Biology subjects

Tang, Y.

Publications and source records attributed to Tang, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

LNP-mediated BCL11A Editing Corrects Sickling Phenotypes and Preserves HSPC Fitness Compared to Electroporation

Hemoglobinopathies, including sickle cell disease (SCD) and thalassemia syndromes, affect millions of individuals worldwide who have limited access to curative therapies. Autologous hematopoietic stem cell transplant following ex vivo CRISPR editing of the BCL11A erythroid enhancer reactivates fetal hemoglobin (HbF) and achieves an effective cure, but the resource constraints of clinically approved procedures for editing by electroporation (EP) severely limit widespread implementation. We directly compared the functional outcomes of EP delivery of Cas9 ribonucleoprotein with lipid nanoparticle (LNP) delivery of Cas9 mRNA in primary human HSPCs obtained from healthy HbAA donors and from patients with SCD. While higher editing rates are achieved with EP, LNP-treated HSPCs exhibited greater viability and cell yields that persisted throughout a multi-stage in vitro erythroid differentiation protocol. By day 20, the yield of mature red blood cells (CD71lowCD235ahigh) was lowest in the EP cohorts. Across treatment groups, we observed HbF induction proportional to indel frequency. LNP editing of SCD patient-derived HSPCs as low as 25% modified alleles still caused HbF production and reduced the propensity for sickling of in vitro differentiated RBCs. These findings highlight the critical trade-offs among manufacturing ease, delivery-associated toxicity, and functional performance across two modalities of therapeutic genome editing for hemoglobinopathies.

bioengineering↗

bioRxiv2026

AKAP5 and Caveolin-1 organize opposing nanodomains that regulate smooth muscle contraction and blood pressure

TRPV4 ion channels in vascular smooth muscle cells (SMCs) are crucial regulators of blood pressure, and their functional effects are differentially shaped by their signaling partners. However, the mechanisms by which TRPV4 channels are compartmentalized into distinct signaling nanodomains with opposite impacts on blood pressure remain unclear. Here, we identify the scaffolding proteins that compartmentalize TRPV4 channels into discrete nanometer-scale signaling domains at the SMC plasma membrane and define how these nanodomains produce opposing effects on vasoconstriction and blood pressure. We show that AKAP5 anchors a nanodomain linking 1-adrenergic receptors, protein kinase C and TRPV4 channels, thereby driving sympathetic vasoconstriction and blood pressure elevation. In contrast, caveolin-1 promotes a mechanosensitive nanodomain comprising Piezo1, TRPV4, and BK channels that mediates vasodilation and a decrease in blood pressure. In hypertension, AKAP5-dependent constrictor nanodomains are hyperactive, whereas caveolin-1-based dilator nanodomains are hypoactive, shifting the balance toward pathological vasoconstriction. These findings reveal fundamental mechanisms that organize smooth muscle TRPV4 channels into spatially and functionally distinct nanodomains regulating blood pressure and show how disruption of this organization contributes to blood pressure elevation in hypertension.

physiology↗

bioRxiv2026

MYC-MIZ1 Complexes at Enhancers Tune Neuroendocrine Identity of Small Cell Lung Cancer

MYC family members have been extensively studied as undruggable transcription factors regulating oncogenic signaling in highly aggressive tumors such as small cell lung cancer (SCLC), via promoter binding. Here, leveraging the previously described Myc-driven SCLC mouse model (RPM), we generated RPM-Miz1{Delta}POZ (RPMM) mice to uncover a Myc-dependent regulation of neuroendocrine (NE) differentiation, via enhancers. Our functional and genomic analyses reveal that Miz1 facilitates Myc binding to low-affinity E-boxes at distal chromosomal regions, thereby enabling Myc occupancy at sites with otherwise limited intrinsic affinity. We further show that SCLC patients and cellular models share an enrichment of low-affinity E-Box Myc binding motifs at enhancer regions that loop to genes of classic neuroendocrine differentiation. Integrated epigenetic and genomic analyses with AI-modeling implicate Myc/Miz1 binding at enhancers as the determinant for the expression of bona-fide neuroendocrine genes. In RPMM tumors, the suppression of neuroendocrine identity is paralleled by a redistribution of Myc protein towards promoter-proximal regions, hyper-activation of Myc transcriptional programs, apoptotic priming and enhanced sensitivity to etoposide. Together, these findings uncover Miz1/Myc-engaged enhancers as a central hub for neuroendocrine lineage programs and provide a mechanistic basis for a targeted inhibition of Miz1 to boost chemosensitivity in SCLC.

cancer biology↗

bioRxiv2026

OTUB1 controls marginal zone B-cell development by stabilizing RelA in a CD40-dependent manner

Ubiquitin-dependent regulation of NF-{kappa}B signaling is essential for B-cell homeostasis and fate decisions, yet the contribution of specific deubiquitinating enzymes remains incompletely defined. OTUB1, a lysine-48-specific deubiquitinase, has been broadly implicated in immune regulation, including control of NF-{kappa}B signaling and prevention of immune hyperactivation. Previous studies have demonstrated that B cell-specific deletion of OTUB1 leads to B cell hyperplasia, increased antibody production, and lupus-like autoimmunity, highlighting its importance in maintaining B cell tolerance and immune homeostasis. Using B cell-specific OTUB1-deficient mice, we show that loss of OTUB1 leads to a marked expansion of marginal zone (MZ) B cells and their precursor populations in the spleen, accompanied by an activated phenotype and enhanced proliferative responses, particularly upon CD40 stimulation. OTUB1 deficiency results in altered CD40-induced NF-{kappa}B signaling, characterized by enhanced I{kappa}B degradation and increased nuclear accumulation of p50-containing NF-{kappa}B complexes, despite reduced RelA stability. Mechanistically, we show that OTUB1 interacts with RelA, restricting its lysine-48-linked ubiquitination and proteasomal degradation, thereby stabilizing this key transcription factor. Collectively, these findings identify RelA as a novel OTUB1 target and uncover an additional layer of ubiquitin-dependent control of NF-{kappa}B signaling that governs splenic B-cell homeostasis and marginal zone B-cell development.

immunology↗

bioRxiv2026

A lipid nanoparticle platform for high yield CRISPR-targeted homology directed repair enables fully non-viral CAR T cell generation

CRISPR-mediated homology directed repair (HDR) enables targeted CAR integration with improved fitness and therapeutic potential of CAR T cells. However, current methods for generating HDR-engineered CAR T cells rely on viral transduction or electroporation, approaches that limit global implementation and constrain patient access due to their cost, toxicity, and requirement for centralized manufacturing. Through a screen of ionizable lipids, we identified LNP systems that enable CRISPR-mediated gene knock-in (KI) in primary human T cells and are amenable to hand mixing by ethanol injection as a research tool or machine formulation for larger scale manufacturing. Modifying the linear dsDNA HDR template with truncated Cas9 target sequences (tCTS) enhanced HDR rates across multiple LNP systems. We optimized two LNP formulations capable of HDR-mediated KI of a large 4kB CD19 CAR-EGFR HDR template into the TRAC locus with rates of [≥]8% and >10x improved edited cell yields compared to electroporation. We demonstrate that LNP-generated CAR T cells exhibited similar growth kinetics, activation states, differentiation states, and killing capacity compared to electroporation-generated CAR T cells. Our LNP platform components are fully disclosed, commercially sourced, and enable efficient fully non-viral CRISPR-HDR cell engineering across diverse applications.

bioengineering↗

bioRxiv2026

The Live Concert of Brains: Performer-Audience Neural Coupling Links Ensemble Coordination to Shared Audience Integration

Collective social events often require coordinated action by one group to become shared experience in another, yet how this transformation is organized across multiple brains remains unclear. Live music provides a tractable model of this problem because ensemble coordination, performer-audience alignment, and shared audience integration unfold within the same event. Here we tested whether performer-audience neural coupling acts as a cross-role neural interface linking ensemble coordination to shared audience integration. We recorded brain activity from a nine-person live performance system, consisting of a fixed three-performer ensemble and four independent audience groups, using synchronized multi-device functional near-infrared spectroscopy hyperscanning across live trio performance sessions. Inter-brain neural coupling was analyzed across three relational layers: performer-performer (PP), performer-audience (PA), and audience-audience (AA) coupling. Behavioral ratings showed strong affective engagement and shared evaluative alignment. Neural coupling during live performance was not expressed as a diffuse increase across channel pairs, but was organized into task-sensitive relational components with interpretable PC-corr network modules. Crucially, path-based mediation analyses revealed that PA components statistically bridged PP coordination and AA coupling, yielding multiple complete and partial PP [->] PA [->] AA pathways. Brain-behavior analyses further suggested that mediation-related PA components were linked to shared performance evaluation and emotional alignment. These findings identify performer-audience coupling as a cross-role neural interface through which coordinated production becomes linked to shared collective reception. Significant StatementHow coordinated actions become shared experiences is a major problem in social neuroscience, yet most studies examine pairs of people. Using live music as a model of group interaction, we found that brain-to-brain alignment was organized across social roles rather than arising as a uniform response to the same event. Performer-audience alignment occupied a bridging position between coordination within the ensemble and integration within the audience. This identifies a systems-level architecture through which collective action may become linked to collective experience. The framework moves multi-brain research beyond dyads and offers a general approach for studying classrooms, public speaking, theater, rituals, and team events, where one group generates structured behavior that another group jointly receives and interprets.

neuroscience↗

bioRxiv2026

Adipose GPD2 Couples Glycolytic Signals to Epigenetic Control of Metabolic Homeostasis

The glycerol-3-phosphate shuttle (G3PS) is a classic reducing equivalent transferring system, yet its role in adipose metabolism remains poorly understood. Here, we identify mitochondrial glycerol-3-phosphate dehydrogenase (GPD2), the core enzyme of G3PS, as a critical orchestrator of adipose thermogenesis and systemic metabolic homeostasis. Adipocyte-specific GPD2 knockout mice exhibited impaired thermogenic capacity and energy expenditure, rendering them susceptible to obesity and metabolic dysfunction. Mechanistically, GPD2 deficiency elevated cytosolic NADH, which suppressed glycolysis and decreased the levels of key metabolites, such as acetyl-CoA, thereby diminishing H3K27ac at thermogenic gene loci and silencing these genes. NADH depletion with an NADH oxidase rescued both glycolysis and thermogenic gene expression. In support of this mechanism, we defined a previously undescribed enhancer of Ucp1 whose H3K27ac was tightly controlled by GPD2. Remarkably, replenishing the acetyl-CoA pool or directly restoring H3K27ac at the Ucp1 enhancer reversed UCP1 expression in GPD2-deficient adipocytes. Importantly, we find that human adipose GPD2 expression is inversely correlated with BMI, WHR, and HOMA-IR, underscoring its clinical relevance. Collectively, our findings establish GPD2 as an essential node in the metabolic-epigenetic axis that governs thermogenic activation and energy balance.

biochemistry↗

bioRxiv2026

Netrin-1 inhibition does not attenuate cancer-induced bone pain in three translational models

1.Cancer-induced bone pain (CIBP) occurs in a majority of patients when primary or metastatic cancer develops within the bone. This pain has a significant impact on quality of life, yet there are limited effective treatment options available. Nerve sprouting is a complex mechanism that has been implicated in CIBP. Netrin-1 is a neuronal guidance molecule that is produced by numerous cell types, including cancer cells. In this study we aimed to determine whether netrin-1 inhibition (with NP137 - a humanized IGg1 monoclonal antibody) could ameliorate nerve sprouting, and nociception by extension, in three models of CIBP - osteosarcoma, metastatic breast cancer, and metastatic prostate cancer. Sustained administration of NP137 failed to produce an anti-nociceptive effect in these models, but a delayed onset was observed in the osteosarcoma model. NP137 did not produce a disease-modifying effect, as micro-computed tomography did not reveal reduced bone destruction in the NP137-treated groups. Additionally, there was no nerve fibre density reduction in any of the groups at the late-stage of the disease, suggesting that nerve sprouting occurs in early- to mid-stage CIBP development. Investigation of NP137 exposure indicated that serum levels of NP137 were comparable between the sham and cancer groups. Our study indicates that netrin-1 may play a role in early-stage CIBP development, but inhibition of this mechanism does not produce robust anti-nociception.

pharmacology and toxicology↗

bioRxiv2026

HnRNPAB-targeted antisense oligonucleotides ameliorate tau pathology and cognitive deficits by modulating Alzheimers disease-associated alternative splicing

Aberrant alternative splicing alters multiple disease-associated splicing events, including MAPT exon 10 inclusion linked to tau pathology, and thereby impacts Alzheimers disease (AD) progression. Heterogeneous nuclear ribonucleoprotein AB (hnRNPAB) functions as a splicing regulator, yet its roles in AD remain poorly defined. Here, we identified AB332, the full-length isoform of hnRNPAB, as a novel repressor of MAPT exon 10 inclusion. AB332 binds a conserved AAUAU motif and recruits RBMX and RBMXL1 through its RRM and glycine-rich domains to assemble a complex. Beyond MAPT, AB332 modulates a network of splicing events in multiple AD-associated genes, including STAG2, ApoER2, MCL-1, PICALM, and zDHHC7. Importantly, the exon 7-skipping isoform AB285 lacks these activities. Transcriptomic analysis of post-mortem brain tissues from AD patients revealed reduced expression of hnRNPAB, while selective downregulation of AB332 was confirmed in the hippocampus of 3xTg AD mice. We performed a systematic antisense oligonucleotide-tiling screen targeting hnRNPAB exon 7 and its flanking intronic regions, identifying ASO30 that specifically upregulated AB332 expression. In 3xTg AD mice, ASO30 restored hippocampal AB332 levels, reduced pathological tau phosphorylation, and rescued cognitive deficits. These findings define a molecular mechanism by which AB332 regulates AD-associated splicing events, thereby providing a therapeutic strategy targeting hnRNPAB for AD. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/736008v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@621096org.highwire.dtl.DTLVardef@2f01b1org.highwire.dtl.DTLVardef@182e6forg.highwire.dtl.DTLVardef@190afd3_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Ginsenoside Ro ameliorates diabetic cardiomyopathy by maintaining ciliary homeostasis and enhancing antioxidation

ObjectiveTo investigate and clarify the role of Ginsenoside Ro (GRo) in diabetic cardiomyopathy (DiaCM) and to elucidate the molecular mechanism by which GRo ameliorates DiaCM. Methods[circled1] The construct of type 2 diabetic mouse model. The bought C57BL/6 male mice were housed in a specific pathogen-free (SPF) animal facility and randomly divided into control, STZ (model), STZ + GRo, and control+GRo groups. The STZ (model) and STZ + GRo groups were fed a high-fat and high-glucose diet combined with intraperitoneal injection of streptozotocin (STZ). The control and control + GRo groups were fed a normal diet, while the control + GRo and STZ + GRo groups were treated with GRo via oral gavage. Then, all groups were evaluated for cardiac function and structure by small animal echocardiography and histological staining including hematoxylin and eosin (HE) and Massons trichrome staining to screen and confirm diabetic cardiomyopathy in mice. Finally, immunofluorescence staining of cilia in mouse heart tissue was performed to determine whether GRo inhibits abnormal ciliary growth. [circled2] The construct of cell models. First, the CCK-8 (Cell Counting Kit-8) assay was used to separately evaluate the cytotoxicity of GRo and the combination of TGF-{beta}1 and PA in myocardial fibroblasts and cardiomyocytes. Subsequently, mouse myocardial fibroblast lines (MCFs) were treated with transforming growth factor-beta 1 (TGF-{beta}1), and H9c2 cardiomyocytes were treated with palmitic acid (PA). Both cell types then received the GRo treatment. [circled3] Molecular and cellular testing. Firstly, we measured serum levels of cardiac injury markers (CK-MB, MYO, and TNNI3), glutathione (GSH), and malondialdehyde (MDA). Secondly, we examined the expression of myocardial fibrosis-related genes (Col1a1, etc.), myocardial hypertrophy markers (Nppa, etc.), cilia-specific genes (Pkd1, etc.), and oxidative stress-related genes (Nrf2, etc.) in both animal and cell samples by Western blotting and RT-qPCR. Finally, we used immunofluorescence staining of myocardial fibroblasts to detect cilia length and phalloidin staining of cardiomyocytes to measure their cross-sectional area. [circled4] The correlation mechanism. Firstly, the cilia-specific inhibitory drug HIP-4 was used to disrupt cilia homeostasis by inhibiting cilia growth. Secondly, small activating RNA (saRNA) was used to upregulate the Pkd1 gene to verify whether GRo exerts its anti-fibrotic effects through the inhibition of PC1. Results[circled1] Animal level. A diabetic cardiomyopathy mouse model was successfully established by combining STZ injection with a high-fat and high-glucose diet, and treatment with GRo significantly ameliorated the associated symptoms. [circled2] Cellular level. We successfully established a myocardial fibrosis model by treating myocardial fibroblasts with TGF-{beta}1, and a myocardial hypertrophy model by treating cardiomyocytes with PA. Immunofluorescence staining demonstrated that GRo significantly decreased cilia length in the fibrosis model, while phalloidin staining showed that GRo significantly attenuated the increase in cardiomyocyte cross-sectional area. [circled3] Molecular level. Compared with the model group, GRo treatment significantly reduced serum levels of cardiac injury markers (CK-MB, MYO and TNNI3), glutathione (GSH) and malondialdehyde (MDA). Western blotting and RT-qPCR analyses of both animal and cell samples revealed that GRo markedly alleviated indicators of myocardial fibrosis and hypertrophy, while also suppressing cilia-specific genes and oxidative stress-related genes. Overall, GRo significantly ameliorated the markers associated with myocardial fibrosis and hypertrophy, and inhibited cilia-specific protein expression as well as oxidative stress parameters. [circled4] The correlation mechanism. The cilia-specific drug hedgehog pathway inhibitor 4 (HPI-4) was used to revealed that cilia homeostasis is closely linked to myocardial fibrosis and shortened cilia inhibit the fibrosis progression. Furthermore, upregulation of the Pkd1 gene by small activating RNA demonstrated that PC1 overexpression abrogates the therapeutic effect of GRo. Finally, GRo can alleviate DiaCM.

Molecular Biology↗

bioRxiv2026

Ergothioneine, alone or combined with vitamin K2, vitamin D3 and magnesium L-threonate, attenuates bone turnover, inflammatory and oxidative disturbances in ovariectomized mice

PurposeEstrogen deficiency drives bone loss through a complex interplay of endocrine, oxidative, inflammatory, and bone-remodeling disturbances. Ergothioneine (EGT) is a diet-derived thiol/thione antioxidant, yet its effects on the estrogen-deficient skeleton remain unknown. This study evaluated whether EGT-alone or combined with vitamin K2, vitamin D3, and magnesium L-threonate-attenuates the skeletal and systemic consequences of ovariectomy (OVX) in mice. MethodsForty-eight female C57BL/6J mice underwent either sham surgery or OVX. For 12 weeks, the mice received a daily oral gavage of one of the following: vehicle, alendronate (1.53 mg/kg), EGT (30 mg/kg/day), EGT with vitamin K2 (40 {micro}g/kg/day) and vitamin D3 (500 IU/kg/day), or EGT with vitamin K2, magnesium L-threonate (350 mg/kg/day), and vitamin D3 (n = 5-6 per group). Outcomes evaluated included the uterine index, tibial micro-computed tomography (micro-CT), distal-femoral histology, serum bone turnover markers (CTX-I, PINP, osteocalcin), sex hormones, TNF-, IL-6, SOD, and MDA. ResultsOVX significantly lowered the uterine index and induced tibial trabecular deterioration. This was accompanied by increased CTX-I, TNF-, IL-6, and MDA, alongside decreased PINP, osteocalcin, and SOD (all P < 0.01 vs. sham). Alendronate successfully restored tibial micro-CT bone-volume fraction (BV/TV) and trabecular number (P < 0.01 vs. OVX). While the EGT-based regimens did not significantly restore tibial micro-CT BV/TV, trabecular thickness, or trabecular number (all P > 0.05 vs. OVX), they significantly increased the trabecular area in distal-femoral histology (14.2-15.0% across regimens vs. 7.6% in OVX; P < 0.05). Furthermore, EGT treatments lowered CTX-I, TNF-, IL-6, and MDA, increased SOD, and partially restored PINP and osteocalcin (P < 0.05-0.01 vs. OVX). Apparent increases in serum estradiol were assay-dependent and are considered exploratory. ConclusionEGT-based nutritional regimens improved the systemic oxidative, inflammatory, and bone-turnover environments associated with estrogen-deficient bone loss and successfully preserved the distal-femoral trabecular area. However, tibial three-dimensional microarchitecture was not restored on micro-CT. Given that histological and micro-CT endpoints were evaluated at different skeletal sites, structural interpretations should be made with caution. These findings support the further evaluation of EGT as a dietary adjunct, warranting subsequent mechanistic and dose-optimization studies.

pharmacology and toxicology↗

bioRxiv2026

Beyond statistical significance: ranking transcription factor binding motifs by effect size

Chromatin immunoprecipitation-sequencing (ChIP-seq) has wide use in identifying transcription factor binding sites. DNA sequence motifs specific to a targeted transcription factor occur more frequently near ChIP-seq peak centres. The most common approach to quantifying relative motif enrichment ranks motifs by p-value. Because sample sizes can vary substantially across examined motifs, p-value magnitudes may reflect this heterogeneity rather than the biological effect of interest. As alternatives, we considered four ranking methods based on effect sizes: (a) a modified Cliffs delta, (b) the lower bound of a frequentist asymptotic confidence interval, (c) the lower bound of a frequentist finite-sample confidence interval, and (d) the lower bound of a Bayesian credible region. Through extensive simulations, the four alternatives better recovered the simulated central-enrichment ordering under heterogeneous sample sizes. Using published ChIP-seq data for GATA3, the effect size methods ranked the known targeted motif highest, even compared to highly similar motifs for other GATA family members, while p-value ranking did not. In a separate SRF application, all four alternative methods also consistently ranked the known motif highest. We recommend the asymptotic confidence interval lower bound for its simplicity, ease of implementation, and intuitive interpretation. The software is freely available (https://github.com/ScottMastro/motif-ranking).

bioinformatics↗

bioRxiv2026

Flow-Induced Yap/Taz Signaling Balances Endothelial and Hematopoietic Stem Cell Fates

Mechanical forces from blood flow are essential for production of hematopoietic stem and progenitor cells (HSPCs) during embryogenesis, but the molecular mechanisms by which hemodynamic cues are sensed and orchestrate endothelial-to-hematopoietic (EHT) transition remain incompletely defined. We previously identified YAP mechanotransduction as a key integrator of physical forces with EHT. Here we show that hemodynamic forces can activate YAP signaling via the mechanoresponsive ion channel Piezo1 in human iPSC-derived hemogenic endothelium (HE) and zebrafish embryos. Investigation of the Piezo1/YAP axis revealed shared and unique roles of YAP and its paralogue TAZ in EHT. Mechanistically, we find a requirement for the Tead DNA-binding co-factor in YAP/TAZ-dependent control of HSPC number, and note that TAZ uniquely augments transcriptional output of the hematopoietic master regulator Runx1 via direct protein-protein interactions. By comprehensive scRNA-sequencing of YAP/TAZ gain-of-function (GOF) and yap-deficient cells from zebrafish, we reveal that YAP/TAZ promotes HSC production by positively regulating gene programs for hematopoietic self-renewal, cell cycle, and glycolysis-to-oxidative phosphorylation switching, while preventing reversion to endothelial identity. Importantly, comparison of GOF transcriptomes and functional analyses suggest decoupling of metabolic/proliferative and endothelial gene regulatory modules between YAP and TAZ: while either can functionally compensate for loss of the other in EHT, indiscriminate overactivation of TAZ enhances an endothelial program over pro-hematopoietic fate, ultimately blunting progression of HSPC production. Given that hemodynamic cues are integrated simultaneously by arterial and HE cells in embryonic vessels in which EHT occurs, these findings have strong implications for strategies designed to introduce biomechanical cues to in vitro hematopoietic differentiation systems to drive HSC production.

Cell Biology↗

bioRxiv2026

Physics-driven self-supervised learning for quantitative high-fidelity structured illumination microscopy

Structured illumination microscopy (SIM) enables rapid, long-term super-resolution (SR) imaging of live-cell dynamics. However, although current state-of-the-art (SOTA) SIM reconstruction methods achieve high-fidelity structural SR, they consistently lack reliable intensity quantification, restricting their use in quantitative biology. Here, we develop qHiFi-SIM, a physics-driven self-supervised learning framework for quantitative high-fidelity SR-SIM imaging. By leveraging the wide-field image as a physical intensity reference, our approach enables self-supervised training without reliance on SR data with ground-truth intensity. qHiFi-SIM achieves high structural fidelity (structural similarity, SSIM > 0.95) with a twofold resolution enhancement, while maintaining excellent intensity linearity (coefficient of determination, R{superscript 2} > 0.99). It also exhibits strong transferability across diverse SIM setups and typical samples, and is compatible with SOTA SIM algorithms, enabling direct quantitative correction of their intensity deviations without retraining. We demonstrate the unique advantages of qHiFi-SIM for live-cell quantitative visualization of mitochondrial structure, intensity, and membrane potential dynamics, as well as for high-fidelity SIM-FRET (Forster resonance energy transfer) functional imaging. We anticipate that qHiFi-SIM will serve as a practical tool for SR structural visualization and quantitative functional imaging in live cells.

Cell Biology↗

bioRxiv2026

Phylogenomic description of three novel species of the Microbulbifer genus, phylum Pseudomonadota, isolated from marine sponges and corals

AO_SCPLOWBSTRACTC_SCPLOWUnderstudied bacterial genera present a dynamic phylogenetic landscape and opportunities for discovering new taxa as more strains are isolated and genomic data is added. Here, through phylogenomic analysis, we describe three novel species of the globally distributed cosmopolitan marine bacterial genus Microbulbifer. This genus is ubiquitous in saltwater microbiomes and is a validated source of biodegradation enzymes as well as high value small molecule natural products. Average nucleotide identity (ANI) to the closest known species, Microbulbifer variabilis ATCC 700307T, was less than 88.4% for all three novel species. Isolates of the three novel species, designated as PAAF003T (T = type strain), ZKSA006T, and SSSA003T were imaged to reveal their phormological characteristics. Based on phylogenetic data, strains PAAF003T, ZKSA006T, and SSSA003T represent three new species of the genus Microbulbifer, for which the names Microbulbifer maximicatervae sp. nov., Microbulbifer regidiadema sp. nov., and Microbulbifer mixtoriginis sp. nov. are proposed, respectively, under the SeqCode. We also reconstructed a robust phylogeny of available Microbulbifer genomes, which should faciliatate future isolation and strain description studies.

microbiology↗

bioRxiv2026

Anthocyanin-associated cellular programs underlying terroir variation in Cabernet Sauvignon grape berry revealed by SEED-based deconvolution

Plant tissues consist of diverse cell populations that collectively contribute to development, metabolism, environmental responses, and phenotype formation. Although single-cell and single-nucleus RNA sequencing have greatly advanced the study of plant cellular heterogeneity, their application to large sample cohorts remains limited by cost, technical complexity, tissue dissociation constraints, and throughput. In contrast, bulk RNA-seq datasets have accumulated extensively across plant species, tissues, developmental stages, and environmental conditions, yet the celltype-level information embedded in these datasets remains difficult to resolve because plant-oriented deconvolution frameworks are still lacking. Existing deconvolution methods have largely been developed in mammalian systems and have not been systematically optimized for plant transcriptomic features, leaving their applicability under plant-specific constraints unclear. Here, we present SEED, an adaptive deconvolution framework optimized for plant transcriptomic data. SEED integrates candidate reference-template construction with seven deconvolution strategies and automatically identifies an optimal combination for a given dataset. In grapevine simulated benchmarking, SEED showed its clearest advantage under low-replication conditions and remained broadly competitive, rather than uniformly dominant, when larger pseudo-bulk sample sizes were evaluated. SEED further performed robustly in public Arabidopsis thaliana and Nicotiana tabacum datasets. Finally, we applied SEED to bulk RNA-seq data generated in this study from Vitis vinifera cv. Cabernet Sauvignon berries collected from Yinchuan and Yantai, identifying terroir-associated cell subtypes and coordinated celltype interaction patterns. Together, these results establish SEED as a practical framework for plant transcriptome deconvolution and provide a new tool for dissecting cellular heterogeneity associated with environmental adaptation and phenotype formation in plants.

bioinformatics↗

bioRxiv2026

Mono-ADP-ribosylation-driven immunosuppression and cross-resistance to therapy through cancer cell intrinsic and extrinsic mechanisms

Mono-ADP-ribosylation (MARylation) is emerging as an important regulator of anti-cancer immunity and immunosuppressive tumor microenvironment (TME). Our previous studies showed that PARP11, one of several enzymes that facilitate MARylation, regulates the activities of intratumoral cytotoxic T lymphocytes (CTLs) and regulatory T cells (Tregs). Here, we demonstrate that stimuli such as adenosine, epinephrine, or glucagon-like peptide-1 (GLP1) induced PARP11 in cancer cells. Upregulation of PARP11 in cancer cells led to PARP11-mediated MARylation, ubiquitination, and accelerated degradation of MHC-I through the autophagy-lysosomal pathway. Induction of PARP11 protected cancer cells from killing by specific CTLs and stimulated tumor growth and progression. Genetic ablation of PARP11 attenuated MHC-I MARylation, ubiquitination, and interaction with autophagy receptors. Pharmacologic inhibition of PARP11 in pancreatic ductal adenocarcinoma (PDAC) cells restored their MHC-I levels, sensitized them to killing by CTLs, inhibited tumor growth, and impeded their initial resistance to chemotherapy and their acquired resistance to targeted therapy with RAS inhibitors. Moreover, inhibition of PARP11 prevented hyperprogressive disease in a mouse melanoma model treated with immune checkpoint inhibitors (ICBs), suggesting that PARP11 is a major therapeutically actionable driver of immunosuppression in tumors. SYNOPSISInduction of PARP11 in the tumor microenvironment mediates immunosuppression. This study reports that PARP11-driven MARylation and ubiquitination of MHC-I in cancer cells drives immune evasion, tumor growth and resistance to therapies.

cancer biology↗

bioRxiv2026

Biosynthetic allene and alkyne formation by enzymatic prenyl demethylation

Allenes and alkynes are versatile functional groups in total synthesis, medicinal chemistry, and bioorthogonal conjugation. The biosynthetic logic of how Nature installs allene or alkyne in natural products, especially that of allenes, is not well understood. Here we uncovered allenes and alkynes can be formed enzymatically through oxidative C(sp2)-demethylation of the common five-carbon prenyl group. Two fungal cytochrome P450 monooxygenases, PpnB and NseB, from the penipratynolene and sinuxylamide biosynthetic pathways, respectively, were shown to catalyze oxidative removal of a C(sp2)-methyl group in O-prenyl-L-tyrosine to afford O-homoallenyl-L-tyrosine and O-but-2-ynyl-L-tyrosine, respectively. Combining density functional theory calculations, heterologous expression, biotransformation and enzymatic assays with isotopically labeled substrates, a mechanism involving selective C-C bond cleavage followed by product-determining hydrogen atom abstraction is presented. An additional P450 enzyme from the penipratynolene pathway, PpnD, acts as an oxidative isomerase that converts the four-carbon terminal allene into a terminal alkyne. This unprecedented enzymatic editing strategy to install allene and alkyne expands the catalytic repertoire of P450 enzymes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/727785v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@54a57dorg.highwire.dtl.DTLVardef@13cb5d0org.highwire.dtl.DTLVardef@c4a2b7org.highwire.dtl.DTLVardef@196b357_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗