Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Age-specific Aβ-Tau interactions underlie spatial memory deficits in an APP/PS1 amyloidosis model

BackgroundAmyloid-{beta} (A{beta}) and tau pathology are key molecular hallmarks of Alzheimers disease (AD), yet how their interaction contributes to cognitive decline remains unclear. We investigated the relationship between A{beta} burden, tau pathology, presynaptic density, and spatial learning and memory in the APPswe/PSEN1{Delta}E9 (APP/PS1) transgenic (TG) mouse model of amyloidosis. MethodsSpatial learning and memory were assessed with the Barnes maze test in male TG and wild-type (WT) littermate mice, aged 6, 12, and 18 months. Gross visual function was assessed indirectly in 18-month-old animals using the light/dark exploration test. Brains were collected for autoradiography of tau pathology and presynaptic density with [18F]Flortaucipir and [3H]UCB-J, respectively, while A{beta} plaque load was measured by immunohistochemistry. Correlation and linear mixed-effects regression analyses were used to assess relationships between behavioral and pathological measures. ResultsAPP/PS1 mice showed normal cognitive performance at 6 months, a selective long-term memory deficit at 12 months, and severe impairments in learning and retention at 18 months, independent of visual confounds. Age-dependent increases in [18F]Flortaucipir binding and A{beta} plaque load were observed in all brain regions of TG compared to WT mice, whereas [3H]UCB-J binding was increased in a region-dependent manner in 18-month-old TG vs. WT animals. Barnes maze performance during the final day of testing correlated negatively with both A{beta} and tau pathology across all areas examined. Linear regression revealed a significant association between tau and age and between tau and A{beta} in the cortex, indicating that memory decline in ageing TG mice was driven by the combined effects of these pathologies. ConclusionsDeficits in memory retention precede impairments in task learning performance in APP/PS1 mice. Spontaneous tau accumulation contributes to the progressive cognitive decline, capturing key aspects of the A{beta}-tau interaction observed in human AD.

neuroscience↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

Reliable delineation of Clostridioides difficile and related members of the family Peptostreptococcaceae using phylogenomics and spore coat protein-specific molecular markers

Traditional bacterial classification relies on phenotypic traits (e.g., morphology, metabolic profiles), but these methods lack resolution for closely related taxa and are biased by culture conditions. While 16S rRNA gene sequencing is a widely used molecular complement, it fails to resolve closely related Peptostreptococcaceae species, including Clostridioides difficile. These limitations have caused family-level taxonomic confusion and ambiguous Clostridioides genus boundaries, hindering clinical identification of pathogenic strains and posing public health risks. To address these limitations, we developed an integrated approach combining multi-scale phylogenomic and protein-based molecular evidence, adopting a hierarchical workflow: first, constructing a 16S rRNA phylogeny of 151 Firmicutes strains to demonstrate traditional marker inadequacies; second, generating a whole-genome protein phylogeny of 51 representative Peptostreptococcaceae genomes and defining taxonomic boundaries via Average Amino Acid Identity (AAI); third, analyzing spore-associated protein patterns across C. difficile isolates and related genomes. Results revealed high conservation of C. difficile spore coat/exosporium proteins and clear genus-level phylogenetic distinctiveness of these proteins. Combined with AAI-validated whole-genome data, our findings support key Peptostreptococcaceae taxonomic revisions: redefining polyphyletic Romboutsia, reassigning Eubacterium tenue to Paeniclostridium, and elevating Alkalithermobacter to genus status. This study establishes spore coat proteins as core taxonomic markers for spore-forming bacteria, with our integrated strategy overcoming traditional limitations to improve classification accuracy and C. difficile surveillance. ImportanceConventional classification struggles to resolve closely related Peptostreptococcaceae species (e.g., C. difficile). We developed an integrated framework combining 16S rRNA sequencing, whole-genome protein analysis, and spore trait assessment, with a key innovation: identifying spore coat/exosporium proteins as robust, conserved taxonomic markers. This approach enabled three pivotal Peptostreptococcaceae revisions--redefining Romboutsia, reassigning Eubacterium tenue to Paeniclostridium, and elevating Alkalithermobacter to genus rank. The findings resolve a longstanding microbial systematics bottleneck for spore-forming bacteria, provide critical taxonomic context for C. difficiles precise monitoring and prevention, and expand taxonomic markers beyond nucleic acid-based methods. This advances classification precision, critical for microbial ecology, pathogenesis, and industrial microbiology research.

genomics↗

bioRxiv2025

α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangements is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangements during branching morphogenesis is poorly understood. Here we used 3D live imaging of mouse ureteric bud branching to show that -parvin, a component of the integrin binding ILK-PINCH-Parvin (IPP) complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, -parvin promotes actin turnover by inhibiting activation of the small GTPases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis. TeaserScaffold protein -parvin limits cell adhesion and actin polymerization, enabling cell rearrangements that drive kidney branching

developmental biology↗

bioRxiv2025

Decoding Prokaryotic Whole Genomes with a Product-Contextualized Large Language Model

Genomes encode the instructions for life, yet their interpretation requires models capable of capturing long-range genome-wide functional context at scale. Existing genomic foundation models have primarily focused on sequence-level representations, providing powerful tools for biological prediction while leaving complementary opportunities for function-level genome modeling. Here, we present GenSyntax, a function-level genome representation learning framework that models prokaryotic genomes as ordered sequences of gene-product descriptors. By treating gene products as semantic units, GenSyntax transforms annotated replicons into interpretable "genetic paragraphs" that capture genome-wide functional context. We trained GenSyntax on 49,250 annotated prokaryotic genomes and evaluated its ability across genome-scale tasks, including plasmid host prediction, gene-product disambiguation, genome contig ordering and gene essentiality prediction. Compared with general-purpose large language models and representative genomic foundation models, GenSyntax achieved competitive performance across multiple benchmarks, with independent external evaluations supporting its generalization beyond the original training datasets. GenSyntax embeddings also captured signals associated with microbial phenotypes, and gene essentiality predictions enabled exploratory design of minimal genomes. Together with the lightweight GenSyntax-Tiny model, GenSyntax provides a complementary, post-annotation framework for function-level analysis of prokaryotic genomes.

genomics↗

bioRxiv2025

Synthetic Modular Cyanobacterial Consortium Enables Carbon-Negative Production of Glycerol and Derivatives

Cyanobacteria offer a direct route for converting solar energy and CO2 into valuable chemicals, yet the metabolic burden of complex heterologous pathways often limits their productivity and stability. Here, we present a modular co-culture strategy that uses glycerol as an efficient mediator metabolite to link cyanobacterial carbon fixation with downstream bioconversion. We first engineered Synechococcus elongatus UTEX 2973 (Syn2973) for high-level glycerol biosynthesis by optimizing synthase selection, eliminating competing pathways, and improving CO2-supply conditions, achieving a production of 14.53 g{middle dot}L-1. In parallel, we constructed glycerol conversion modules in Syn2973 and Gluconobacter oxydans enabling production of 1,3-propanediol (1,3-PDO), 3-hydroxypropionic acid, and dihydroxyacetone, with exogenous glycerol yielding up to 30.07 g{middle dot}L-1 1,3-PDO. Integrating the two modules resulted in a fully autotrophic co-culture that produced all three target chemicals directly from CO2, including semi-continuous 1,3-PDO production at 6.02 g{middle dot}L-1{middle dot}day-1, corresponding to a net carbon fixation efficiency of 3.43 kg CO2 eq/kg 1,3-PDO.

synthetic biology↗

bioRxiv2025

Improved cloning-free one-step CRISPR-Cas12a-assisted tagging of mammalian genes using PCR generated reagents (PCR tagging)

Precise DNA integration in mammalian genomes using CRISPR/Cas based strategies remains challenging due to competing DNA repair pathways. We present an update for our CRISPR/Cas12a-assisted PCR-tagging method using linear donor cassettes and self-targeting gRNAs for gene tagging. By incorporating 2A-linked selection markers and chemically modifying PCR cassettes with phosphorothioate and biotin, along with the inhibition of NHEJ, we improve precise insertions while reducing unwanted integration products and we devise a variant of the method for seamless gene tagging. To profile integration outcomes, we further developed our integration site sequencing protocol (Tn5-Anchor-Seq, Meurer et al., 2018) to obtain a protocol using long-read (ONT) sequencing coupled with a custom computational pipeline. This enables high-resolution quantification of all integration events with respect to integration by HDR or NHEJ, as well as the presence of concatemers and off-target integrations. Our data reveal gene-specific editing profiles and demonstrate that combining cassette design with DNA repair modulation yields up to 5-fold increases in HDR and suppression of concatemers and indels. Together, our improvements outline an robust strategy for efficient and high-fidelity gene tagging in mammalian cells, facilitating functional genomics and cell engineering applications.

molecular biology↗

bioRxiv2025

Full-length structure of CPR-containing self-sufficient cytochrome P450

Cytochrome P450 (P450s) are heme-thiolate monooxygenases that exploit electrons sourced from pyridine nucleotide to reduce the oxygen and heme iron to catalyze hydroxylation of inactivated C-H bond1-4. Self-sufficient P450s that contain the substrate-binding heme-domain and the electron-donating NADPH:cytochrome P450 reductase (CPR) domain in the same polypeptide chain are highly effective and have been engineered to catalyze various challenging reactions. The high efficacy attributes to the effective electron transfer rate, but how the electrons travel among the redox centers remains elusive owing to the lack of structural information of the full-length protein. Here, we report the structure of a homologue of the most extensively studied P450BM3 from Shimazuella soli (SoP450) resolved by single particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. SoP450 primarily exists as a homodimer formed via the intertwined CPR-domains. The spatial alignment of the heme-domain that is linked via an extensive loop was also determined. Notably, a class of structure that lacks one heme-domain was identified from the cryo-EM analyses, indicating that the heme-domain is mobile. We suspected that the heme-domain could move to reach the CPR-domain for electron acquisition and built a model of putative catalytic state to reveal how the electrons are relayed from NADPH to heme. These results are of fundamental importance to understand the catalytic reaction of CPR-containing self-sufficient P450s, which shall provide critical information to the engineering and applications of these enzymes.

synthetic biology↗

bioRxiv2025

PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy

Distinguishing among neuronal cell types is crucial for deciphering complex neural networks and brain functions. However, the current repertoire of cell-labeling tools compatible with light microscopy (LM) and/or electron microscopy (EM) is limited compared to the vast number of cell types in the brain. Here, we introduce PKU (polymer king-size unit) tags, genetically encoded "shape tags" that leverage the polymerization of self-assembling proteins, spectrally distinct fluorescent proteins and, optionally, a nuclear targeting sequence to generate a series of multi-shaped (spherical or filamentous), multi-colored (blue, green, red, near-infrared) and multi-localized (cytosolic or nuclear) tags. By co-expressing multiple PKU tags within the same cell, a combinatorial strategy further expands the repertoire, which can theoretically yield hundreds of unique labeling patterns. Expressing PKU tags in vivo provides multi-cell-type labeling and neuronal circuit tracing, without altering the animals behavior or transcriptomic profiles. Moreover, when fused to the peroxidase APEX2, PKU tags maintain their shape-specific features, providing shape "barcoding" using EM. Thus, PKU tags represent a versatile and efficient toolkit for studying connectomics using both LM and EM.

neuroscience↗

bioRxiv2025

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution

The rapid emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) threatens global TB control, yet the mechanisms enabling rapid evolution of drug resistance in Mtb remain poorly understood. Here we reveal that pre-existing mutations in oxidative stress response genes create permissive genomic backgrounds that accelerate high-level isoniazid resistance (INHR) without fitness costs, challenging the paradigm that resistance mutations always precede their fitness compensatory adaptations. Using M. smegmatis mc2155 (Msm) as a model, we show that brief exposure to sublethal INH (2x IC50) enriches for "low-level resistance and tolerance" (LLRT) mutants in a single step. These LLRT mutants, particularly those with ohrR loss-of-function mutations, acquire high-level resistance (> 500x IC50) at 6-fold higher rates than wildtype, primarily through otherwise-deleterious mycothiol biosynthesis mutations that become tolerable in the oxidative stress-buffered background. Crucially, we demonstrate that sublethal oxidative stress alone, mimicking host immune pressure, nearly tripled the rate of INH resistance evolution in Msm. Bayesian analysis of 1,578 clinical Mtb isolates from Vietnam confirmed that mutations in oxidative stress response genes were significantly associated with the emergence of INHR strains (p-value = 1.09x10-7). Independently, reanalysis of genome-wide CRISPRi screens revealed that the OSR network and high Bayes probability genes are functionally associated with treatment escape and survival with multiple antibiotics, including isoniazid, rifampicin, ethambutol, bedaquiline, vancomycin, clarithromycin, linezolid, and streptomycin. Our findings that host-imposed oxidative stress and inadequate drug penetration may synergistically prime Mtb populations for rapid resistance evolution suggest that targeting pre-resistance mechanisms, such as oxidative stress defenses, could help slow the emergence of antibiotic resistance in tuberculosis.

microbiology↗

bioRxiv2025

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogenic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet to be expressed they must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA present in multiple copies (up to nine) in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes and is enriched in E. coli strains that carry the locus of enterocyte effacement (LEE). We show that HnrS directly base-pairs with the ribosome-binding site of the hha mRNA, repressing its translation and thereby reducing Hha-enhanced H-NS silencing. This counter-silencing de-represses the LEE type III secretion system and concomitantly represses motility. Transcriptomic profiling further revealed that HnrS indirectly activates genes involved in nitrate/nitrite respiration and nitric oxide resistance, metabolic pathways that contribute to survival in the inflamed gastrointestinal tract. Deletion of hnrS reduced expression of nitrate reductase genes and impaired actin pedestal formation on host epithelial cells. Our results indicate that prophage-encoded, multicopy hnrS provides a counter-silencing mechanism that reduces Hha-H-NS repression at specific virulence loci. This likely enables expression of horizontally acquired genes without broadly disrupting the core H-NS regulon. HnrS illustrates how mobile genetic elements deploy sRNAs to counteract xenogenic silencing and promote virulence gene expression, enhancing colonisation of the host. Importance statementHorizontally acquired genes are often silenced to protect bacterial genomes, but this defence also limits the expression of new traits. We identify a prophage-encoded small RNA, HnrS, that counteracts this restriction by repressing the xenogenic silencer Hha, lifting Hha-H-NS-mediated repression of virulence and metabolic genes. HnrS activates the locus of enterocyte effacement, nitrate/nitrite respiration, and nitric oxide resistance--pathways that help E. coli survive and colonise the inflamed gut. Our findings reveal an RNA-based counter-silencing mechanism encoded by mobile genetic elements, showing how phages can reprogram bacterial regulatory networks to promote adaptation and pathogenicity.

microbiology↗

bioRxiv2025

SPARP-seq reveals poly(A) tail shortening as a hallmark of the active human translatome

The poly(A) tail at the 3 end of mRNAs plays a critical role in the synthesis of proteins, but its dynamic relationship with the translation process has been unclear. Here, using a novel single-molecule approach SPARP-seq that integrates poly(A) assessment with ribosome profiling, we demonstrate that poly(A) tail shortening is a universal hallmark of active translation in human cells. We find that most mRNAs begin translation on single ribosome (monosome) with long tails that progressively shorten as additional ribosomes are recruited. In contrast, highly expressed housekeeping genes are translated efficiently on monosomes and possess intrinsically short poly(A) tails. Furthermore, we find that translationally repressed transcripts, such as those retaining introns, are trapped on monosomes with long tails. Pharmacological inhibition of translation induces global poly(A) tail lengthening, confirming that deadenylation is coupled to ongoing translation. These findings reveal a dynamic system where the poly(A) tail integrates mRNA status with translational fate, defining the monosome as a central hub for post-transcriptional control.

molecular biology↗

bioRxiv2025

AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination

Analyzing the structure of the helical assembly is very important to excavate the mechanism of base life activities such as cell morphology maintaining, cargo transportation, et. al. However, the structure determination of helical assembles still challenging due to ambiguous of helical parameters. Here, we developed automatic, fast and accurate helical parameter and structure calculation method AI-HEAD, which perform diffraction indexing and parameter calculation automatically in seconds, and determine the final structure unambiguously by sorting parameters semi-automatically. AI-HEAD is open source and also provides a user-friendly graphical interface.

biophysics↗

bioRxiv2025

Vectorial boundary representation of 3D layout in human visual cortex

Human spatial navigation relies on the brains ability to visually represent the 3D layout of the environment. To understand how the brain encodes the layout information, it is crucial to identify the key features of environmental layout and how they are processed in the human brain. The vector coding principle, which highlight the role of boundary distance and orientation, provides a theoretical framework supported by physiological evidence from rodents. In this study, we developed a reconstruction approach to quantitatively estimate 3D layout information from natural indoor scene images. This approach enabled analyses of fMRI data from the large-scale Natural Scenes Dataset (NSD) using vector-based models of 3D layout. To validate the NSD-based results and examine task-related dynamics, we further conducted fMRI and MEG experiments with navigation-related and non-navigational tasks. Controlling for low-, mid-, and high-level visual and semantic features of natural indoor scenes, we found a spatiotemporal dissociation between boundary distance and orientation representations in the human brain. Relative distance was encoded in the early visual cortex during early processing in a task-invariant manner, whereas orientation was represented in scene-selective higher visual areas during later processing and was modulated by navigation-related tasks. Importantly, task modulation manifested as feedback-induced enhancement of orientation coding in the early visual cortex. Together, these findings provide a novel perspective on how the human brain represents navigation-relevant information about the immediate surrounding environment, advancing our understanding of the neural mechanisms that link perception to action in spatial navigation.

neuroscience↗

bioRxiv2025

Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of vitamin D receptor (VDR) in the epigenomic network

Identifying the factors that regulate female reproduction is crucial to understanding how the environment affects female reproductive health. The vitamin D receptor (VDR) and its ligands (primarily 1,25(OH)2D3) have a recognized role in calcium homeostasis; however, their broader impact on female reproduction remains underexplored. We demonstrate that the VDR and its ligands are involved in the hormonal induction of uterine decidualization. Mice fed a vitamin D-deficient diet displayed an impaired hormonally induced decidual response. In a human telomerase reverse transcriptase-immortalized human endometrial stromal cell line (T-HESC), VDR decreased during in vitro decidualization. Small interfering RNA (siRNA) knockdown of VDR in T-HESC enhanced in vitro decidualization, while overexpression of VDR inhibited it. Chromatin accessibility and histone modification analyses revealed that VDR functions as a chromatin regulator, restricting accessibility and repressing transcription in specific genomic regions. Transcriptomic analyses confirmed that VDR broadly modulates gene expression, with most ligand-mediated effects occurring through the VDR. These findings identify VDR as a key regulator of transcriptional and chromatin landscapes in human endometrial stromal cells, offering novel insights into vitamin D signaling in reproduction. This study highlights the potential of targeting vitamin D pathways to treat uterine disorders associated with impaired decidualization and reduced fertility. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/688535v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@6b048org.highwire.dtl.DTLVardef@11f7b4corg.highwire.dtl.DTLVardef@1d7dbfaorg.highwire.dtl.DTLVardef@ab3894_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

Functional annotation of proteins from extreme environments represents a major bottleneck for bioresource discovery, as a vast reservoir of functional dark matter defies existing homology-based methods. We demonstrate that environmental pressures impart conserved physicochemical energy signatures that co-determine protein function with sequence and structure. Here we developed ACCESS, a multimodal graph neural network employing hierarchical contrastive learning with a tailored label-sample co-embedding to fuse energy, sequence, and structural information and overcome homology scarcity. ACCESS surpasses state-of-the-art methods including BLASTp and CLEAN in annotating low-identity enzymes. Applied to extreme environmental metagenomics, we constructed a function map of extremophile enzymes to expand the biocatalyst library, pinpointed functionally critical residues to guide rational design, and enabled large-scale, function-based macro-evolutionary analyses. This paradigm transcends the limitations of homology, illuminating protein dark matter and accelerating the exploration of the biospheres functional diversity for applications in biotechnology and therapeutic development.

bioinformatics↗

bioRxiv2025

Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS

Hematopoietic stem cell transplantation (HSCT) offers the best curative option for acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), yet relapse remains common. Current relapse detection methods are often too late for effective intervention. To identify earlier predictors and therapeutic targets, we performed longitudinal single-cell RNA and T cell receptor (TCR) sequencing of bone marrow from 33 AML/MDS patients during post-transplant immune reconstitution, comparing those who relapsed to those who remained in remission. Persistence of recipient hematopoietic stem and progenitor cells (HSPCs) in the marrow was associated with relapse months later. These residual recipient HSPCs harbored copy number variations (CNVs), supporting their leukemic origin, and overexpressed PRAME and CALCRL compared to coexisting donor HSPCs. Further, in a subset of TP53-mutant disease, low TCR diversity with skewing toward dominant clonotypes foreshadowed relapse. These findings lay the groundwork for improved relapse prediction and nominate therapeutic targets for early post-transplant intervention.

cancer biology↗

bioRxiv2025

CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction

BackgroundCellular repressor of E1A-stimulated genes 1 (CREG1) is an evolutionarily conserved endolysosomal glycoprotein that enhances lysosomal biogenesis and autophagy, suppresses proliferation, and promotes differentiation. A prior gene targeting strategy that produced truncated N-terminal fragments resulted in embryonic lethality, limiting the ability to assess the physiological role of complete CREG1 loss. We hypothesized that CREG1 regulates cardiac autophagy, thereby maintaining cardiac structure and function under both physiological and stress conditions. MethodsWe generated true Creg1 knockout (KO) mice by deleting the entire open reading frame and established a gain-of-function model by inserting human CREG1 into the Rosa26 locus. Cardiac structure and function were assessed in global and cardiomyocyte-specific Creg1 knockout (cmCreg1KO) and knock-in (cmCREG1KI) mice. Autophagy was evaluated using biochemical assays, immunofluorescence, electron microscopy, and the CAG-EGFP-RFP-LC3 reporter analysis. ResultsGlobal Creg1 knockout mice developed progressive cardiac hypertrophy, fibrosis, and diastolic dysfunction at [~]80 weeks of age. At younger ages, CREG1 deficiency increased susceptibility to nutritional stress, resulting in mitochondrial damage and myofiber disruption in cardiomyocytes. cmCreg1KO mice exhibited dilated cardiomyopathy, left atrial thrombosis, and lethality around 50 weeks of age; however, interpretation of disease severity is confounded by Myh6-Cre-associated cardiotoxicity, which may mask additional pathogenic effects attributable to CREG1 loss. In contrast, cmCREG1KI mice demonstrated enhanced exercise capacity under nutritional stress. Mechanistically, CREG1 was localized to endolysosomal and autophagosomal compartments. Loss of CREG1 impaired autophagy flux and mitophagy, likely due to defective autophagosome membrane expansion and degradation. In contrast, CREG1 overexpression enhanced autophagy in cardiomyocytes. ConclusionsCREG1 is a key regulator of cardiac autophagy, protecting the heart against nutritional stress-induced injury and age-associated cardiac hypertrophy, fibrosis, and diastolic dysfunction. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/687936v1_ufig1.gif" ALT="Figure 1000"> View larger version (60K): org.highwire.dtl.DTLVardef@1b9fc05org.highwire.dtl.DTLVardef@150e48aorg.highwire.dtl.DTLVardef@1cc47adorg.highwire.dtl.DTLVardef@75ed53_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗