Biology subjects

Ma, Q.

Publications and source records attributed to Ma, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A novel and evolutionarily distinct flavoprotein monooxygenase drives skatole degradation in Rhodococcus

Skatole (3-methylindole), a persistent and toxic N-heterocyclic aromatic pollutant, poses significant bioremediation challenges due to poorly defined biodegradation processes. This study systematically investigated the genetic determinants and metabolic mechanisms of skatole degradation in the environmentally versatile Gram-positive genus Rhodococcus. We demonstrated that skatole degradation was a broadly conserved trait across diverse Rhodococcus species, including R. aetherivorans, R. pyridinivorans, R. ruber and R. qingshengii. Genomic and functional analyses uncovered a novel flavoprotein monooxygenase (FPMO) SkaA as the initial catalyst for skatole catabolism. Heterologous expression in Escherichia coli confirmed SkaAs essential catalytic role, with high-resolution liquid chromatography-tandem mass spectrometry identifying the key product 3-methyloxindole and 3-hydroxy-3-methyloxindole. Distribution studies revealed SkaA homologs predominantly in Actinobacteria, particularly Nocardia and Rhodococcus, indicating conserved metabolic capacity for skatole transformation within this phylum. Notably, Rhodococcus strains lacking the skaA gene also retained skatole degradation activity, implying the existence of alternative genetic determinants. Crucially, phylogenetic analysis positioned SkaA as a distinct subclass within Group E FPMOs, exhibiting [≤]40% sequence identity to reported styrene/indole oxygenases. The phylogenetic segregation of skatole, indole, and styrene monooxygenases provides a predictive framework for functional annotation of Group E FPMOs. Our findings elucidate a novel skatole transformation pathway, establish Rhodococcus as environmentally versatile biocatalysts, and provide new insights into the study of Group E FPMOs. IMPORTANCESkatole is a notorious, foul-smelling compound generated by the anaerobic breakdown of tryptophan, presenting substantial risks to both the environment and public health. Despite its prevalence, the enzymatic machinery initiating its biodegradation remains poorly characterized. Our study resolves this critical gap by identifying SkaA as a functionally validated enzyme catalyzing skatoles initial oxidation step. Distribution analyses revealed SkaA homologs predominantly in Actinobacteria, particularly Rhodococcus and Nocardia. Phylogenetic analysis positioned SkaA as a novel third subclass within Group E flavoprotein monooxygenases. These breakthroughs provide molecular tools for engineering targeted bioremediation solutions and new insights into the study of Group E FPMOs.

microbiology↗

bioRxiv2025

Discovery and characterization of a lactonase in gut microbiota that initiates the metabolism of ellagic acid

Ellagic acid (EA), a natural plant polyphenol, and its metabolite urolithin (Uro) exhibit significant bioactivity, with Uro being recognized as the active compound responsible for the in vivo effects of EA. Although specific intestinal microorganisms that can metabolize EA have been discovered, the corresponding biochemical routes and genetic mechanisms involved in these processes have yet to be fully elucidated. In this study, we employed bioinformatics, biochemical assays, and genetic analyses to discover and characterize an EA lactonase (EAL) from the intestinal bacterium Gordonibacter urolithinfaciens DSM 27213. EAL specifically catalyzes the cleavage of the ester bond in EA, yielding Uro-M5. Notably, EAL and its extensive homologs form a unique subclass within the lactonase and amidohydrolase families. Structural predictions indicate that the active pocket of EAL comprises a propeller-like structure formed by seven {beta}-strands. Additionally, molecular modeling analyses further revealed that EA establishes specific interactions with key catalytic residues within the enzymes binding site. These insights enhance our understanding of the role of intestinal microbial communities in metabolizing plant-derived phenolic compounds, potentially shaping health outcomes and disease management through dietary interventions. Significance StatementEllagic acid (EA), which is abundant in the human gut microbiome, can be metabolized by gut microbes into urolithin A (Uro-A), however, the biochemical mechanisms underlying these transformations remain incompletely understood. In this study, we identified and characterized an EA lactonase (EAL) from the gut bacterium Gordonibacter urolithinfaciens DSM 27213, which serves as a key enzyme in the initial metabolic breakdown of EA. We elucidate the function, distribution, and structure of the EAL. This discovery advances our understanding of Uro-A production within the human body and may provide a foundation for further investigations into the relationship between Uros and human health.

biochemistry↗

bioRxiv2025

Lateral plate mesoderm directs human amnion and ventral skin organoid formation

Summary ParagraphEngineering organoids that faithfully replicate the intricate architecture and region-specific features of bodily organs and extraembryonic tissues remains a significant scientific challenge. Previously, we demonstrated that craniofacial skin organoids (cSkOs)--containing epidermis, dermis, and hair--could be generated by co-developing epidermal progenitors with cranial mesenchyme. Building on this approach, we precisely adjusted cellular composition and signaling environments to generate ventral skin organoids (vSkOs) with lateral plate mesoderm (LPM) progenitors, successfully recapitulating features of abdominal or groin skin. Modulating early BMP and FGF signaling redirected these vSkOs toward an extraembryonic fate, producing human amnion-like tissues, termed Amnioids. Like native human amnion, Amnioids rapidly expanded into large, avascular, hairless cysts, in sharp contrast to the primitive vasculature and abundant hair follicles of vSkOs. Single-cell RNA sequencing identified divergent molecular signatures and developmental trajectories, highlighting key roles for NOTCH, WNT, and YAP/Hippo signaling pathways. Functional studies further underscored mesenchymal-epithelial interactions and mechanical forces as critical regulators of epithelial expansion. Together, these models provide potent tools to investigate human development at the embryonic-extraembryonic interface, offering critical insights into congenital skin and amniotic disorders and opening new avenues for precision regenerative therapies.

developmental biology↗

bioRxiv2025

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

Hybridization-based spatial transcriptomics technologies have advanced our ability to map cellular and subcellular organization in complex tissues. However, existing methods remain constrained in gene coverage, multimodal compatibility, and scalability. Here, we present MERFISH+, an enhanced version of Multiplexed Error-Robust Fluorescence in Situ Hybridization (MERFISH), which integrates chemical probe anchoring in protective hydrogels with high-throughput microfluidics and microscopy. This optimized design supports robust and repeated hybridization cycles across an entire centimeter-scale tissue sample. MERFISH+ allowed to simultaneously quantify over 1,800 genes and resolve the 3D organization of chromatin loci and their associated epigenomic marks in developing human hearts. Using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omic atlas of the developing human heart at subcellular resolution capturing 3.1 million cells across 34 distinct populations. This 3D atlas provides a holistic view of an entire organ enabling the characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Thus, MERFISH+ offers a robust, large-format platform for spatial multi-omics that enables high resolution mapping of gene expression at subcellular resolution and the characterization of cellular organization within 3D organs. One Sentence SummaryMERFISH+ is an spatial multi-omics platform that integrates hydrogel-based probe anchoring, automated high-throughput microfluidics, and large-format multimodal data production to enable comprehensive, subcellular resolution mapping of gene expression and chromatin organization across millions of cells within complex developing human organs. HighlightsO_LIMERFISH+ expands MERFISH capabilities to measure >1,800 genes and at whole-organ 3D imaging scale C_LIO_LICombines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics C_LIO_LIGenerates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution C_LIO_LIIntroduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets C_LI

genomics↗

bioRxiv2025

Structural and functional insights into QueC-family protein in QatABCD anti-phage system

QatABCD is a widespread prokaryotic anti-phage defense system comprising four protein components, out of which QatC, a QueC-family protein is the signature component. QueC family proteins are nucleoside biosynthesis enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine derivative. Recently, QueC-family proteins were shown to catalyze a deazaguanylation protein-nucleobase conjugation reaction in type IV CBASS antiphage defense. However, the mechanism of QatABCD, even the function of QatC in this system, remains unknown. Here, we demonstrate that QatBCD forms a complex in which QatD is highly flexible. Crystal structures of the QatBC complex in apo and ATP-bound form support a shared role for QueC-family proteins in targeting protein substrates for N-terminal modification as in type IV CBASS. We show that the QatB N-terminal loop, its binding with QatC and QatC catalytic site are essential for QatABCD defense in vivo, suggesting a modification might occur analogous to CBASS. These findings provide structural and functional insights into QueC-family protein in QatABCD system, suggesting the conserved mechanisms and critical roles of QueC-family in prokaryotic immunity.

biochemistry↗

bioRxiv2025

FveOCRs - a database for open chromatin prediction in wild strawberry based on a large language model

BackgroundWoodland strawberry (Fragaria vesca) is a widely used model system for cultivated strawberries and Rosaceae for molecular genetic studies. Nevertheless, available databases for its cis-regulatory element identification are limited. With the emergence of large language models in plant research, strawberry research could benefit significantly from applying these models. One such model derived from Plant DNA Large Language Models (PDLLMs) effectively predicts open chromatin regions (OCRs), which are nucleosome-depleted areas typically associated with cis-regulatory elements. However, improvement of the models accessibility and utility will be needed to facilitate the models application in strawberry as well as other plant species. ResultsWe developed the FveOCRs database (http://liulab.online:33838/FveOCRLiuLabTestVer25), which predicts open chromatin regions located within 5,000 bp upstream sequences, the first and second introns and exons, and the longest introns in Fragaria vesca genes. Predictions were generated using a sliding-window approach based on one of the PDLLMs. In the database, users could predict open chromatin regions for input DNA sequences from any plant species and obtain visual graphs with precise predicted regions of open chromatins. ConclusionsThe FveOCRs database is the first database for open chromatin region prediction in Fragaria vesca based on a Plant DNA Large Language Model. It can also predict OCRs in user-provided DNA sequences from any plant species. The resource and its accessible visual graphs will facilitate discovery of cis-regulatory elements and engineering of gene expression in strawberry and other plant species.

bioinformatics↗

bioRxiv2025

Environmental Regulation of Toxin Production in Bacillus anthracis

Pathogenic Bacillus anthracis strains carry two plasmids - pX01, which encodes a tripartite protein exotoxin complex (PA, LF, and EF); and pX02, which encodes a poly-D-gamma-glutamic acid capsule. A multidomain transcription factor, AtxA, regulates the expression of these virulence genes. AtxA has two DNA-binding Helix-Turn-Helix (HTH) domains, two phosphoenolpyruvate:carbohydrate phosphotransferase system regulatory domains (PRD1 and PRD2), and a putative EIIB domain (a component of PTS sugar transport EII-complexes). Previous studies showed that glucose and CO2 increase AtxA-dependent toxin gene transcription, along with histidine phosphorylation of PRD1 and PRD2. Our transcriptional profiling of virulence factors, PA secretion, and fluorescent reporter strain analyses confirms a synergistic effect of glucose and CO2 on AtxA-dependent toxin production. Deletion of AtxA ({Delta}atxA) significantly reduced glucose uptake in bacteria, suggesting that AtxA may act within the glucose-PTS system. Mutation analysis of the EIIB domain of AtxA identified the cysteine at position 402 as essential for the transcriptional activity of AtxA. Deletion of glucose PTS permease PtsG ({Delta}ptsG) significantly reduced the expression of PA, LF, and EF. Loss of PtsG also caused attenuation in a mouse model of infection. Intracellular imaging using FLIM confirms a physical interaction of PtsG and AtxA through EIIB domain of AtxA. Using phosphomimetic and phosphoablative mutants of AtxA, we confirmed that the physical interaction of PtsG and AtxA is essential for AtxA activity. Finally, the synergy between glucose and CO2 was targeted by deleting pyruvate carboxylase Pyc ({Delta}pyc), which regulates anaplerosis. This deletion confirms that Pyc stimulates the level of phosphoenolpyruvate (PEP) and increases the phosphorelay in glucose-PTS to enhance AtxA activity. Therefore, we propose that a histidine-phosphorelay from PEP regulates AtxA via PTS enzymatic activity, impacting AtxA activity through physical interaction of AtxA and PtsG. Finally, we propose AtxA as an integral component of the glucose-PTS, where transcriptional activity of AtxA is regulated by environmental signals including glucose and CO2.

molecular biology↗

bioRxiv2025

Transcriptional and epigenetic repression of hematopoietic stem cells underlies bone marrow failure after spinal cord injury

Spinal cord injury (SCI) triggers systemic pathology beyond the nervous system, including bone marrow failure that can worsen infection risk, anemia, and motor recovery. Here we identify a neuroendocrine mechanism that rapidly imprints long-lasting dysfunction in hematopoietic stem cells (HSCs), which sustain lifelong production of immune cells, red blood cells, and platelets. Rather than mounting a canonical stress-hematopoietic response, SCI HSCs enter a broadly repressed state marked by chromatin closure and suppression of programs required for cell-cycle entry, genome maintenance, and redox defense. This maladaptive state leads to persistent DNA damage, impaired oxidative stress resolution, pancytopenia, and loss of long-term HSC regenerative capacity. Mechanistically, SCI-induced glucocorticoid surges drive glucocorticoid receptor-dependent repression of DNA repair genes, including Lig1 and Fen1. Acute glucocorticoid receptor blockade after SCI restores durable hematopoiesis, revealing an early therapeutic window to preserve hematopoietic integrity after neurotrauma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/680535v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1627bb3org.highwire.dtl.DTLVardef@a73e19org.highwire.dtl.DTLVardef@1ddf85dorg.highwire.dtl.DTLVardef@1dcd8fe_HPS_FORMAT_FIGEXP M_FIG C_FIG Key FindingsO_LIAcute SCI prevents induction of normal stress-induced repair programs in HSCs. C_LIO_LISCI HSPCs exhibit increased chromatin compaction. C_LIO_LISCI compromises HSC genome-maintenance and redox capabilities. C_LIO_LISCI HSCs have defects in normal cell cycle regulation, are hypersensitive to genotoxic stress, and are deficient in long-term reconstitution. C_LIO_LIEarly glucocorticoid receptor (GR) blockade restores long-term hematopoiesis, supporting a GR-dependent but reversible repression mechanism. C_LI

cell biology↗

bioRxiv2025

Lipodystrophy and recovery are mediated by the Wnt/lipogenesis axis during skin fibrosis.

Acquired lipodystrophy in the dermal white adipose tissue (DWAT) is a salient feature of skin fibrosis, and is followed by accumulation of extracellular matrix (ECM). Lipodystrophy syndromes, often associated with metabolic co-morbidities, are estimated to affect 1 in 20,000 people. We recently showed that fibrosis-associated lipodystrophy is dependent on sustained Wnt signaling, but the mechanism is unclear. Transcriptomic profiling of mature dermal adipocytes in vivo reveal that Wnt activation downregulates the de novo-lipogenesis (DNL) axis enzymes within 48 hours. We found that protein expression of Fatty Acid Synthase (FASN), a key DNL enzyme, is dependent on sustained Wnt activation in vitro and in vivo. In human systemic sclerosis, FASN mRNA is significantly downregulated during two years of disease. Remarkably, pharmacological inhibition of FASN enzyme during reversal from Wnt induced fibrosis impedes recovery of DWAT lipid content as well as ECM accumulation and topography. All together, we demonstrate that acquired lipodystrophy in the context of skin fibrosis is mediated by a new role of the Wnt-DNL axis. These findings underscore the importance of this pathway in lipodystrophy and fibrosis, opening new avenues for therapeutic targets in skin fibrosis.

cell biology↗

bioRxiv2025

A cross model spatial and single-cell atlas reveals the conserved involvement of osteopontin in polycystic kidney disease

Polycystic kidney disease (PKD) arises from mutations in cilia-associated genes, such as PKD1 and PKD2, expressed in renal epithelial cells, leading to progressive kidney dysfunction and end- stage kidney disease (ESKD). PKD patients exhibit significant heterogeneity in disease progression, largely due to genetic and environmental modifiers. Like patients, mouse models of PKD also exhibit significant heterogeneity with regards to the gene mutated, age of disease onset, and rate of disease progression. To elucidate the cellular and molecular consequences of these variables, we constructed an integrated single-cell and spatial transcriptomics atlas across mouse models of PKD, mapping changes in cell type composition, gene expression, and intercellular signaling networks across the whole atlas and within individual models. Consistently across models, single cell RNA sequencing (scRNAseq) data revealed increased Spp1 (osteopontin) expression and signaling from PKD-enriched clusters to Ly6clo monocytes. Global deletion of Spp1 in Pkd1RC/RC mice resulted in reduced cyst severity, improved kidney function, and reduced Ly6clo monocyte numbers, suggesting that SPP1 signaling to Ly6clo monocytes promotes PKD progression. We also created a freely available, searchable website (https://bmblx.bmi.osumc.edu/scPKD/) that can be used to identify cross- and intra-model specific changes in gene expression, guiding researchers to new therapeutic targets for treating PKD.

bioinformatics↗

bioRxiv2025

Nicotinamide opposes ET-1's adverse effect on uterine decidualization via EDNRB

Endothelin-1 is involved in pathogenesis of preeclampsia. Mice (Edn1H/+) having excess endothelin-1 developed preeclampsia-like phenotypes during pregnancy in a maternal genotype-dependent manner. Here, we investigate whether decidualization is impaired in Edn1H/+ dams, and whether nicotinamide (a potent inhibitor of endothelin-1) exerts beneficial effect. We compared implantation sites between wild type (WT) and Edn1H/+ dams with or without nicotinamide treatment. Implantation sites of Edn1H/+ dams exhibited abnormal ectoplacental cone and sinusoids with reduced vascular density in mesometrial regions of deciduae. There was more VEGF in decidua of Edn1H/+ dams than WT dams. Markers of decidualization were decreased in Edn1H/+ dams. Nicotinamide supplementation corrected this abnormality. During differentiation (decidualization) of cultured human endometrial stomal cells, endothelin-1 impaired the upregulated expression of decidualization markers. The endothelin-1s effect was reversed by nicotinamide. These results show nicotinamide counteracts ET-1s detrimental effects on endometrial decidualization and has potential to improve embryo implantation and subsequent pregnancy outcomes.

developmental biology↗

bioRxiv2025

MNase stratification reveals heterogeneous 5hmC in naive B cells

DNA demethylation is essential for gene activation and is primarily mediated by the Ten-Eleven-Translocation (TET) dioxygenase family. TET initiates the demethylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), a chemically stable derivative that is not only an intermediate in demethylation but also an epigenetic mark. 5hmC is enriched at active gene bodies, promoters, and enhancers that exist at accessible chromatin. Yet, 75-90% of genomic DNA is physically packaged in nucleosomes, raising the question about where 5hmC resides relative to nucleosomes. To address this question, we used micrococcal nuclease (MNase) to biochemically stratify 5hmC according to nucleosome protection in naive mouse B cells. Using multiple approaches, we showed that [~]95% of 5hmC peaks are retained after MNase digest, suggesting that 5hmC is nucleosome-associated. Despite the majority of 5hmC being similar in nucleosomal DNA compared to total DNA, we identified minor subsets that were MNase-sensitive (accessible 5hmC, [~]3%) or further MNase-resistant (protected 5hmC, [~]1-2%). Integrative analyses revealed that the accessible 5hmC is preferentially located at promoters and enhancers, and the presence of promoter-proximal accessible 5hmC showed a stronger correlation with gene expression than total 5hmC. In contrast, protected 5hmC is enriched in chromatin states with mixed active and repressive features. These results shed new light on the relationship between 5hmC and accessible chromatin, suggesting 5hmC is predominantly associated with nucleosomes and revealing heterogeneous 5hmC subsets with potential distinct regulatory roles.

molecular biology↗

bioRxiv2025

2-Methoxyestradiol Treatment Prevents Graft-versus-Host Disease While Preserving Graft-versus-Leukemia Effect in Mice

2-Methoxyestradiol (2ME2, Panzem) is an endogenous metabolite that is well-tolerated in phase I/II clinical trials for variety of tumors. The plasma levels of 2ME2 may increase up to 1,000-fold during pregnancy and correlate temporally with the remission of rheumatoid arthritis (RA) and multiple sclerosis (MS) symptoms. The anti-inflammatory properties of 2ME2 were recently established in the mouse model of MS, and the mechanism of action is the ability of 2ME2 to inhibit lymphocyte proliferation, cytokine production and T cell polarization. Herein, we have demonstrated that 2ME2 treatment can significantly reduce the mortality and morbidity associated with graft-versus-host disease (GVHD). There is a lower number of donor-derived CD4+ and CD8+ T cells in the peripheral lymph node and Peyers patches of 2ME2-treated mice compared to control recipients. Moreover, 2ME2 exposure can significantly decrease the production of IFN-{gamma} and IL-2 in donor-derived CD4+ T cells and serum in GVHD mice. However, 2ME2 treatment has no effect on the differentiation of CD8+ effector T cells in vivo and their cytolytic activity remains intact. Furthermore, 2ME2 therapy is effective in preventing GVHD while preserving graft-versus leukemia (GVL) activity in mice. Our findings indicate that 2ME2 could be a novel and effective treatment for GVHD patients.

immunology↗

bioRxiv2025

Intracellular auto-circularizing RNA using human tRNA splicing elements

Circular RNAs (circRNAs), a type of covalently closed RNA, have emerged as crucial regulatory factors in gene expression and development across various organisms. Understanding their formation and functional mechanisms holds potential for therapeutic applications, including novel RNA vaccines against diseases such as COVID-19. However, practical challenges still exist in the preparation of circRNAs. In this study, we explored the influence of human tRNA splicing elements on circRNAs formation and identified effective sequences for intracellular auto-circularization. We developed a generic auto-circularizing RNA (acRNA) framework template, optimized various key components of circRNAs formation, and proposed a more efficient and precise intracellular auto-circularization method. This study provides novel insights into the production mechanism of circRNA and establishes a simple and effective method for intracellular auto-circularization.

cell biology↗

bioRxiv2025

Copper Sulfide Nanoparticle-Mediated Photothermolysis Induces Immunogenic Cell Death in Ovarian Cancer Cells

Immunotherapy has only limited efficacy against ovarian cancer because of dysfunctional T cells in an immunosuppressive tumor microenvironment. Selective photothermolysis is a technique in which short pulsed laser is used to ablate tissue in targeted regions in a precise spatiotemporally controlled manner. This technique allows targeted tissue ablation without damage to surrounding tissue. In the current study, we demonstrated that ovarian cancer cells treated with photothermolysis mediated by near-infrared-absorbing CuS nanoparticles and 15-ns laser pulses were ingested by human monocyte-derived dendritic cells (MoDCs) more efficiently than were ovarian cancer cells treated with ionizing radiation. Moreover, ingestion of ovarian cancer cells treated with CuS NP-mediated photothermolysis promoted MoDC activation. Immature MoDCs that had been exposed to photothermolysis-treated cancer cells caused greater clonal expansion of co-cultured human CD4+ and CD8+ T cells than did immature MoDCs that had been exposed to ionizing radiation-treated tumor cells. These data indicate that photothermolysis may be used to selectively target and destroy tumor cells and cause them to release antigens and danger signals, which can be recognized by DCs to activate T cells.

immunology↗

bioRxiv2025

An artificially selected cytokinin-pathway transcription factor balances soybean yield and pathogen resistance

Soybean contributes to sustainable food and feed production, but some modern varieties favor yield at the cost of disease resistance. Using a bottom-up approach, we demonstrate that the RR2b transcription factor activates cytokinin signaling for plant growth and reproductive fitness but represses disease-resistance and root-nodulation pathways. RR2b was artificially selected during domestication and improvement, and its expression levels correlate with ATT repeat polymorphisms in its promoter. Most wild soybeans and landraces have either more or less ATT repeats: more lead to weak RR2b expression with lower yield and enhanced resistance to soybean bacterial blight, and fewer cause strong RR2b expression, higher yield but reduced disease resistance. Elite cultivars instead balance yield and defense via moderate RR2b expression and several ATT repeats. This confers contrasting RR2b functionality across haplotypes in response to contrasting selection pressures and offers insights into decoupling trade-offs between yield and disease resistance to enhance crop productivity.

genetics↗

bioRxiv2025

An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation

Cellular senescence is a primordial driver of tissue and organ aging, and the accumulation of senescent cells (SnCs) has been implicated in numerous age-related diseases. A major barrier to studying senescence is the rarity and heterogeneity of SnCs, which are not a uniform population but instead comprise diverse senotypes shaped by cell-of-origin and microenvironmental context. Such heterogeneity exceeds what classical senescence hallmarks can resolve at single-cell resolution, motivating the need for computational frameworks that can capture senotype-level diversity intrinsically. Here, we introduce DeepSAS, a deep graph representation learning framework that robustly identifies cell-type-specific SnCs and their senescence-associated genes (SnGs). DeepSAS incorporates a heterogeneous graph that integrates intracellular transcriptional states with intercellular communication cues, enabling the joint inference of senescent cells and senescence-linked genes through attention-based contrastive learning. Applied to public healthy eye and lung atlases, DeepSAS identified SnCs whose proportions positively correlate with aging. From in-house idiopathic pulmonary fibrosis (IPF) patient scRNA-seq data, DeepSAS detected 1,678 SnCs (out of 24,125 cells) and 263 SnGs across 26 cell types, including 43 SnGs that are uniquely associated with a single cell type. We generated high-resolution Xenium spatial transcriptomics data to further validate SnGs in IPF, revealing NFE2L2 as a SnG specifically enriched in CTHRC1+ fibroblasts. Notably, the ex vivo bleomycin-induced senescence in human precision-cut lung slice (hPCLS) samples similarly identified NFE2L2 as an SnG in CTHRC1+ fibroblasts, albeit with stronger transcriptional signals, suggesting mechanistic differences in senescence cells associated with chronic and acute injury. Overall, DeepSAS uncovers distinct senescence programs and infers cell-type-specific SnGs that are difficult to resolve using existing marker-based approaches. We believe it offers a generalizable and translationally relevant strategy for advancing senescence biology and therapeutic development.

bioinformatics↗

bioRxiv2025

Sephin1 alleviates white matter injury by protecting oligodendrocyte after intracerebral hemorrhage

BackgroundWhite matter injury (WMI) caused by intracerebral hemorrhage (ICH) is a major neuropathological feature closely associated with neurological impairments such as motor and sensory dysfunction. Oligodendrocytes (OLs), which are responsible for repairing WMI, also suffer severe death resulting from the compression of hematoma and secondary neuroinflammation after ICH. Sephin1, a selective inhibitor of PPP1R15A, has been shown to reduce general protein synthesis and protect OLs by prolonging the integrated stress response (ISR). We aimed to evaluate the effectiveness of Sephin1 in protecting OLs in experimental ICH mice and primary OLs and microglia co-cultures. MethodsWe first determined the performance of ICH mice treated with Sephin1 or vehicle in multiple behavioral tests. To investigate dynamic changes in the number of OLs surrounding the hematoma after ICH, we labeled and tracked apoptotic, proliferating, and mature OLs using immunofluorescence staining. ResultsSephin1 treatment improved long-term neurological function after ICH, which was accompanied by a significant alleviation of WMI in the perihematomal region. Our data indicated that Sephin1 dramatically increased the population of OLs in the perihematomal region after ICH by inhibiting OL apoptosis and promoting OL proliferation. Moreover, Sephin1 treatment attenuated neuroinflammation after ICH by inhibiting microglial polarization to the M1 phenotype. In vitro, a co-culture model of primary OLs and microglia demonstrated that Sephin1 preserved the viability of OLs under pro-inflammatory conditions. ConclusionsOur observations suggest that Sephin1 is a promising therapeutic drug to preserve the OLs and alleviate WMI around the hematoma in ICH, highlighting its translational potential to improve long-term neurological recovery in hemorrhagic stroke.

neuroscience↗