Biology subjects

Zhang, R.

Publications and source records attributed to Zhang, R..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex

The dorsolateral prefrontal cortex (dlPFC) is central to cognitive dysfunction in schizophrenia (SCZ), yet how molecular changes are organized across cortex remains unclear. Here, we applied complementary spatial transcriptomic approaches spanning laminar domains, microenvironments, and cell types in postmortem human dlPFC. At the laminar level, SCZ-associated transcriptional changes were strongest in glia-enriched domains (layer 1/meninges and white matter), including down-regulation of microglia-associated genes, whereas genetic risk localized to neuronal-rich gray matter. We next analyzed SCZ-linked microenvironments including neuropil, neuronal, perineuronal net, and vascular compartments. Within these, neuronal and synaptic transcriptional changes were most prominent in neuropil, showing down-regulation of activity-dependent synaptic genes and inhibitory neuron markers. At the cellular level, these signals reflected intrinsic alterations localized to cell types. Across analyses, patterns converged on altered BDNF-TrkB signaling and inhibitory circuit dysfunction. Together, our findings highlight spatial scale as a key determinant in resolving neuronal and non-neuronal aspects of SCZ-associated biology.

neuroscience↗

bioRxiv2026

TRIM32-UBQLN2-p62 axis promotes TDP-43 inclusion formation and amyloid aggregation through shuttle condensates

Aberrant protein aggregation is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), which share overlapping genetic and pathological features. Similar aggregates are increasingly recognized in Alzheimers disease (AD) and limbic-predominant age-related TDP-43 encephalopathy (LATE). However, it remains unclear whether a shared molecular pathway drives this pathological aggregation. Here, we report that the E3 ubiquitin ligase TRIM32, together with the shuttle factor UBQLN2 and the autophagy adaptor p62/SQSTM1, form condensates that depend on E3 ligase activity and a network of intermolecular interactions. These condensates act as scaffolds that capture UBQLN2 client proteins, including TDP-43 and ANXA11, and modulate their mobility. A unique hydrophobic loop within TRIM32s substrate-binding domain mimics low-complexity motifs in ANXA11 and TDP-43, enabling selective retention via competitive binding mediated by UBQLN2 STI1 domain. Moreover, TRIM32 condensates promote amyloid aggregation of TDP-43, an effect that is exacerbated by pathogenic UBQLN2 mutation. In brains from individuals with diverse neurodegenerative diseases, TRIM32 co-localizes with pathological phospho-TDP-43 (pTDP-43) inclusions, supporting a model in which TRIM32-driven condensates function as selective proteostasis sorting compartments that broadly contribute to TDP-43 proteinopathy.

neuroscience↗

bioRxiv2026

The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

genomics↗

bioRxiv2026

Lipid monounsaturation confers cold tolerance and improves tissue viability during hypothermic storage

The rapid loss of tissue viability during hypothermic storage frequently results in organ failure and high discard rates in transplantation. In contrast, ectothermic animals can tolerate prolonged exposure to low temperatures in their natural environments. Elucidating the mechanisms underlying this cold tolerance may therefore inform improved strategies for tissue preservation. Here, we investigate proteomic and metabolomic responses to cold exposure in the livers of two frog species from distinct habitats: the cold-sensitive African clawed frog (Xenopus laevis) and the cold-tolerant Northeastern Asian brown frog (Rana dybowskii). Cold exposure induced lipid mobilization in X. laevis, whereas it promoted phospholipid mono-unsaturation in R. dybowskii. Notably, treatment with monounsaturated fatty acids (MUFAs) or overexpression of stearoyl-CoA desaturase (SCD) reduced cell death during cold storage. Moreover, MUFA infusion significantly improved cell viability in mouse liver tissue under hypothermic conditions. Together, these findings suggest that lipid mono-unsaturation, an adaptive feature of cold-tolerant frogs, can be leveraged to enhance tissue preservation during cold storage.

biochemistry↗

bioRxiv2026

3D Cell-Matrix Mechanical Interaction Models for Cancer Invasion and Drug Evaluation

Cancer cells breach the extracellular matrix (ECM) using both protease-driven degradation and force-driven physical remodeling, yet most anti-metastatic drug screens still rely on biochemical assays that overlook cell-matrix mechanical reciprocity. Here, we present a fully synthetic 3D invasion platform based on cellular force-responsive polyisocyanide (PIC) hydrogels that isolates biophysical invasion mechanisms. Cell-generated forces align and densify the PIC fibrous network, reproducing hallmark matrix remodeling seen in the tumor microenvironment. A constitutive model, parameterized by the critical stress for strain stiffening effect, links matrix nonlinear elasticity to pericellular stiffening, long-range mechanotransmission, and intercellular coupling. Using this system, we show that breast cancer cells invade by pulling and pushing the network even when matrix metalloproteinases are inhibited, revealing a physical bypass of protease blockade. Accordingly, broad-spectrum metalloproteinase inhibitors that suppress invasion in Matrigel fail to inhibit invasion here, exposing a limitation of current drug-evaluation pipelines. In co-culture, cancer-associated fibroblasts markedly accelerate invasion by generating aligned fiber tracks through higher contractility, implicating CAF-driven mechanical remodeling as a key route for breaching barriers during metastasis. The platform is thermoresponsive, compatible with standard Transwell formats, enables direct imaging of fiber architecture and invasion fronts, and decouples biophysical from biochemical cues for mechanism-aware, animal-free assessment of anti-metastatic therapies.

cancer biology↗

bioRxiv2026

Reciprocal adipose-heart regulation of NRAC

Fatty acids (FAs) are a major energy substrate, and their storage and utilization must be balanced across tissues to maintain metabolic homeostasis. White adipose tissue (WAT) and the heart play opposing roles in FA metabolism, with WAT serving as the primary site of FA storage and the heart relying heavily on FAs as an energy source. However, the molecular factors regulating FA handling between the two tissues remain incompletely understood. We previously identified NRAC as a nutritionally regulated adipose- and cardiac-enriched protein; however, how its expression is regulated between these tissues across nutritional states, and how this relates to systemic FA homeostasis, remains unclear. Here, we integrate analyses of human transcriptomic datasets with nutritional and genetic perturbations in mice to examine the association between NRAC and FA metabolism. Human single-cell transcriptomic data from GTEx show enrichment of NRAC expression in adipocytes and cardiomyocytes, and analysis of subcutaneous adipose tissue from the UK Twins cohort reveals strong associations between NRAC expression and the abundance of multiple adipose lipid species. In mice, NRAC expression in WAT and heart was reciprocally regulated by fasting and refeeding and showed opposing associations with circulating free fatty acid (FFA) levels; moreover, whole-body deletion of NRAC elevated circulating FFA. Together, these findings support a role for NRAC in nutritionally responsive inter-organ regulation of FA between WAT and the heart, with implications for systemic lipid homeostasis.

physiology↗

bioRxiv2026

Leptin Receptor+ cells create a perisinusoidal niche for thrombopoiesis in the bone marrow by synthesizing CXCL14

Leptin Receptor-expressing (LepR+) stromal cells in the bone marrow are a critical source of growth factors for the maintenance of hematopoietic stem cells (HSCs) and most restricted hematopoietic progenitors. An important unresolved question is whether they also regulate terminal differentiation in some hematopoietic cells. We found that LepR+ cells promote thrombopoiesis by synthesizing the chemokine CXCL14, which is expressed in the bone marrow by a subset of LepR+ cells. Cxcl14-expressing LepR+ cells extend fine processes that wrap around perisinusoidal megakaryocytes. Deletion of Cxcl14 from LepR+ cells did not significantly alter HSC function or most aspects of bone marrow hematopoiesis, including megakaryocyte generation; however, it significantly reduced the numbers of proplatelet-forming megakaryocytes in the bone marrow and platelets in the blood. CXCL14 promoted platelet formation by remodeling lipid metabolism in megakaryocytes, increasing fatty acid transporter expression and enabling megakaryocytes to take up more polyunsaturated fatty acids from circulation. A high fat diet rescued the formation of proplatelet-forming megakaryocytes and platelets in Lepr-cre; Cxcl14 fl/fl mice. CXCL14 protein was sufficient to promote platelet formation by megakaryocytes in vitro and in vivo. LepR+ cells thus create a perisinusoidal niche for thrombopoiesis by producing CXCL14, which regulates lipid metabolism and terminal differentiation in megakaryocytes. Key pointsO_LILeptin Receptor+ stromal cells regulate terminal differentiation in megakaryocytes in addition to maintaining stem and progenitor cells C_LIO_LICXCL14 from Leptin Receptor+ cells promotes the formation of platelets by remodeling lipid metabolism in megakaryocytes in the bone marrow C_LI

cell biology↗

bioRxiv2026

Getting over ANOVA: Estimation graphics for multi-group comparisons

Data analysis in experimental science mainly relies on null-hypothesis significance testing, despite its well-known limitations. A powerful alternative is estimation statistics, which focuses on effect-size quantification. However, current estimation tools struggle with the complex, multi-group comparisons common in biological research. Here we introduce DABEST 2.0, an estimation framework for complex experimental designs, including shared-control, repeated-measures, two-way factorial experiments, and meta-analysis of replicates.

bioinformatics↗

bioRxiv2026

PC-index, a composite metric for gene expression in single-cell RNA-seq

Single-cell RNA sequencing enables analysis of gene expression heterogeneity, but summarizing gene expression across large cell populations remains challenging. Gene expression is commonly described using average expression (counts per 10,000 transcripts, CP10K) and cellular prevalence (the fraction of cells expressing a gene), which can be difficult to interpret jointly. Here, we introduce the PC-index, a single, intuitive metric that integrates expression magnitude and prevalence. The PC-index is defined as the largest value X such that at least X% of cells express a gene at [≥]X/10 CP10K. Using human adipocytes from GTEx single-nucleus RNA-seq as an illustrative example, we show that adipocyte genes exhibit distinct PC-index profiles. For example, adiponectin has a PC-index of 21, indicating that at least 21% of adipocytes express it at [≥]2.1 CP10K. Conceptually, the PC-index reflects both percentage and CP10K, yielding a stable and interpretable single-number summary of gene expression behavior in single-cell data.

genomics↗

bioRxiv2026

CTLA-4 inhibitors drive colitis through metabolic reprogramming-mediated Treg/Th17 imbalance

Immune checkpoint inhibitors (ICIs), especially CTLA-4 inhibitors (CTLA-4), exhibit a high incidence of colitis as an immune-related adverse event (irAE) during cancer treatment, severely limiting patient benefit. Clinically, both treatment interruption and existing intervention drugs for ICI-mediated colitis may compromise antitumor efficacy. However, there is inadequate research on the pathogenesis of ICI-mediated colitis, with findings often conflicting. Here, we first established multiple clinically relevant animal models, including an immuno-humanized ICI-mediated colitis model. Through time-series transcriptomics, we discovered that CTLA-4-induced colonic toxicity exhibits characteristics ranging from early metabolic reprogramming represented by glycolysis to later immune disorders represented by Th17 responses. By targeting colonic CTLA-4+ T cells, CTLA-4 blocked CD80/CD86-CTLA-4 interaction, thereby activating the PI3K-AKT-mTOR pathway. Subsequently, mTOR mediated metabolic reprogramming in T cells, shifting them from Treg-biased oxidative phosphorylation to Th17-biased glycolysis. The colonic toxicity of CTLA-4 has also been demonstrated to depend on the PI3K-AKT-mTOR pathway, glycolysis, and Th17 responses. Notably, metformin significantly relieved ICI-mediated colitis by inhibiting mTOR without impeding antitumor efficacy. Collectively, these findings highlighted the metabolic-immune axis in the colonic toxicity of ICI and provided a clinically superior intervention strategy.

pharmacology and toxicology↗

bioRxiv2026

Locus coeruleus noradrenaline elicits response profiles distinct from natural arousal in hippocampal neurons and astrocytes

The locus coeruleus (LC)-noradrenaline (NA) system is a central component of the brains response to arousal and stress. Yet how LC activity contributes to the cellular response profiles observed during natural arousal remains unclear. Here, we directly compared natural arousal with selective LC activation in mouse CA1, using physiologically titrated optogenetics, fiber photometry of NA and calcium signals, chronic two-photon imaging, and behavioral monitoring. While natural arousal robustly activated astrocytes, pyramidal cells, and interneurons, direct LC stimulation revealed a striking divergence in cellular response polarity and sensitivity. At levels of LC activation that correspond to arousal and moderate stress, we observed strong and reliable calcium responses in astrocytes, whereas pyramidal neurons and interneurons remained largely unaffected. Only at high-intensity LC stimulation did neurons exhibit a response, characterized by broad population-level inhibition of both pyramidal cells and interneurons, alongside the transient activation of an interneuron subpopulation that occupied distinct laminar positions in CA1. Thus, LC-driven NA release produces cell-specific effects in hippocampal CA1 that are distinct from and, at the population level for neurons even opposite to, cellular dynamics during natural arousal. Together, our results reveal a divergence in how astrocytes and neurons respond to LC-driven NA release and suggest that noradrenergic effects in the hippocampus at moderate levels of arousal and stress are predominantly mediated by astrocytes.

neuroscience↗

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

Haemagglutinin 162-164 deletions enhance influenza B/Victoria virus fitness and virulence in vivo

Influenza B viruses cause substantial respiratory disease and seasonal outbreaks. Despite decades of circulation in humans, only the B/Victoria lineage persisted after the COVID-19 pandemic. Continual evolution has generated hemagglutinin deletion variants at residues 162-164 that drive successive epidemics, yet their functional consequences remain poorly understood. Using integrated phylodynamics and reverse genetics, we show that Clade V1A.1 viruses carrying a two-amino acid deletion exhibit enhanced replication and increased virulence compared with ancestral viruses lacking deletions. The recently prevailing Clade V1A.3, which harbors a three-amino acid deletion together with the K136E substitution, has completely displaced V1A.1 and causes more severe disease in mice. Both clades bound efficiently to alpha 2-3 and 2-6 sialylated glycans and exhibited broad tolerance to acidic pH and elevated temperatures. These findings reveal that specific combinations of HA deletions and substitutions confer pronounced fitness advantages to emerging variants, driving global selective sweeps, evolutionary success and long-term persistence of B/Victoria lineage, and posing challenges for vaccine efficacy and influenza control.

microbiology↗

bioRxiv2025

MLL3 and MLL4 sustain hematopoietic stem cell multipotency by opposing a B-cell default state

Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) are sustained by networks of transcription factors and epigenetic regulators that prime lineage-specific programs yet maintain multipotency. Two epigenetic regulators, MLL3 and MLL4, play important but opposing roles in maintaining this balance. MLL3 promotes HSC differentiation, whereas MLL4 opposes differentiation. These opposing functions are essential for both normal homeostasis and leukemia suppression, yet it is not clear how MLL3 and MLL4 regulate HSC and MPP gene expression to control HSC/MPP fate decisions. To resolve these mechanisms, we performed an extensive series of single cell genomic studies after conditionally deleting Mll3, Mll4 or both genes together. Mll3 deletion had only limited effects on HSC/MPP enhancer networks at steady state, whereas Mll4 deletion led to precocious activation of myeloid enhancers. Surprisingly, compound Mll3/4 deletion eliminated all myeloid, erythroid and megakaryocytic potential within the hematopoietic hierarchy and caused all progenitors to rapidly default to a B-cell-like identity. These changes were accompanied by widespread inactivation of HSC/MPP enhancers and superenhancers, and ectopic activation of B-cell superenhancers. Disabling MLL3/4 histone methyltransferase activity did not recapitulate the pervasive changes in cell identity that were observed when MLL3 and MLL4 were fully inactivated, indicating that MLL3 and MLL4 activate HSC/MPP enhancers independently from their enzymatic activities. Our findings show that HSC/MPP multipotency requires sustained tension between MLL3/4-dependent enhancers that maintain myeloid, erythroid and megakaryocyte potential, and MLL3/4-independent enhancers that prime B-cell identity. MLL3 and MLL4 therefore serve as critical linchpins of multilineage hematopoiesis. KEY POINTSO_LIMLL3 and MLL4 act redundantly in HSCs to sustain transcription factor and enhancer networks that support multipotency C_LIO_LISimultaneous loss of MLL3 and MLL4 drives hematopoietic progenitors into a uniform B-cell-like default state C_LI

cell biology↗

bioRxiv2025

DIME: Data-driven Importance MEtric Guides Localization of the Seizure Onset Zone from Intracranial EEG Data

Epilepsy affects over 50 million individuals, many of whom require surgical treatment that is dependent on accurate localization of the seizure onset zone (SOZ). Conventional SOZ biomarkers are based on strictly defined intracranial electroen-cephalography (iEEG) phenomena and cannot benefit from increased datasets. The scarcity of SOZ-labeled iEEG data impedes biomarker development. We introduce the Data-driven Importance MEtric (DIME) to guide SOZ localization in an interpretable pipeline that improves with ictal-labeled iEEG data. We apply DIME to an open-source dataset (n=21; 13 successful; 8 failed) for SOZ localization and surgical outcome prediction. The highest DIME-ranked electrode belonged to the clinically annotated SOZ for 69.2% of patients with successful surgery (p < 0.001). DIME scores were significantly higher in SOZ electrodes than nonSOZ electrodes in both successful and failed surgeries (p < 0.001), though the DIME distribution for successful cases differed from failed cases (p = 0.002). DIME predicted surgical outcome with 92.3% recall and 66.7% accuracy.

neuroscience↗

bioRxiv2025

Excitatory nicotinic signaling drives action potential bursting in dopaminergic axons

Nicotinic acetylcholine receptors (nAChRs) facilitate striatal dopamine transmission but also suppress dopamine release during high-frequency stimulation, suggesting they act as as low pass filters of dopamine release. Because axonal excitability is key a determinant of transmission, we combined axonal recordings and calcium imaging to define the physiological conditions under which nAChRs bidirectionally control dopaminergic axons. Activation of cholinergic interneuron (CINs) recruited nAChRs to enhance dopaminergic axon signals under moderate activation but suppressed signals after strong high-frequency stimulation. Axonal recordings revealed that single-pulse striatal stimulation triggered a rapid ([~]125 Hz) burst of 2-3 nAChR-driven spikes in dopaminergic axons followed by a brief refractory period that inhibited further axon spiking. In sum, we show that nAChRs mainly enhance local excitability of striatal dopaminergic axons but also trigger axonal bursting that suppresses axonal excitability. This mechanism expands the computational power of dopaminergic axons and explains the apparent nAChR-mediated low-pass filtering of dopamine release.

neuroscience↗

bioRxiv2025

Temporal single-cell profiling uncovers age-associated delays in immune resolution to respiratory viral infection

Aging is a major risk factor for increased morbidity and mortality following acute respiratory virus infections. To elucidate the immune determinants underlying viral pathogenesis and delayed lung repair in the aged lung, a comprehensive time-course study was conducted. Single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry were utilized to compare lungs from young and aged mice infected with influenza A virus (IAV). Aged hosts displayed diminished alveolar macrophage (AM) and dendritic cell (DC) but elevated monocyte-derived macrophage (MoM) and interstitial macrophage (IM) presence following infection. Additionally, enhanced accumulation of adaptive immune cells, including CD4+ tissue-resident helper (TRH) cells, CD8+ tissue-resident memory (TRM) cells, and a B cell subset resembling age-associated B cells, was observed in the memory phase. Pathway analysis revealed that elevated type I and II interferon (IFN/{gamma}) signaling, especially in MoM/IM subsets, distinguished the aged hosts from the young. Inhibition of IFN/{gamma} signaling after viral clearance improved long-term respiratory outcomes and reduced both IM and TRH populations in aged mice. These findings highlight the pivotal role of IFN/{gamma} signaling, likely within MoM/IM subsets, in driving the exuberant persistence of adaptive immune cells and chronic immunopathology in the aged lung following acute viral infection.

immunology↗