Biology subjects

Zhou, Y.

Publications and source records attributed to Zhou, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

A human gut-BBB-brain microphysiological model for studying neurodegenerative diseases

The gut-brain axis has emerged as a crucial factor in neurodegeneration, with growing evidence linking gut dysbiosis and metabolic dysfunction to Alzheimers disease (AD) progression. Unfortunately, the lack of human-relevant in vitro models limits our ability to effectively explore the mechanism of this axis. To address this gap, we have developed a human induced pluripotent stem cell (iPSC)-derived gut-blood-brain barrier (BBB)-brain microphysiological system that enables systematic investigation of gut-brain interaction in the context of AD under controlled conditions. Our findings reveal that the interaction between gut and brain organoids can promote the maturation of brain organoids, making them more similar to their physiological characteristics in vivo. Additionally, co-culture gut and brain organoids better recapitulates the pathological features of AD. We also discovered that gut organoids of AD can trigger neurodegenerative disease manifestations in healthy brain organoids. In summary, our microphysiological system provides a novel and versatile in vitro platform for studying the interaction between the gut and brain in neurodegenerative diseases.

neuroscience↗

bioRxiv2026

ProteinConformers: large-scale and energetically profiled descriptions of protein conformational landscapes

Modeling protein conformational landscapes is essential for understanding dynamics, allostery, and drug discovery, yet existing resources lack diverse conformational coverage, energetic annotations, or benchmarking standards. ProteinConformers (https://zhanggroup.org/ProteinConformers) provides 2.7 million geometry-optimized conformations generated with a multi-seed molecular dynamics strategy, paired with 13.7 million energy evaluations and 5.5 million similarity annotations. It delivers continuous landscapes from non-native to near-native states, benchmarking framework for multi-conformation generators, and an interactive analysis platform.

bioinformatics↗

bioRxiv2026

NRMLncR, a myocyte-enriched long non-coding RNA, enhances myogenesis in mouse

Myogenesis is a stepwise process encompassing myogenic progenitor proliferation, lineage commitment, differentiation, myocyte fusion, and myotube maturation, and it is orchestrated by myogenic regulatory factors (MRFs) together with signaling pathways that coordinate these transitions. Long noncoding RNAs (lncRNAs) have emerged as important regulators of muscle development and regeneration, yet how lncRNAs integrate with canonical signaling networks to shape myogenic progression remains incompletely defined. Here, we identify a novel myocyte-enriched, Notch-repressed myogenic lncRNA (NRMLncR, known as A930003A15Rik), as a previously uncharacterized regulator of mouse myogenesis. The expression of NRMLncR is robustly induced during primary myoblast activation and differentiation. Loss-of-function analyses show that knockdown of NRMLncR impairs myogenic differentiation, accompanied by reduced expression of key myogenic genes. In contrast, adenovirus-mediated overexpression of NRMLncR enhances myogenic differentiation in vitro and is associated with increased muscle fiber size in vivo. Mechanistically, MyoD and MyoG occupy the NRMLncR promoter and promote its transcription during myogenic differentiation. NRMLncR knockdown alerts the transcription of nearby genes, suggesting its function through a cis-regulatory mechanism. RNA pull-down assays further identify an interaction between NRMLncR and the RNA-binding protein CELF1. Together, these findings establish NRMLncR as a novel Notch-associated lncRNA that promotes myogenic differentiation and provide insight into lncRNA-dependent regulation of the myogenic program.

genetics↗

bioRxiv2026

Large-scale quantum computing framework enhances drug discovery in multiple stages

Coherent Ising machines (CIMs) excel at solving large-scale combinational optimization problems (COPs), but their insufficient long-term stability has hindered their applications in compute-intensive tasks like computer-aided drug discovery (CADD). By improving fiber vibration isolation and temperature control system, we have implemented a 2000-node CIM named QBoson-CPQC-3Gen achieving stable solutions over one hour on large-scale COPs. Graph-based encoding schemes were further introduced to realize a CIM-based CADD workflow including allosteric site detection, protein-peptide docking and intermolecular similarity calculation. CIM-based methods demonstrated superior speed and accuracy than heuristic algorithms. Especially, QBoson-CPQC-3Gen identified 2 novel druggable sites and bioactive compounds for 6 targets, which were further validated in vitro, in-cell and by crystal structures. Our contributions established a quantum-computing framework for multi-stage drug discovery, representing a significant advancement in both quantum computing applications and pharmaceutical research.

bioinformatics↗

bioRxiv2026

Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation

DNA methylation is a conserved epigenetic modification crucial for silencing genes and transposable elements (TEs). However, the mechanisms that cause silencing remain unclear, partly because methyl reader protein mutants in both plants and animals show minimal transcriptional changes. To explore the possibility of redundancy among these silencing mechanisms, we generated combinatorial mutants of H1.1, H1.2, ADCP1, MOM1, MBD2, MBD5, and MBD6 lacking key methyl readers and related silencing pathways. We observed massive derepression of genes and TEs at DNA-methylated loci, showing that these pathways account for 73% of silencing compared to DNA methylation-free mutants. We also observed that immune response genes were upregulated, causing an imbalance between growth and defense. Loss of downstream silencing pathways further disrupted 3D genome organization, leading to increased euchromatin-heterochromatin interactions. These findings highlight the cooperative action of multiple downstream mechanisms in DNA methylation-mediated silencing and genome organization.

molecular biology↗

bioRxiv2026

Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants

In mammals, cohesin-mediated chromatin loop extrusion is blocked at boundaries, where CTCF, WAPL, and PDS5s co-bind and regulate cohesin, establishing an impermeable barrier with no exceptions. In contrast, our study revealed that in Arabidopsis, some noncanonical contacts have emerged between the boundary flanking regions, which suggest that cohesin is not absolutely blocked but enables sliding beyond boundaries. We identified these interactions as noncanonical loops and clarified their regulatory proteins. Firstly, the plant-specific boundary binding protein EMF1 is essential for noncanonical loops formation. Surprisingly, although both Arabidopsis WAPLs and PDS5s inhibit loop extension as mammals, PDS5s do not co-bind and cooperate with WAPLs at boundaries. Instead, PDS5s bind to boundary-flanking regions enriched with H3K4me1 through their Tudor domains, restricting further extension of noncanonical loops. Consequently, pds5a/b/c mutants lose noncanonical loops, resulting in emergence of larger canonical loops but anchored on boundaries and co-upregulation of anchored gene pairs. Collectively, our findings reveal that the plant-specific noncanonical loop, regulated by plant-specific EMF1 and PDS5 proteins, is the fundamental structure of the distinctive chromatin organization of plants, which provides novel mechanistic insights into eukaryotic chromatin architecture regulation.

plant biology↗

bioRxiv2026

Rapid and Quantitative Phage Susceptibility Test by Ramanome

Antimicrobial resistance poses an escalating global threat, renewing interest in bacteriophage therapy as a precision alternative to antibiotics. However, clinical translation remains hindered by the lack of rapid and quantitative phage susceptibility testing (PST) platforms capable of evaluating host range, infection potency, and effective multiplicity of infection (MOI). Here we present RPST, a ramanome-based phenotypic platform that captures infection-induced remodeling of bacterial macromolecular composition to unify these diagnostic requirements within a single workflow. RPST integrates four Raman biomarkers into a Composite Infection Index (CII), enabling rapid and lysis-independent discrimination between susceptible and resistant bacterial populations within [~]1 hour, with 96.0% categorical concordance (24/25) to plaque assays. As a continuous population-level metric, CII quantifies the proportion of infected cells, allowing quantitative ranking of phage potency against shared hosts. By resolving CII trajectories across the MOI and time, RPST further determines the minimal effective MOI, which is the lowest phage-to-bacterium ratio sustaining self-propagating infection, thereby defining the lower boundary for therapeutic feasibility. Together, these capabilities transform PST from static compatibility assays into a dynamic and quantitative framework that bridges in vitro infectivity assessment and infection dynamics relevant to phage therapy. Impact StatementBased on the rapid emergence of antimicrobial resistance, this study introduces RPST, a novel ramanome-based phage susceptibility testing platform. RPST detects phage-induced biochemical remodeling in bacteria within [~]1 hour, achieving 96.0% concordance with gold-standard plaque assays. By integrating four Raman biomarkers into a Composite Infection Index, it not only distinguishes susceptible from resistant strains but also quantifies phage potency and determines the minimal effective multiplicity of infection required for self-sustaining infection. This transformative approach moves beyond binary diagnostics to offer a dynamic, quantitative framework for precision phage therapy, significantly accelerating therapeutic decision-making and enhancing our ability to combat resistant infections.

microbiology↗

bioRxiv2026

Cell type-resolved proteomics reveals intra- and intercellular signalingin Alzheimers disease

Alzheimers disease (AD) arises from pathological interactions among diverse brain cell types, but cell-specific proteomic changes remain underexplored. Here, we present deep proteomic profiling of sorted or proximity-labeled brain cells from AD mouse models (5xFAD and AppNL-G-F) at multiple ages, quantifying 13,411 proteins in microglia (three subtypes), astrocytes, oligodendrocyte precursor cells, and neurons. We identified 3,028 differentially abundant proteins across these cell types, the majority of which were not detected in bulk proteomic datasets, and constructed cell type-specific networks to define functional modules and hub proteins. Comparison with transcriptomic data revealed that [~]30% of proteomic changes are RNA-independent. Further analyses uncovered cross-cell type signaling proteins conserved in human AD brains, such as pleiotrophin (Ptn), which is transcriptionally enriched in astrocytes but accumulates in microglia. Importantly, recombinant PTN directly activates induced microglia-like (iMG) human cells. Thus, these findings provide a comprehensive cell type-resolved proteomic atlas of AD models, highlighting novel intra- and intercellular signaling events. HighlightsO_LIA high-resolution cell type-resolved proteomic atlas of Alzheimers disease mouse models C_LIO_LI[~]3,000 cell type-specific protein alterations identified beyond bulk tissue analyses C_LIO_LIProteomic profiling of microglial subtypes reveals subtype-specific changes in Alzheimers disease C_LIO_LIAstrocyte-microglia signaling is highlighted and validated through PTN-mediated interactions C_LI

neuroscience↗

bioRxiv2026

Prostaglandin E2 Reverses Myofibroblast Differentiation in Eosinophilic Esophagitis

Background & AimsUnchecked inflammation in Eosinophilic esophagitis (EoE) leads to esophageal fibrosis and eventual stricture. Differentiated fibroblasts, termed myofibroblasts, are the main effector cells in fibrosis, responsible for secreting extracellular matrix proteins leading to tissue stiffness. Regulating myofibroblasts has not been explored as a therapeutic possibility in the fibrostenotic esophagus. Herein, we aim to investigate the efficacy of Prostaglandin E2 (PGE2) in dedifferentiation of the EoE myofibroblast. MethodsWe evaluated the efficacy and mechanism of myofibroblast dedifferentiation using fetal esophageal fibroblasts (FEF3), patient-derived fibroblasts, and a murine model of EoE. ResultsFibrosis markers (SMA, FN1, and COL1A1) and contractility of myofibroblasts were significantly decreased by PGE2 via the cAMP pathway. PGE2 treatment decreased nuclear accumulation of phospho-Smad2/3-YAP complex and induced phospho-YAP proteasomal degradation. Transcriptome analyses of FEF3 treated with TGF{beta} or PGE2 revealed that the Integrin1 pathway, and specifically thrombospondin 1 (THBS-1), was significantly upregulated by TGF{beta} and downregulated by PGE2, as supported by pseudo-bulk single-cell RNA-seq of EoE biopsies. THBS-1 was shown to be regulated by PGE2 via the cAMP/YAP pathway, and its knockdown induced myofibroblasts dedifferentiation. In a murine model of EoE, Butaprost, agonist of the E-prostanoid G protein-coupled receptor 2, treatment significantly reduced the expression of THBS-1, SMA, and FN1 along with a decrease in YAP nuclear translocation. Additionally, collagen fiber organization in the lamina propria was markedly reduced. ConclusionPGE2 promotes dedifferentiation of myofibroblasts in EoE via the cAMP/YAP/ THBS-1 pathway. Our data suggest that PGE2 is a promising treatment strategy for EoE with stenosis. What You Need to KnowO_ST_ABSBackground and ContextC_ST_ABSIn Eosinophilic esophagitis, unchecked inflammation and tissue stiffness drives fibroblast differentiation and fibrostenosis of the esophagus, yet targeting myofibroblasts as regulators of extracellular matrix deposition in fibrostenotic disease remains clinically unexplored. New FindingsProstaglandin E2 promotes dedifferentiation of myofibroblasts in eosinophilic esophagitis via the cAMP/YAP pathway, with Thrombospondin-1 identified as a critical YAP regulated target driving fibrostenosis. LimitationsThis study focused on fibroblast-specific mechanisms. The effects of PGE2 on esophageal epithelial differentiation, barrier function, and immune cell recruitment in EoE remain to be determined. Clinical Research RelevanceThis study demonstrates proof-of-concept that pharmacological reversal of established fibrosis is achievable in EoE. PGE2 and its EP2-selective agonists represent translatable therapeutic targets for fibrostenotic EoE--a patient population that remains treatment-refractory to current immunosuppressive approaches. Basic Research RelevanceThe cAMP/YAP/THBS-1 signaling in fibroblasts emerges as a critical therapeutic target for esophageal fibrosis. Importantly, this work demonstrates that terminally differentiated myofibroblasts retain remarkable plasticity and can dedifferentiate--challenging the paradigm that fibrosis is irreversible.

cell biology↗

bioRxiv2026

LANA-dependent Interaction of Host Factors DAXX and BRD4 Impact KSHV Lytic Replication

Kaposis Sarcoma-Associated Herpesvirus (KSHV) is an oncogenic gammaherpesvirus that causes Kaposis Sarcoma (KS). KSHV alternates between latent and lytic phases. Latency is marked by limited viral gene expression and absence of virion production, whereas the lytic phase is characterized by the expression of all viral genes in a temporally and sequentially regulated cascade of immediate-early, early, and late genes, culminating in viral genome replication and infectious virion production. Both KSHV latent and lytic viral phases contribute to its pathogenesis and the development of KS. KSHV proteins hijack host proteins, rewiring host cellular processes and signaling pathways, and modulating host gene expression. KSHV establishes latency through stable interactions between viral proteins and host factors, with the Latency Associated Nuclear Antigen (LANA) serving as a key regulator that interacts with host machinery to maintain the viral episome and regulate viral replication. However, the consequences for host proteins binding viral proteins, including changes in their interaction networks and their impact on viral replication, remains poorly understood. Here, using Immunoprecipitation Mass Spectrometry (IP-MS), we identified and validated the host death domain-associated protein (DAXX) and DNA ligase 3 (LIG3) as major LANA-associated factors and discovered a LANA-dependent recruitment of Bromodomain-containing protein 4 (BRD4) to DAXX. This remodeling of the DAXX interactome guided functional analyses demonstrating roles for DAXX and BRD4 in supporting KSHV infection. Functional studies show that siRNA knockdown of DAXX or BRD4 in iSLK.BAC16 cells, followed by lytic reactivation, significantly induced viral gene transcription and protein expression of KSHV lytic genes ORF45, ORF59, ORF26, and K8.1. Conversely, siRNA knockdown of LIG3 reduced the transcription and protein expression of KSHV lytic genes. Viral genome replication and infectious virion production were elevated upon knockdown of DAXX or BRD4 and reduced after the knockdown of LIG3. Additionally, chemical inhibition of BRD4 activity by the drug JQ1 in iSLK.BAC16 cells, followed by lytic reactivation, resulted in elevated KSHV lytic gene expression, genome replication, and infectious virus production. Together, these data suggest that both DAXX and BRD4 host genes contribute to KSHV latency maintenance, while LIG3 is required for lytic reactivation. Understanding the functional significance of these LANA-interacting host factors in regulating KSHV infection is critical for identifying therapeutic targets and developing potential treatment strategies.

microbiology↗

bioRxiv2026

Antigen presentation requirements for effective cDC1-based cancer immunotherapy

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma. As expected, MHC-I- or MHC-II-deficiency had minimal impact on the transcriptional state of cDC1s in homeostasis or following stimulation with the adjuvant poly dI:dC. Moreover, in vitro-derived cDC1s cultured under steady-state conditions closely resembled tumor-infiltrating cDC1s, whereas their poly dI:dC-stimulated counterparts resembled CCR7+ tumor-infiltrating DC populations, also referred to as mregDCs or LAMP3+ DCs. Our data further show that both MHC-I and MHC-II contribute to tumor control upon cDC1 vaccination, and coexpression of MHC-I and MHC-II on the same cDC1 is necessary for a robust vaccine response. We also identified an important function for host cDC1s in supporting the efficacy of vaccination with in vitro-derived cDC1s, as judged by impaired tumor control in Irf8+32-/- mice, which lack endogenous cDC1s. Overall, these results indicate that effective antitumor responses depend on MHC-I and MHC-II antigen presentation by vaccine-delivered cDC1s, with additional contributions from host cDC1s. Key pointsO_LIIn vitro-generated cDC1s resemble intratumoral DC populations found in mice and humans. C_LIO_LIMHC-I and MHC-II antigen presentation by vaccine-delivered cDC1s contribute to antitumor efficacy. C_LIO_LICoexpression of MHC-I and MHC-II on the same cDC1 enhances vaccine responses. C_LIO_LIAntitumor responses reflect the activity of vaccine and endogenous cDC1s. C_LI

immunology↗

bioRxiv2026

Starve-Feed Cycles Direct Quiescence to Proliferation Transitions in Drosophila Follicle Stem Cells via Transcriptional Regulation

Stem cell quiescence is a reversible state in which cells temporarily exit the cell cycle but remain poised to reenter, on cue. Robust protection of the balance between stem cell quiescence and proliferation (Q->P) is critical for long-term tissue health. Proliferation without proper resources drives disease states including cancer or birth defects. Conversely, extended periods of quiescence can lead to irreversible senescence, causing stem cell loss, aging symptoms, and vulnerability to oncogenic transformation. Diet is a central regulator of Q->P. Tissue stem cells are particularly impacted, entering periods of quiescence during nutrient restriction, with rapid induction of proliferation upon feeding. We demonstrated previously that the Hedgehog (Hh) signaling pathway is necessary and sufficient for controlling Q->P responses to dietary changes in epithelial Follicle Stem Cells (FSCs) in the fly ovary. The Hh effector, Cubitus Interruptus (Ci), is a transcriptional regulator that mediates the feeding response. To identify Ci-induced Q->P regulators, we labeled transcripts that are induced in FSCs during the 6-hour Q->P timecourse using thiouracil tagging (TU-tagging), and sequenced TU-tagged messages versus Input to prioritize candidates. Unexpectedly, cell cycle regulators were not induced, suggesting that other mechanisms control Q->P in FSCs. We describe a sequential screening approach that uncovered seven novel, feeding-dependent Q->P regulators, including a cholesterol transporter and, surprisingly, glial and neuronal regulators. Our results highlight the importance of dynamic regulation of gene expression for translation of dietary signals by stem cells, uncovering new pathways for mechanistic investigation.

genetics↗

bioRxiv2026

3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network

Spatially resolved transcriptomics (SRT) is a promising new technology that enables simultaneous analysis of gene expression and spatial information for biomedical research. However, the existing statistical and deep learning algorithms used for analyzing SRT data rely solely on two-dimensional (2D) spatial coordinates, which limits their ability to accurately identify spatial domains, spatially variable genes, cell-to-cell communications, and developmental trajectories in a three-dimensional (3D) spatial manner. To address these limitations, we introduced Spa3D, which utilized the anti-leakage Fourier transform and graph convolutional neural network model to reconstruct 3D-based spatial structures from multiple 2D SRT slices. We demonstrate that Spa3D is appliable to analyze data from various SRT technology platforms and outperforms state-of-art methods by: (I) improving spatial domain identification through 3D reconstruction, (II) elucidating cell-cell communication landscape in the 3D cellular organization, (III) modeling of organ-level tempo-spatial development patterns in a 3D fashion, and (IV) annotating 3D spatial trajectory that are not captured by 2D spatial coordinates. Key pointsO_LIMost existing spatial omics analysis methods rely on 2D data, limiting their ability to capture full spatial and developmental tissue complexity C_LIO_LISpa3D incorporates physical z-axis distances, enabling accurate 3D modeling even when adjacent slices vary in tissue structure and composition C_LIO_LISpa3D reconstructs true 3D spatial structures from 2D SRT slices using graph convolutional networks and anti-leakage Fourier transforms C_LIO_LISpa3D enhances spatial domain detection, revealing detailed cell-cell communication and organ-level development patterns across multiple spatial omics platforms C_LIO_LISpa3D enables novel biological discoveries by revealing spatial features and trajectories not detectable using traditional 2D transcriptomic analysis approaches C_LI

bioinformatics↗

bioRxiv2026

Deep learning-guided design of cell type-specific AAV promoters

Precise cell type targeting is critical for both clinical and experimental applications of adeno-associated viral (AAV) vectors, yet engineering vectors with cell type-specific activity remains a challenge. Here, we compared three strategies leveraging single-cell chromatin accessibility data to design cell type-specific AAV promoters, including a deep learning-based method to generate de novo regulatory sequences. When applied to target retinal ganglion cells or horizontal cells in mouse retina, deep learning-guided design consistently outperformed rational approaches, yielding synthetic promoters with stronger and more specific expression in vivo. Synthetic AAV promoters supported diverse transgenes, enabling the recording and ablation of targeted cells. Promoter activity was also maintained in human retinal organoids, suggesting that deep learning-designed sequences may be suitable for translation. Our findings highlight the potential of deep learning to synthesize cell type-specific AAV promoters and establish a versatile platform for cell type targeting with broad implications for gene therapy and basic research.

synthetic biology↗

bioRxiv2026

Molecular Mechanisms Associated With Amelioration Of Radiation Induced Gastrointestinal Mucositis By Compound Kushen Extracts

Radiation induced gastrointestinal mucositis (GIM) is a severe complication of radiotherapy that compromises patient quality of life and treatment efficacy. This study assessed the therapeutic potential and molecular mechanisms of two forms of herbal extracts, Compound Kushen Powder (CKP) and Compound Kushen Injection (CKI) in a rat model of GIM. Administration of either CKP or CKI to irradiated animals significantly reduced the severity of GIM symptoms. Transcriptomic analysis of jejunum and colon mucosa identified candidate mechanisms as well as common pathways between CKP and CKI. CKP modulated innate immune activation and inflammatory signalling, affecting genes such as Socs3 and Tlr4, while CKI promoted tissue repair and oxidative stress resistance through genes including Osm, Epha2, and Stat3. However, both forms of herbal extract enhanced stress response and stimulus regulation in our GIM model. These findings reveal common mechanisms shared by CKP and CKI that suppress symptoms of radiation induced GIM, along with extract specific effects on distinct pathways, acting on different set of genes.

molecular biology↗

bioRxiv2026

Lysosomal Aspartylglucosaminidase Couples Glycoprotein Catabolism to Cell-Surface GlycoRNA Production

GlycoRNAs, small non-coding RNAs covalently linked to N-glycans, reveal an unexpected intersection between RNA biology and glycosylation, with potential roles in immunity and cell-cell communication. The origins and biogenesis of their glycans remain unclear. Using CRISPR-Cas9 screening, metabolic glycan labeling and lysosome-targeted proteomics, we reconfirm canonical N-glycosylation enzymes (STT3A/B) and identify components of the mannose-6-phosphate (M6P) lysosomal sorting pathway (GNPTAB, M6PR) as essential contributors. Strikingly, lysosomal aspartylglucosaminidase (AGA) acts as a rate-limiting regulator, linking glycoprotein catabolism to glycoRNA formation. Loss of AGA collapses both abundance and diversity of RNA-linked N-glycans, while pulse-chase tracing shows glycoprotein-derived glycans are repurposed for RNA glycosylation. These findings position lysosomes as active participants in RNA modification and redefine glycoRNA biogenesis as a metabolically integrated process.

cell biology↗

bioRxiv2026

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii

Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that hospital network architecture functions as a primary selective pressure, driving pathogen evolution through infrastructure-dependent virulence-transmission trade-offs. Phylogenomic analysis of 5,023 Acinetobacter baumannii isolates across Chinas centralized healthcare system identifies two co-existing evolutionary strategies: a virulence-optimized clade (ESL2.4) that spread slowly (20.4 km per year) in low-connectivity hospitals, and a transmission-optimized clade (ESL2.5) that disseminate rapidly (65.2 km per year) through mega-city healthcare hubs, likely attributed to its capsule conversion and increased upper respiratory colonization. Comparative analysis with European A. baumannii populations demonstrates that healthcare connectivity, not geography, governs pathogen distribution through convergent genomic adaptations. Our simulation suggests competitive asymmetries of the two clades, following the ecotype principle and enabling stable coexistence. The COVID-19 pandemic provided a natural experiment validating these mechanisms: outpatient restrictions reduced transmission-optimized lineage spread by 89%, while virulence-optimized lineage persisted through inpatient networks. These findings establish healthcare infrastructure as a critical evolutionary driver with immediate implications for predicting and controlling antimicrobial resistance emergence across diverse healthcare systems.

microbiology↗

bioRxiv2026

Dual Inhibition of MYRF Cleavage by Its JM Region and PAN-1 CCT Gates Developmental Timing in C. elegans

Post-embryonic development proceeds through discrete stages, yet the mechanisms that coordinate transitions between stages remain incompletely defined. The transmembrane transcription factor MYRF undergoes intramolecular cleavage to release a nuclear-localized fragment essential for developmental progression in C. elegans. Previously, we showed that PAN-1 as a key partner required for MYRF activity during development. PAN-1 promotes MYRF trafficking to the cell membrane--an essential step for MYRF cleavage--through interactions between their extracellular domains (Xia et al., 2021). Here, we show that MYRF-1 cleavage and nuclear translocation oscillate with larval stage transitions in C. elegans, peaking mid-to-late stage and being suppressed during molts. Using endogenous gene editing and mutant reporters, we identify an uncharacterized juxtamembrane (JM) region in MYRF-1 that self-inhibits cleavage. JM deletion triggers premature MYRF-1 nuclear entry, early lin-4 activation, growth defects, and adult lethality. We further demonstrate that the cytoplasmic tail (CCT) of the transmembrane protein PAN-1 acts as a predominant trans-inhibitor of MYRF-1 cleavage, coupling extracellular association with cytoplasmic inhibition. PAN-1 CCT deletion causes near-constitutive MYRF-1 nuclear accumulation, leading to premature lin-4 activation, accelerated M-cell division, and larval lethality. Removing these inhibitory mechanisms on MYRF-1 cleavage overrides nutrient-responsive developmental checkpoints. These findings uncover dual inhibitory mechanisms governing MYRF-1 cleavage and establish MYRF-1 cleavage as a key gatekeeper of developmental timing.

developmental biology↗