parietal cortex

Cognitive neuroscience has identified brain systems that reliably underpin specific abilities, including verbal short-term memory. However, there is no simple mapping between anatomy and function; moreover, brains are differently organised across people. In two functional magnetic resonance imaging studies, and using transcranial magnetic brain stimulation to test causality, we characterised differences in the neural processes supporting verbal short-term memory in healthy participants who varied in their use of semantic information. In group analyses, left anterior inferior parietal cortex showed the expected pattern for a "phonological buffer" -- this site was responsive to phonological tasks and verbal short-term memory for meaningless items. However, the functions of this site differed across the sample; individuals with the strongest "semantic reliance" in short-term memory (showing higher imageability effects and poorer nonword performance) showed weaker phonological responses. They also showed more activation when maintaining meaningful word sequences in short-term memory, compared with nonwords. In these semantically-reliant participants, left anterior inferior parietal cortex showed stronger functional connectivity to limbic and default mode regions during nonword rehearsal. While inhibitory stimulation to phonologically responsive regions disrupted nonwords more than words in people with good phonological short-term memory, these effects were reversed when verbal short-term memory was more semantically reliant. These findings show that left anterior inferior parietal cortex supports the maintenance of different kinds of verbal information across individuals.

neuroscience↗

bioRxiv2025

Microglia coordinate activity-dependent protein synthesis in neurons through metabolic coupling

De novo protein synthesis is required for long-lasting synaptic plasticity and memory, but it comes with a great metabolic cost. In the mammalian brain, it remains unclear which cell types and biological mechanisms are critical for sensing and responding to increased metabolic demand. Here we demonstrate that microglia, resident macrophages of the brain, coordinate metabolic coupling between endothelial cells, astrocytes, and neurons to fuel protein synthesis in active neurons. Increasing metabolic demand via a motor task stimulates microglia to secrete the hypoxia-responsive protein CYR61, increasing glucose transporter expression in brain vasculature. Depleting microglia reduces training-induced metabolic fluxes and neuronal protein synthesis, which can be reproduced by blocking CYR61 signaling. Thus, we define a neuroimmune metabolic circuit required for on-demand protein synthesis in mouse motor cortex.

neuroscience↗

bioRxiv2025

The disordered JM motif in RTKs promotes classical DFGout conformation formation via dynamic effect

Receptor tyrosine kinases (RTKs) are validated anti-cancer targets, and targeting their DFGout conformations represents a mainstream strategy for developing highly selective type II inhibitors. RTKs can adopt various DFGout conformations, but only the classical ones with a fully formed back pocket are structurally validated to accommodate type II inhibitors. However, such classical DFGout conformations are scarce, presenting a significant obstacle for selective RTK inhibitor design. Recently, a conserved disordered motif N-terminal to the kinase domain of RTKs, called the juxtamembrane (JM) motif, has been reported to regulate inhibitor binding to the DFGout conformation of VEGFR2, an RTK involved in angiogenesis. In this study, we performed extensive MD simulations to explore the impact of the disordered JM motif on the conformational space of the DFG motif in RTKs and its relationship to inhibitor binding at the active site of VEGFR2. We revealed that in VEGFR2, the disordered JM is highly dynamic and forms transient contacts with the kinase domain, and consequently fine-tunes the DFGout sub-conformational space to shift populations from non-classical to classical DFGout conformations. This dynamic model provides the structural basis underpinning the reported regulatory effects of JM on inhibitor binding toward VEGFR2. Addtionally, we demonstrated that in other RTKs beyond VEGFR2, the disordered JM similarly promotes classical DFGout conformations. Such role of JM is particularly favorable for creating druggable DFGout conformations that can be exploited for designing high-selectivity type II inhibitors.

biophysics↗

bioRxiv2025

Cardiomyocyte-specific plakophilin-2 loss is sufficient to induce aging and senescence of nonmyocytes. Relevance to arrhythmogenic cardiomyopathy.

IntroductionPathogenic variants in PKP2 are the most common cause of familial arrhythmogenic right ventricular cardiomyopathy (ARVC). ObjectiveTo test whether PKP2 deficiency only in cardiomyocytes is sufficient to provoke premature aging and pro-inflammatory senescence in non-myocytes, cardiac resident cells. MethodsWe studied mice with cardiomyocyte-specific, tamoxifen-activated loss of PKP2 (PKP2cKO) using conventional and multiplex imaging, cytokine arrays, epigenetic clocks, spatial transcriptomics, expansion and structured illumination microscopy, and correlative data analysis. We examined non-myocytes and cardiomyocytes for premature aging and senescence. ResultsWe observed senescence-associated heterochromatin foci (SAHFs) and p21 staining in non-myocytes. Cytokines in media of non-myocyte cells were consistent with senescence-associated secretory phenotype (SASP). Epigenetic clocks identified premature aging. Multiplex immunohistochemistry showed non-myocyte cells in niches, intermingled with cardiomyocytes. Spatial transcriptomics showed over-representation of SASP-related transcripts, predominantly in myocyte-rich areas of the left ventricle. SAHFs, p21 staining and increased epigenetic age were not found in cardiomyocytes from PKP2cKO hearts, though we observed structural features associated to premature aging. Cross-reference analysis showed correlation between the PKP2cKO cardiac proteome and that of mice 5 or 6 times their chronological age, as well as transcriptional signatures of neurodegenerative diseases. ConclusionLoss of PKP2 expression only in adult cardiac myocytes is sufficient to induce pro-inflammatory senescence in non-myocytes, and overall premature cardiac aging. This is the first study to intersect cellular senescence and premature aging in desmosomal arrhythmogenic cardiomyopathies. We speculate that cell-agnostic molecular signatures, biomarkers, and pharmacology of senescence and of neurodegenerative diseases may be relevant to diagnose or treat PKP2-ARVC. UNSTRUCTURED ABSTRACTPathogenic variants in PKP2 are the most common cause of familial arrhythmogenic right ventricular cardiomyopathy. We used the PKP2cKO model (cardiomyocyte-specific, tamoxifen-activated PKP2 knockout) to examine whether PKP2 deficiency only in cardiomyocytes is sufficient to provoke premature aging and pro-inflammatory senescence in non-myocyte, cardiac resident cells. Through a variety of methods, we identified senescence-associated heterochromatin foci (SAHFs), p21 staining, and cytokines consistent with senescence-associated secretory phenotype (SASP) in cells and media of non-myocytes. Epigenetic clocks identified premature aging. Spatial transcriptomics showed over-representation of SASP-related transcripts, predominantly in myocyte-rich areas of the left ventricle. SAHFs, p21 staining and epigenetics suggesting advanced age were not found in cardiomyocytes, though we observed structural features associated to premature aging. Cross-reference analysis showed correlation between the PKP2cKO cardiac proteome and that of mice 5 or 6 times their chronological age, as well as transcriptional signatures of neurodegenerative diseases. HIGHLIGHTSO_LIPKP2-ARVC is a leading cause of sudden unexpected death in the young. C_LIO_LIThe molecular path from the variant of a gene to the clinical disease remains unclear. An inflammatory component has been postulated. C_LIO_LIWe show that loss of PKP2 only in myocytes is sufficient to induce a pro-inflammatory senescence in non-myocytes and premature aging of cardiac cells. C_LIO_LISimilarities to the molecular profile of neurodegenerative diseases and novel paths to therapy are discussed. C_LI

physiology↗

bioRxiv2025

Abnormally increased intrinsic neural timescales in sensory and default mode networks in cocaine use disorder

Cocaine use disorder (CUD) is associated with abnormal structural and functional brain changes. However, the neurodynamics and molecular underpinnings remain unclear. In this study, we mapped whole-brain intrinsic neural timescales (INTs), reflecting temporal neural processing, using resting-state functional magnetic resonance imaging data from 44 CUD patients and 44 healthy controls (HC). CUD showed increased INTs in visual, somatomotor, and default mode networks compared with HC. Mediation analysis linked local INTs abnormalities to altered dorsal attention network neurodynamics, associated with inhibitory control deficits. Notably, these changes were primarily correlated with alterations in gamma-aminobutyric acid type A receptors and the noradrenaline transporter. Machine learning classifiers based on INTs achieved a maximum accuracy of 75.5% in distinguishing CUD from HC, with a generalization accuracy of 65.0% on an independent dataset. This study elucidates aberrant neural mechanisms underlying CUD and highlights INTs as promising diagnostic biomarkers for clinical detection and intervention. TeaserSpatiotemporal neuroscience reveals intrinsic neural timescale disruptions underlying cocaine use disorder, offering novel diagnostic biomarkers.

neuroscience↗