Biology subjects

Zhang, J.

Publications and source records attributed to Zhang, J..

At least 397 records · Page 22Linked to original sources

bioRxiv2025

Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow

Spaceflight induces physiological changes that resemble accelerated aging, however, how age influences bone marrow response at the cellular level remains poorly understood. Here, we perform single-cell transcriptomic profiling of murine femur and humerus bone marrow from young (12-week-old) and old (29-week-old) mice that underwent a 32-day spaceflight mission followed by a 24-day Earth recovery, with age-matched ground controls. Our analysis reveals that, compared with young cohorts, old mice exhibit persistent dysregulation after spaceflight, most prominently in erythroid and B cell lineages. In erythroid cells, old flight mice show pronounced aging signatures, characterized by impaired maturation, inhibited mitophagy, and increased oxidative stress. In B cells, old flight mice show dysregulation associated with failure of the AP-1 stress-response pathway and complete collapse of the intercellular CXCL signaling network. Our findings dissect the age-dependent effects of spaceflight on the bone marrow hematopoietic and immune system at single-cell resolution, and demonstrate that spaceflight imposes a disproportionate burden on the aged hematopoietic system and blunts post-flight recovery. These insights provide candidate pathways and biomarkers for health monitoring and countermeasures in long-duration missions.

bioinformatics↗

bioRxiv2025

Proteolytic activation of diverse antiviral defense modules in prokaryotes

Linked protease-effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules--metallo-{beta}-lactamase (MBL)-fold hydrolase, /{beta}-hydrolase, Pepco, and EACC1--form latent death effectors that are unleashed by site-specific proteolysis. Genetic, biochemical, and structural analyses reveal novel modes of effector licensing. MBL and /{beta}-hydrolase are zymogens activated by cleavage at two distinct sites, and upon proteolysis, MBL becomes a Zn2+-dependent double-stranded DNA nuclease. In contrast, Pepco and EACC1 act as pore-forming toxins via distinct mechanisms: Pepco constitutively oligomerizes into a denaturation-resistant beta barrel that is activated by cleavage after a specific isoleucine in its C-terminal tail, whereas EACC1 monomers assemble into large membrane pores following removal of an autoinhibitory domain. All four modules are fused to diverse sensors to detect a wide range of phage signals, and EACC1-DnaK chaperone fusions suggest a convergence between defense and general stress responses. These findings establish proteolysisgated activation as a dominant, modular logic for anti-phage defense and reveal parallels with eukaryotic innate immunity.

molecular biology↗

bioRxiv2025

A Deep Learning Framework for Quantifying Dynamic Self-Organization in Myxococcus xanthus

Under starvation, Myxococcus xanthus bacteria initiate a multicellular developmental program in which cells move to form fruiting bodies and differentiate into distinct cell types. Many genes affecting this process have been identified, and it is assumed that perturbing genes within the same pathway induces similar changes in the phenotype, although those changes may be subtle or obscured by pleiotropic effects. However, these pathways cannot be systematically mapped, as there are no systematic methods for quantifying phenotype similarity. Here, we applied deep learning techniques to quantify the phenotype patterns and self-organization dynamics of 292 genetically distinct strains. By integrating ResNet and StyleGAN2 to construct a Variational AutoEncoder (VAE) and utilizing a Siamese network for phenotypic similarity metrics, we efficiently encoded high-resolution microscopy images into 13-dimensional feature vectors, capturing phenotypic variability in aggregation patterns across time and strains. Human evaluation confirmed that our models reconstructions were visually indistinguishable from real images and closely aligned with input phenotypes. Importantly, the feature space is interpretable: individual dimensions correlate with biological features such as aggregate number and size, and extrapolation along these dimensions produces predictable morphological changes. Remarkably, our model revealed that developmental phenotypes are predictable from the earliest stages before visible aggregate formation begins. This predictability held across both genetic and environmental sources of variation, suggesting fundamental constraints on developmental trajectories and indicating that subtle phenotypic variations carry important information. These results demonstrate how machine learning can reveal hidden structure in complex multicellular dynamics and provide scalable methods for phenotypic analysis without manual annotation.

systems biology↗

bioRxiv2025

Hidden Spirals Reveal Neurocomputational Mechanisms of Traveling Waves in Human Memory

While traveling waves are often described as planar propagations across cortex, recent theoretical work predicts that more complex spatial patterns, including spiral dynamics, could organize large-scale neural computations but remain difficult to detect in the human brain. To investigate this, we analyzed direct brain recordings from humans performing a working memory task. To characterize traveling wave patterns, we used independent component analysis, and showed that traveling waves propagated along the cortex in complex spatial patterns that correlated with behaviors such as memory encoding, maintenance, and retrieval. We then developed a novel computational framework based on coupled phase oscillators to model these distinct wave patterns. This computational approach revealed hidden spirals that were not visible in the original recordings. The center of these hidden spirals shifted across the cortex to distinguish separate behavioral states, such as memory encoding and retrieval. Together, these findings reveal that cortical traveling waves are governed by latent spiral attractor dynamics and suggest that rotating wave architectures provide a fundamental neurocomputational mechanism for flexible human memory processing.

neuroscience↗

bioRxiv2025

Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling

Mosaic variants, defined as postzygotic mutations occurring during an organisms development from zygote to adult, play critical roles in developmental biology, aging, and diseases such as cancer and neurological disorders. However, their accurate detection remains challenging due to low abundance in the genome and low variant allelic fractions (VAF). While current mosaic variant callers are primarily designed for short-read sequencing, no method is available for long-read sequencing, which can generate tens of kilobase-long reads to cover complex genomic regions inaccessible to short reads. To fill the gap, we present Clair-Mosaic, a deep-learning-based method for detecting mosaic small variants from long-read data. Clair-Mosaic was trained on hundreds of millions synthetic variants encompassing diverse read coverages and allelic fractions, enabling it to detect low-VAF mosaic variants with high sensitivity in paired-sample and single-sample modes. In addition to neural network prediction, Clair-Mosaic distinguishes genuine mosaic variants from sequencing artifacts by leveraging their inherent haplotype relationship in phased long reads. Furthermore, a Bayesian mosaic-germline discriminator is introduced to distinguish mosaic variants from germline variants. It also employs multiple post-calling filters, including a mosaic variant database and multiple germline population resources, to tag common germline and mosaic variants. Comprehensive benchmarking on synthetic datasets and real samples demonstrated Clair-Mosaics outstanding performance in ONT and PacBio. Clair-Mosaic is also applicable to short-read data and outperforms methods like MosaicHunter, MosaicForecast, DeepMosaic, and DeepSomatic. Clair-Mosaic is open-source and available at https://github.com/HKU-BAL/Clair-Mosaic.

bioinformatics↗

bioRxiv2025

In-Cell Synthesis of Nε-acetyl-L-lysine for Facile Protein Acetylation

N{varepsilon}-acetylation of proteins is a crucial post-translational modification (PTM) that occurs across all kingdoms of life and plays key roles in nearly every cellular process. Due to its broad significance, there is a strong demand for chemical biology tools that enable efficient, site-specific acetylation of target proteins in live cells. Genetic code expansion (GCE) has emerged as a powerful tool for introducing N{varepsilon}-acetylation at specific lysine residues in proteins. However, achieving adequate expression levels typically requires adding 2-10 mM of chemically synthesized N{varepsilon}-Acetyl-L-lysine (AcK) to the culture medium, which can be cumbersome and costly. To overcome this limitation, we present the first proof-of-concept for a one-pot acetylation platform that simplifies protein acetylation in both E. coli and mammalian cells. Our approach begins with the discovery of 10 novel lysine acetyltransferases (KATs) capable of biosynthesizing AcK from basic carbon sources. When these enzymes are co-expressed with the genetic incorporation machinery for AcK, they facilitate streamlined, site-specific acetylation of any target protein without compromising E. coli viability. This innovative platform not only broadens the range of unnatural amino acids (UAAs) that can be biosynthesized and incorporated but also provides a powerful tool for probing the histone and non-histone acetylation events in live cells. In addition, this technique offers an eco-friendly and scalable method to produce synthetic acetylated proteins, which will provide practical value in acetylation/deacetylation-related research such as chemical biology, biotechnology, and drug development.

synthetic biology↗

bioRxiv2025

Screening of Oyster Peptides for Anti-Muscle Atrophy Based on Machine Learning and Computer Simulation: Guided by Antioxidant Pathways

Muscle atrophy poses a serious threat to human health, with its primary pathogenic mechanisms closely linked to oxidative stress. This study focuses on the potential of oyster peptides in alleviating dexamethasone (DEX)-induced skeletal muscle atrophy and their underlying antioxidant mechanisms. Utilizing efficient integrated machine learning and computer simulation methods, a systematic screening of active peptides and mechanistic research was conducted. The results revealed that oyster peptides at concentrations of 25-50 g/mL significantly improved the decline in cell viability and myotube atrophy induced by DEX, while downregulating the expression of muscle atrophy markers Atrogin-1 and MuRF1. Through LC-MS/MS, 220 high-activity peptide sequences were identified. Following the replication and extension of the iAnOxPep integrated learning model, 15 potential antioxidant peptides were selected. Among them, the short peptide AWPGPQ demonstrated the strongest binding affinity with Keap1 and PPAR{gamma} targets. Molecular dynamics simulations confirmed its stability, suggesting that AWPGPQ may exert its dual effects--antioxidant and anti-muscle atrophy--by modulating the Keap1-Nrf2 and PPAR{gamma} signaling pathways. This study established a systematic and efficient strategy for screening natural active peptides, providing theoretical support and technical pathways for the discovery of multifunctional short peptide candidates, with significant theoretical value and application prospects.

molecular biology↗

bioRxiv2025

Targeting homologous recombination repair to potentiate fluoroquinolone efficacy in Mycobacterium abscessus

Synthetic antibiotics, fluoroquinolones (FQs), are extensively important treatment options for fast growing mycobacterial infections. However, their widespread use has led to decreased efficacy due to intrinsic or acquired resistance. FQs exhibit antimicrobial activity by stabilizing type II topoisomerases-generated DNA breaks, thereby inducing lethal double-strand breaks (DSBs) and leading to bacterial death. Escalating resistance among mycobacterial pathogens highlights the need to elucidate resistance mechanisms and identify novel strategies to restore or enhance the drug activity. Here, we revealed homologous recombination (HR) as a key determinant of FQ tolerance in Mycobacterium abscessus, a notoriously drug-resistant pathogen. Through a transposon mutagenesis screen, we identified that disruption of adnB - an HR-associated gene, markedly sensitized M. abscessus to FQs. This finding prompted a systematic dissection of DSB repair pathways in M. abscessus. Targeted deletion of HR core components (adnB, recO, recA, recR, ruvB) significantly increased FQ susceptibility in vitro, while inactivation of alternative DSB repair pathways - single-strand annealing (SSA) and non-homologous end joining (NHEJ) - had no effect, revealing a unique reliance on HR for FQ tolerance. Furthermore, the complementation of gene knock-out M. abscessus strains {Delta}adnB, {Delta}recO, {Delta}recA, {Delta}recR or {Delta}ruvB with the corresponding genes from M. abscessus, as well as homologous genes from Mycobacterium tuberculosis restored the resistance phenotype, indicating a conserved HR-dependent tolerance mechanism in M. abscessuss. In a murine infection model, genetic abrogation of HR significantly improved the therapeutic efficacy of FQs against M. abscessus, demonstrating translational relevance. Collectively, our findings position HR as a conserved and actionable vulnerability in M. abscessus, and provide a compelling rationale for developing HR-targeted adjuvant therapies to resensitize drug-refractory strains to FQ treatment. Impact statementFluoroquinolone (FQ) resistance poses a major challenge in the treatment of Mycobacterium abscessus infections. This study identifies homologous recombination (HR) as a key defense mechanism that limits FQ efficacy across multiple mycobacterial species. Genetic inhibition of HR not only sensitizes M. abscessus to FQs in vitro but also enhances antibiotic activity in vivo. These results highlight HR repair as a promising therapeutic target to potentiate FQ activity and combat drug resistance in M. abscessus infections.

molecular biology↗

bioRxiv2025

Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming

The therapeutic promise of tumor microbial peptides faces a critical safety paradox: tumors and peritumor tissues harbor compositionally similar microbiomes, yet safe immunotherapy demands tumor-specific targeting. We performed comprehensive transcriptomic analysis of microbial communities from 1,868 tumor and peritumor samples across 11 cancer types. Although 88.5% of microbial species are present in both tissue types, tumor and peritumor tissues exhibit profound transcriptional divergence: only 34.1% of microbial genes are expressed in both tissue types, and merely 18.2% of predicted HLA-binding peptides overlap. This transcriptional divergence represents microbial transcriptional reprogramming (MTR) in tumor tissues, through which microbes activate distinct genomic regions while adapting to tumor microenvironmental pressures, thereby generating tumor-specific peptide repertoires. Using Microbial Transcriptional Reprogramming Index (MiTRI) to quantify MTR, we found that higher MiTRI values correlate with expanded immunogenic peptide repertoires. Mass spectrometry-based immunopeptidomics confirmed that 25% of naturally presented microbial peptides originate from MTR regions. Crucially, in microsatellite-stable colorectal cancer, neo-adjuvant therapy responders exhibited significantly higher MiTRI values. T cell receptors (TCRs) recognized MTR-derived epitopes at 2.10-fold higher rates than genome-wide epitopes, accounting for 79.1% of clonally expanded TCRs. These findings establish MTR as the principle that ensures the tumor-specificity and safety of micorbiome-directed immunotherapy.

cancer biology↗

bioRxiv2025

Regulatory T cells inhibit CD8+ TRM-like cells during the early stages of tumor immune escape

How the immune system surveys nascent tumors and how this surveillance is subverted remain poorly understood. Using high-plex cyclic immunofluorescence and 3D imaging, we identified regulatory T (Treg) cells that co-localize with tissue-resident memory (TRM)-like T cells in early-stage human melanoma. In an autochthonous Braf/PTEN melanoma model expressing a defined tumor antigen, the initial CD8+ T cell infiltrate adopts a CD103+CD101+ TRM-like fate, establishing active immunosurveillance within nascent lesions. TRM-like cells dominate early tumors, occupy a stable epidermal niche, express effector molecules, and initiate T cell recruitment. However, Treg cells adopt a parallel tissue-resident phenotype, co-localizing with TRM-like cells and restraining both cytotoxic and sentinel functions. Tumor-site-specific Treg depletion reactivated TRM-like cells, drove robust T cell recruitment, expanded tumor-specific responses, and limited tumor growth. These findings reveal how early immunosurveillance is established through tissue-resident programs and identify Treg co-option of this response as a critical mechanism of tumor immune evasion. One Sentence SummaryNascent melanoma imprints a tissue-resident program on the initial CD8+ T cell infiltrate, which is suppressed by regulatory T cells as a critical checkpoint in immune evasion.

immunology↗

bioRxiv2025

Multiple Allosteric Sites Allow for Synergistic Enhancement of GPCR Signaling

Allosteric modulation of G protein-coupled receptors (GPCRs) is an emerging therapeutic paradigm that has proven effective, yet the cooperative action of multiple modulators remains unexplored. Here, we reveal how positive allosteric modulators (PAMs) synergistically enable extraordinary signal amplification through the D1 dopamine receptor (D1R). We developed UNC9815 and UNC10062 as enhanced D1R PAMs from the parent compound MLS6585, and then employed cryo-electron microscopy to reveal concurrent occupancy of three distinct allosteric sites by PAMs of different scaffolds, including LY3154207, BMS-A1, and our UNC compounds. Remarkably, we discovered two adjacent allosteric pockets at the transmembrane helix (TM) 1-7 interface: BMS-A1 occupies an intracellular site promoting activation through TM7 conformational shifts, while the UNC compounds complementarily stabilize the extracellular side of the interface. When combined with LY3154207, this cooperative architecture enhances dopamine potency by more than 1,000-fold. These findings elucidate the first structural blueprint for multi-site GPCR cooperativity, unlocking transformative therapeutic strategies inaccessible to orthosteric and single- site allosteric drugs.

molecular biology↗

bioRxiv2025

High-Power Dual-Channel Chamber for High-Frequency Magnetic Neuromodulation

ObjectiveSeveral novel methods, including magnetogenetics and magnetoelectric stimulation, use high frequency alternating magnetic fields to precisely manipulate neural activity. To quantify the behavioral effects of such interventions in a freely moving mouse, we developed a dual-channel magnetic chamber, specifically designed for rate-sensitive magnetothermal-genetic stimulation, and adaptable for other uses of alternating magnetic fields. ApproachThrough an optimized coil design, the system allows independent control of two spatially orthogonal uniform magnetic fields delivered at different frequencies within a 10 x 10 x 6 cm3 chamber suitable for mouse studies. The two channels have nominal frequencies of 50 and 550 kHz with peak magnetic field strengths of 88 and 12.5 mT, achieved with resonant coil drives having peak voltages of 1.6 and 1.8 kV and currents of 1.0 and 0.26 kA, respectively. Additionally, a liquid cooling system enables magnetic field generation for second-level durations, and an observation port and camera allow video capture of the animals behavior within the chamber. Main ResultsThe system generates high-amplitude magnetic fields across two widely separated frequency channels with negligible interference (< 1%). Relatively uniform magnetic field distribution ({+/-}10% across 94% of the chamber volume) is maintained throughout the chamber, and temperature increase of the inner side of the coil enclosure during the operation is limited to < 0.35 {degrees}C/s to ensure in vivo safety. Using cobalt-doped and undoped iron oxide nanoparticles, we demonstrate channel-specific heating rates of 3.5 {degrees}C/s and 1.5 {degrees}C/s, respectively, validating frequency-selectivity. Both channels can run continuously for 4 seconds stably. SignificanceWe present a novel magnetic stimulation platform that combines high-frequency, high-power capability with two independently-controlled channels generating different frequencies, along with a real-time behavioral observation system for freely moving animals. The system supports frequency-multiplexed stimulation strategies for precise modulation of neural activity, making it a versatile tool for advancing magnetogenetics, neural circuit interrogation, and noninvasive stimulation approaches in neuroscience and bioengineering.

bioengineering↗

bioRxiv2025

ACE2 Phosphorylation Modulates Angiogenesis via the Activator Protein-1

BackgroundAngiogenesis plays a crucial role in organ development. However, aberrant blood vessel growth is involved in various diseases, including tumors and neovascular eye diseases. Angiotensin-converting enzyme 2 (ACE2) is a critical enzyme regulating the health of cardiovascular system, and its post-translational modifications (PTMs) are crucial to determine ACE2 expression level and activity. Here, we studied how the PTM of ACE2 in vascular endothelial cells (ECs) affect pathological retinal neovascularization and tumor angiogenesis. MethodsThe angiogenic capabilities of ECs were assessed by tube formation, sprouting assays, and 5-ethynyl-2-deoxyuridine (EdU) and filopodia staining. EC angiogenesis was examined by poteome profiler array and aortic ring assays in vitro and by the oxygen-induced retinopathy (OIR) and tumor angiogenesis models in vivo. High-throughput screening involving data from RNA-seq, ATAC-seq, and ChIP-seq were used to explore the epigenetic and transcriptional regulations of pro-angiogenic genes regualtged by ACE2 PTMs. ResultsACE2 Ser-680 dephosphorylation in connection with Lys-788 ubiquitination increased EC angiogenic phenotype, which were manifested by aberrant vascularization in mouse OIR and tumor models. ACE2 Ser-680 dephosphorylation led to the activation of activator protein-1 (AP-1), which transactivated multiple genes involved in angiogenesis. AP- 1 inhibition mitigated such angiogenesis in vivo. ConclusionOur findings show a novel PTM mechanism of ACE2 involved in pathological angiogeneis. Specifically, ACE2 Ser-680 dephosphorylation facilitated AP-1 transactivation of the downstream pro-angiogenic genes in ECs.

cell biology↗

bioRxiv2025

New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study

BACKGROUNDSarcoidosis is a heterogeneous disease with unknown mechanisms, nonspecific therapies, and multiple etiologies. The role of blood extracellular vesicles (EVs) in the diagnosis and pathogenesis of sarcoidosis remains obscure. AIMS/OBJECTIVES. This study aims to test the hypothesis that the EV proteins in the blood can serve as phenotypic biomarkers of sarcoidosis. METHODS. We combined EV proteomics with machine learning algorithms to identify and prioritize biomarkers, enrich their functions, and cluster networks in case-control matched ACCESS patients. RESULTS. In total, 278 plasma EV proteins were significantly upregulated or downregulated in 40 sarcoidosis patients compared with 40 matched healthy controls. We identified 97 proteins that could serve as biomarkers with an AUC > 0.75. Of these, the AUC was > 0.90 for 13 proteins. 62 differentially expressed EV proteins strongly correlated with 20 clinical variables of severity, chest X-ray findings, and/or laboratory results. Functional annotation and network analysis suggest that these differentially expressed proteins regulate endocytosis, host responses to external stimuli, and transcription processes. Moreover, the top three ranked pathways were clathrin-mediated endocytosis, Hsp90 chaperone cycle, and spliceosome. CONCLUSIONS. This study demonstrates that plasma EV proteins can serve as biomarkers of various clinical phenotypes of the disease. At a Glance CommentaryCurrent Scientific Knowledge on the Subject: Sarcoidosis is a heterogeneous condition affecting multiple organs. The role of blood extracellular vesicles in the diagnosis and pathogenesis of this condition remains unknown. What This Study Adds to the Field: We identified differentially expressed proteins in plasma EVs by combining proteomics and machine learning algorithms. Top-ranked proteins can serve as diagnostic biomarkers and potential mechanisms for the development of sarcoidosis.

molecular biology↗

bioRxiv2025

Global Insights into Evolution and Adaptation in KPC and NDM Coproducing Carbapenem-Resistant Klebsiella pneumoniae.

ObjectivesThe worldwide dissemination of carbapenem-resistant Klebsiella pneumoniae co-producing KPC and NDM (KPC-NDM-CRKP) poses a substantial clinical challenge. MethodsThis study characterized 5 KPC-NDM-CRKP isolates from a tertiary hospital in southern China and integrated 460 global isolates genomes to demonstrate the population framework of this epidemic pathogen. Results5 clinical isolates were multidrug resistance, exhibiting high level resistance to first-line drugs including carbapenems and ceftazidime/avibactam. Globally, KPC-2-NDM-1 (50.3%) were the most common and an increasing trend of ST11-KL64 (20%) isolates carrying iucA and rmpA/A2. Resistance and virulence genes were positively associated with specific mobile elements including blaKPC-3 with Tn4401, iucABC with IncHI1B, iroBCDN with IncQ1. The phylogenetic analysis revealed distinct lineage-specific mutations and pan-genome enrichments synergistically promoted adaptive evolution: cluster 1 had membrane transport and secretion but enhanced immune evasion and horizontal gene transfer, cluster 3 adapted metabolically for nutrient-limited niches; cluster 4 reprogrammed metabolism for host adaptation, cluster 6 displayed membrane repair and reduced virulence (e.g., KC187). High-risk iucA/rmpA-positive isolates in cluster 2 acquired enhanced virulence and metabolic adaptive capacity through recombination hotspots (ABC transporters DdpABCD, efflux systems MdtABCD, metabolic enzymes XylB and MtlD, regulators BaeR and OmpR) and pan-genome enrichment (siderophore biosynthesis, toxin-antitoxin VapC and restriction-modification systems). Functionally, these traits correlated with high mucoviscosity, serum resistance, siderophore production and lower survival rates in G. mellonella that contribute to epidemiological success. ConclusionsThese findings demonstrated the discrete mutation, horizontal transfer, and accessory genome plasticity collectively drove the epidemiological success of KPC-NDM-CRKP.

microbiology↗

bioRxiv2025

Atlas of Breast Cancer in Chinese Young Women Revealed by Single-cell RNA and ATAC Sequencing

Young women with breast cancer (YBC, age[<=]40) are particularly prevalent in Asian. YBCs usually show more aggressive pathology and poorer outcomes than non-young patients. However, YBCs are underrepresented in current BC risk models, with their tumor intrinsic subtypes and microenvironments lacking a systematic elucidation at the single-cell level, thereby limiting the young-specific therapies. We established a single-cell Chinese YBC landscape baseline, including 246,659 cells, by applying scRNA-seq and scATAC-seq on untreated patients. We developed a cross-modal feature selection algorithm to construct a young-intrinsic subtype classifier BCYtype, outperforming existing classifiers in pseudobulk, cellular, and external cohorts. Comparative analyses with non-young samples revealed a direct differentiation trajectory from mammary stem cells to mature luminal cells. Pseudotemporal analysis also demonstrated that tumor cells in younger patients undergo earlier carcinogenesis. Mechanistically, we found that CDH1 interacts with pTex and NKT cells, serving as a young-specific marker and a potential therapeutic target for HR+ young patients. The interaction between exhausted T cells and antigen-presenting cells revealed NKG2A as a candidate therapeutic target for triple-negative breast cancer in young patients.

cancer biology↗

bioRxiv2025

Dynamic S-acylation of GSDMA regulates pyroptosis

GSDMA, the primary member of the gasdermin family found in the skin, is critical for pathogen-induced pyroptosis during infection. Recent studies revealed that another gasdermin, GSDMD, undergoes palmitoylation during pyroptosis. However, whether and how the other gasdermin members undergo lipid modification remains poorly understood. Here, we demonstrate that GSDMA is S-acylated at the conserved cysteine residues in its N-terminal domain. We show that S-acylation of GSDMA promotes pyroptosis by facilitating its membrane anchoring and protein oligomerization, a mechanism distinct from the palmitoylation of GSDMD at the N-terminal C191 residue. Additionally, we present evidence that recombinant proteins of GSDMA and GSDMD can undergo S- acylation in vitro via direct interaction with palmitoyl-CoA, suggesting they potentially possess auto-acylation capacity. Furthermore, we identify ABHD17A as one of the deacylating enzymes that regulate the dynamic fatty acylation cycle of GSDMA. Overall, our studies reveal new molecular mechanisms underlying GSDMA function through S- acylation and underscore its important role in regulating pyroptosis mediated by GSDMA. HighlightsO_LIGSDMA is S-acylated at N-terminal conserved cysteine residues. C_LIO_LIGSDMA S-acylation facilitates membrane anchoring and protein oligomerization. C_LIO_LIGSDMA and GSDMD recombinant proteins can undergo S-acylation in vitro C_LIO_LIThe ABHD17A enzyme is involved in GSDMA deacylation. C_LI

biochemistry↗

bioRxiv2025

Xenophagocytosis blockade enhances interspecies chimerism

Organ shortage remains a major challenge in transplantation medicine. Interspecies blastocyst complementation is a promising approach to generate human organs in livestock hosts. However, getting xenogeneic donor cells to engraft and expand at early stages remains challenging. Here we identify an innate immune barrier, wherein host macrophages selectively recognize and eliminate viable xenogeneic donor cells. These events represent a form of phagoptosis and highlight a xenogeneic clearance process that we term xenophagocytosis. We identify the mechanism by which host macrophages selectively phagocytize xenogeneic donor cells: xenogeneic cells display elevated phosphatidylserine, an "eat-me" signal recognized by host macrophages through phagocytic receptor Axl. Xenophagocytosis blockade improves both rat and human donor chimerism in mouse embryos, indicating a conserved mechanism. These findings reveal potential mechanisms by which innate immune cells eliminate xenogeneic cells in early embryogenesis to preserve species integrity and offer improved strategies for generating human organs in livestock.

immunology↗