Biology subjects

Chen, Q.

Publications and source records attributed to Chen, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Multidimensional variation and population stratification across 8000 complete human centromeres

Human centromeres are indispensable for the faithful segregation of chromosomes during cell division, yet their highly repetitive nature has historically precluded comprehensive characterization, leaving fundamental questions about their sequence diversity, evolution trajectories and function dynamics unresolved. Here, we generated 6,312 complete human centromere sequences from 320 phased genome assemblies in Asian Pan-Genome project phase 1. By integrating the assemblies from the Human Pangenome Reference Consortium (HPRC) and Human Genome Structural Variation Consortium (HGSVC), we constructed a multidimensional genetic variation map encompassing over 8,000 gapless centromeres. Centromeric satellite arrays account for 4.19% to 6.01% of the whole genome, with substantial variations in size and architecture across chromosomes. Using a refined alpha satellite clustering approach that captures global diversity, we identified 195 higher-order repeat (HOR) arrays, 56.4% of which are absent from the T2T-CHM13 reference genome. Extensive structural variations across multiple dimensions exhibit population stratification, including centromeric haplotypes (CenHaps), ultra-large pericentric inversions spanning up to 36.6 Mbp, and inter-chromosomal HOR sharing that reflects sequence exchange among chromosomes. Integrating CENP-A CUT&Tag experiments and long-read-based DNA methylation profiles, we demonstrate that 16.8% of centromeres harbor multiple potential kinetochore assembly sites, and CenHap-specific local HOR homogenization is associated with kinetochore positioning. Despite global suppression of recombination at centromeres, we observed asymmetric linkage disequilibrium flanking centromeres and an ancient recombination event within the centromere of chromosome 19. Furthermore, contrary to the prevailing assumption of high mutation rates in centromeres, our estimates based on stringent orthology reveal no significantly higher single-base substitution rates for centromeres relative to flanking pericentromeric regions with substantial variations across chromosomes, despite extraordinary structural plasticity. Collectively, these multi-scale centromeric variations provide a global view of human centromere diversity and population stratification, fundamentally redefine centromere evolution through a dual-track model balancing structural innovation with mutational constraint, and establish an essential resource for investigating centromere biology and a baseline reference for diagnosing centromere-associated disorders.

genomics↗

bioRxiv2026

Deciphering complete archaic introgression sequences in modern human genomes

Genetic introgression from archaic hominins has profoundly reshaped the genetic diversity and adaptive potential of modern humans, yet the full catalog of introgressed sequences, particularly those residing in structurally complex regions has remained elusive. Here, we present ASMaid (ASseMbly-based archaic introgression detector), a Hidden Markov Model-based framework that leverages haplotype-resolved pangenome assemblies to identify archaic-derived sequences with unprecedented completeness. By integrating both single-nucleotide genotype and structural variation (SV) signals, ASMaid captures significantly more intact archaic segments than conventional reference-based approaches. Applying ASMaid to a global panel of 610 phased human genome assemblies, we show that non-African individuals carry approximately 79.8 Mbp of Neanderthal and 8.3 Mbp of Denisovan sequences, representing substantial increases over previous estimates, respectively. Notably, we detected several centromere-spanning archaic segments, including EAS-specific calls on chromosomes 5 and 7. Our assembly-based approach uncovered 1,701 archaic-derived SVs, revealing a previously overlooked layer of archaic functional legacy. High-frequency introgressed loci are enriched in pathways associated with metabolism, immunity, and nervous system (e.g. CTNNA2 linked to early-onset schizophrenia risk), underscoring the fundamental role of introgression in modulating modern human traits. Notably, we identified dozens of loci potentially facilitating local adaptation, such as PRDM16 involved in adipocyte differentiation and cold tolerance, and CSGALNACT2 associated with chondroitin sulfate synthesis. Furthermore, our analysis delineates three distinct Denisovan introgression pulses in Eastern Eurasian genomes, in which the first two pulses are shared across East Eurasian and Oceanian populations, while the third remain primarily exclusive in East Asians. Reflecting these complex introgression events, 31 Denisovan-derived segments, including the TBX15-WARS2 locus, are inferred to have been introduced via at least two events. This comprehensive map of archaic introgression provides a fundamental resource for understanding how ancient gene flow continuously shapes human phenotypic diversity and adaptation.

evolutionary biology↗

bioRxiv2026

A Metabolic Enzyme, Pyruvate Carboxylase, Functions as a Sequence-Selective Small RNA Sensor for Antiviral Immunity

Interleukin-27 (IL-27) is an anti-HIV cytokine that induces 14 novel microRNAs (miRNAs) in primary CD4(+) T cells. We previously reported that transfection of two of these miRNA mimics, miRTC10 and miRTC14 into human primary macrophages, differentially induced interferon (IFN)-2, -8, -13, and -{lambda}1 expression. However, the mechanism underlying this activation remains unclear. Here, we demonstrate that miRTC14 does not directly target canonical IFN-regulatory genes but instead engages with pyruvate carboxylase (PC) and laboratory of genetics and physiology-2 (LGP2/DHX58) as direct binding partner proteins. Functional analysis revealed that miRTC14 transfection induces IFN expression by more than 100-fold (p<0.001), whereas PC or LGP2 depletion by siRNAs markedly attenuated this response (50-100-fold reduction, p<0.01). Reconstitution of PC and LGP2 in deficient HEK293 cells restored miRTC14-driven IFN induction. Notably, IFN activation depended on sequence features at the duplex termini. However, PC-miRTC14-LGP2 axis activates TBK1-dependent phosphorylation of IRF3/7, similarly to canonical RNA sensors (RIG-I/MDA5), but this process induced differential IFN subtype. These findings establish PC as a miRNA-binding protein and define a previously unrecognized RNA-sensing mechanism, linking metabolic enzymes to RNA sequence-dependent innate immunity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/735367v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ea70d3org.highwire.dtl.DTLVardef@1953a73org.highwire.dtl.DTLVardef@305f16org.highwire.dtl.DTLVardef@1b2daff_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO microRNA sequence-dependent activation of innate immunity by pyruvate carboxylase (PC). PC-miRTC14-LGP2 axis induces TBK1 phosphorylation via an as-yet-unidentified adapter(s). The activated TBK1 (p-TBK1) subsequently phosphorylates IRF3 and/or IRF7 leading to selective IFN subtypes (IFN-2, IFN-8, IFN-13, and IFN-{lambda}1). (Created in BioRender. Kariyawasam, U. (2027) https://BioRender.com/u82s04p) C_FIG

immunology↗

bioRxiv2026

A post-mitotic bistable switch actively safeguards mature neurons against reciprocal transdifferentiation in vivo

How mature cells actively defend their identity against alternative fates is poorly understood. Here we show that two types of fully differentiated Drosophila somatosensory neurons, derived from distinct lineages, are continuously prevented from transdifferentiating into one another by a post-mitotic bistable switch. Two homeodomain transcription factors, Hmx and Cut, are co-expressed in both neuronal types but adopt opposite stoichiometric dominances through mutual repression, each defining one identity. Disrupting this balance in mature neurons triggers deterministic, lineage-crossing reprogramming of transcriptome, dendritic and axonal architecture, and sensory behavior without reversion to a progenitor state. This regulatory logic is evolutionarily conserved: Drosophila sensory identities share transcriptomic signatures with distinct human A{delta} mechanoreceptors, and human CUX and HMX proteins functionally replace their fly counterparts. Mature neuronal identity is thus not a fixed endpoint but a poised equilibrium actively maintained by ongoing competition between opposing selectors. TEASERMature somatosensory identity is a poised equilibrium actively maintained by continuous competition between opposing terminal selectors.

Developmental Biology↗

bioRxiv2026

Lipid mediated ER-stress contributes to the pathogenesis of mitochondrial myopathies

Mitochondrial diseases are a heterogeneous group of genetic disorders caused by impaired oxidative phosphorylation (OxPhos). When skeletal muscle is predominantly affected, they are defined as primary mitochondrial myopathies. Although the genetic causes of mitochondrial myopathies and the resulting bioenergetic impairments are well established, the metabolic drivers behind progressive muscle dysfunction remain poorly defined. This gap in knowledge may contribute to the lack of effective treatments for these disorders. OxPhos defective muscle initiates a metabolic response coordinated by systemic signals which invokes the mobilization of fatty acids from white adipose tissue despite muscle inability to fully oxidize fatty acids due to OxPhos impairment. Here, we show that in human patients with mitochondrial disease and mice with OxPhos defective muscle, increased fatty acid mobilization from white adipose tissue leads to ectopic lipid accumulation and lipotoxicity in skeletal muscle. We find an increase in very long chain ceramides which are mechanistically linked to chronic ER stress, phosphorylation of eIF2, and activation of ATF4 signaling. We propose that Ph-eIF2-mediated attenuation of global protein synthesis and ATF4-initiated atrophy pathways contribute to muscle wasting and weakness. Importantly, inhibition of de novo synthesis of ceramides with myriocin reduces ER stress and improves muscle proteostasis, body weight, and motor functions in a conditional COX10 KO mouse model of mitochondrial myopathy. Together, these findings highlight altered lipid metabolism as a contributor of mitochondrial myopathy pathogenesis and identify lipid-mediated stress pathways that can be targeted therapeutically.

Molecular Biology↗

bioRxiv2026

Scalable generation of pure CD103⁺ cDC1 from iDC1 cultures

Conventional type 1 dendritic cells (cDC1) specialize in cross-presentation and interleukin-12 production and are critical for immunity against intracellular pathogens and tumors, but remain rare in vivo, limiting mechanistic and translational studies. Existing bone marrow-derived dendritic cell (BMDC) methods do not achieve highly selective enrichment of cDC1 or scalable production at high purity. Here, we established a novel in vitro culture system for selective generation of CD103+ cDC1 from mouse bone marrow using defined media conditions together with recombinant FLT3L, GM-CSF, and Kit ligand (KitL), termed iDC1. iDC1 cultures enabled scalable generation of an estimated 1.5 x 109 CD103+ cDC1 at greater than 95% purity from a single mouse, representing at least a 75-fold increase relative to previous recombinant cytokine-based methods. Phenotypic and transcriptional analyses demonstrated that iDC1 closely align with the CD103+ cDC1 lineage while remaining clearly distinct from macrophage populations. Functionally, iDC1 responded robustly to innate stimulation, produced interleukin-12 and inflammatory chemokines, and efficiently cross-presented cell-associated antigen to CD8+ T cells. Mechanistically, KitL and GM-CSF regulated distinct stages of cDC1 generation, whereas proteomic, phospho-proteomic, and functional analyses demonstrated that GM-CSF suppresses apoptosis and oxidative stress while promoting cDC1 proliferation. iDC1 generation was dependent on the +32 kb Irf8 enhancer required for bona fide cDC1 development, and STAT5-and BRD4-associated regulatory programs were identified as important regulators of efficient iDC1 generation. Together, these findings establish iDC1 cultures as a scalable platform for studying cDC1 biology and developing cDC1-based immunotherapeutic strategies.

immunology↗

bioRxiv2026

Targeting melanosome pH is an effective method for the treatment of oculocutaneous albinism

Oculocutaneous albinism (OCA) is a genetic condition associated with impaired visual acuity and increased skin cancer risk. When OCA is due to defects in melanosome ion transport, abnormally acidic conditions in the melanosome lumen inhibit tyrosinase, the critical pigment synthetic enzyme. Hence, a therapeutic approach that optimizes melanosome pH to increase pigment production presents a potential treatment for OCA and a method for decreasing skin cancer risk. Here, we report that reduction in sAC (ADCY10) activity via naturally occurring human variants in ADCY10 restores OCA pigmentation, and sAC inhibition increases melanin synthesis in both human and mouse OCA models. These findings demonstrate that targeting melanosome pH is an effective, previously untapped therapeutic strategy for OCA and elevated skin cancer risk.

physiology↗

bioRxiv2026

Learning molecular determinants of selective small-molecule partitioning across biomolecular condensates

The functional role of biomolecular condensates is shaped by the composition of constituent proteins, nucleic acids, ions, and small molecules. Selective partitioning of small molecules into condensates has therefore emerged as a potential route to condensate-specific chemical probes and therapeutics. Although partitioning is influenced by differences in solvation environments between coexisting dense and dilute phases, a molecular framework connecting small-molecule structure to condensate-specific enrichment remains lacking. Here, we use existing experimental partitioning data for a library of FDA-approved drugs and metabolites across four biomolecular condensates to develop an interpretable graph-based model of small-molecule partitioning. By combining multitask pretraining, condensate-specific fine-tuning, evidential uncertainty quantification, and atom-level attribution analysis, our model predicts continuous partition coefficients with improved accuracy over descriptor-based approaches. Atom-level attributions reveal that condensate partitioning is not governed by a universal chemical rule: the same molecular scaffold can be read differently by distinct condensate environments, with local atomic context and connectivity determining whether specific atoms promote or suppress enrichment. We further apply the trained model to ~1.7 million drug-like molecules from ChEMBL, identifying a chemically diverse space of predicted condensate-selective partitioners and mapping regions where predictions are confident versus where new measurements would be most informative. Together, this work establishes condensate partitioning as a chemically learnable property shaped by the interplay between small-molecule structure and condensate-specific microenvironments, providing an interpretable and uncertainty-aware framework for defining molecular determinants of partitioning and guiding the discovery of condensate-selective small molecules.

biochemistry↗

bioRxiv2026

STID: A Standardized Spatial Transcriptomic Analysis Framework for Infectious Diseases

Spatial transcriptomic studies of infectious diseases still rely on fragmented data analysis processes. Here, we developed STID, a standardized framework for spatial transcriptomic analysis of infectious diseases that leverages the Seurat ecosystem and incorporates Python-based modules. STID provides an extensible infection-specific data structure and supports a full suite of analyses, such as pathogen background correction, infection-associated spot and niche identification, single-sample niche characterization, and multi-sample comparative and temporal analyses. Moreover, STID is broadly applicable to spatial transcriptomic data from infectious diseases caused by bacteria, viruses, and parasites, and enables systematic characterization of the structural features, cellular composition, molecular functions, and host-pathogen interactions within pathogen-infected and/or host-responsive niches. Overall, STID provides an accessible, reproducible, and extensible framework for analyzing infection-associated spatial transcriptomic data and for dissecting host-pathogen interactions in their native spatial microenvironments. MotivationSpatial transcriptomics technologies have emerged as powerful approaches for dissecting the structural and functional features of spatial microenvironments. However, the current general-purpose tools remain fundamentally inadequate for resolving the spatial heterogeneity of infectious disease samples, where the intricacies of host-pathogen interactions render spatial microenvironments both challenging to dissect and largely inaccessible. Tools tailored to infectious diseases are critically lacking, including those for reducing pathogen-derived background noise, identifying and isolating infection{square}associated spots or niches, dissecting host-pathogen interactions, and supporting systematic multi-sample analyses. We therefore developed STID, a unified framework that integrates standardized workflows and addresses the analytical bottlenecks in spatial transcriptomic analysis of infectious diseases. HighlightsO_LISTID standardizes spatial transcriptomic analysis in infectious diseases C_LIO_LISTID improves pathogen-infected spot detection by correcting pathogen background C_LIO_LISTID distinguishes pathogen-infected and host-responsive niches C_LIO_LISTID supports multi-sample comparative and temporal analyses of niches C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/727492v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@167d351org.highwire.dtl.DTLVardef@1628848org.highwire.dtl.DTLVardef@1e157aforg.highwire.dtl.DTLVardef@143ca1b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Ribophorin-1 Governs Spike Abundance of Highly Pathogenic Coronaviruses by ER-associated degradation

The spike protein of highly pathogenic coronaviruses is indispensable for viral entry, pathogenesis, and immune evasion. However, specific host factors governing spike protein degradation and abundance on progeny virions remain largely uncharacterized. Here, we identify Ribophorin-1 (RPN1), a non-catalytic subunit of the oligosaccharyltransferase (OST) complex, as an ER-localized host restriction factor that selectively depletes spike to inhibit coronavirus infection. Conditional knockout of Rpn1 in mouse lung markedly exacerbates SARS-CoV-2 pathogenesis, increasing viral load, immune cell infiltration, and syncytium formation. In cells, RPN1 knockdown enhances susceptibility to diverse variants, whereas its overexpression attenuates infection. Nano-flow cytometry, cryo-EM and LSCM show that RPN1 reduces spike abundance on progeny virions, resulting in reduction in subsequent syncytium formation across SARS-CoV, SARS-CoV-2, and MERS-CoV. Mechanistically, RPN1 promotes VCP/p97-dependent retrotranslocation and AMFR-mediated ubiquitination of spike protein. Heterologous expression of RPN1s functional domain (residues 180-307) confers significant protection against SARS-CoV-2 both in vitro and in vivo. Collectively, our findings define an RPN1-initiated ERAD pathway that selectively targets coronavirus spike for proteasomal destruction, and provide proof-of-concept evidence that targeting this RPN1-dependent pathway represents a promising broad-spectrum antiviral strategy.

microbiology↗

bioRxiv2026

Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation

Despite the fundamental role of spatial context in driving tumor progression, most current computational models for virtual perturbation have largely overlooked its importance. Here, we introduce TMEformer, a tumor microenvironment-aware deep learning framework that leverages high-resolution spatial transcriptomics to jointly model intrinsic tumor cell programs and local microenvironmental signals by explicitly incorporating spatial architecture. Validated across diverse tumor spatial transcriptomic cohorts, TMEformer enables virtual perturbations that capture functional dependencies within local cellular ecosystems. Despite being trained on cancer-specific spatial datasets, TMEformer outperforms baseline models pretrained on large-scale corpora in capturing key tumor transitions, including lineage plasticity and the emergence of therapy resistance. Systematic perturbation analyses prioritize tumor-intrinsic transcription factors and TME-derived ligands that drive disease progression, recovering established regulators and revealing novel candidates. Furthermore, TME- derived embeddings improve the spatial stratification of tumor cells and align more closely with pathological architecture. Together, TMEformer establishes a general framework for modeling tumors as spatially coupled, perturbable ecosystems. An online TMEformer web platform for perturbation prediction, analysis, and visualization is available at http://www.pradcellatlas.com.

bioinformatics↗

bioRxiv2026

Distributed Clonal Deletion Prevents Autoimmune Disease Progression

Self-reactive B cells are generated during normal development and can acquire increased pathogenicity through activation-induced cytidine deaminase (AID)-mediated diversification following activation. Clonal deletion is thought to eliminate these cells, yet how deletion is distributed across developmental and activation stages to prevent autoimmune disease remains unclear. Here, we show that clonal deletion is enforced through temporally distinct mitochondrial apoptosis (MOMP) checkpoints that differentially regulate autoreactive B cell fate and disease progression. Using conditional Bcl-2 expression to inhibit MOMP either before or after B cell activation, we find that early inhibition permits the survival and maturation of autoreactive B cells after peripheral egress, expanding the pool of cells available for activation. These cells subsequently undergo AID-dependent diversification, producing class-switched IgG autoantibodies with expanded antigen breadth that target a wider range of self-antigens and drive lethal, female-biased autoimmune disease characterized by complement activation and kidney pathology. In contrast, inhibition of MOMP only after activation allows the accumulation of germinal center, switched memory, and plasma cells and promotes autoantibody production, but results in more restricted IgG autoreactivity, limited complement activation and limited tissue damage, and normal survival. Notably, early MOMP inhibition does not expand immature bone marrow B cells, indicating that a major clonal deletion checkpoint operates in the periphery rather than during initial B cell generation. Together, these findings support a Distributed Clonal Deletion Model in which early checkpoints restrict the entry of autoreactive B cells into diversification pathways, while later checkpoints limit the persistence of diversified autoreactive clones, thereby constraining autoimmune disease progression. One Sentence SummaryDistributed clonal deletion prevents autoimmune disease progression by restricting the breadth of autoreactive clones entering immune responses, with early MOMP checkpoints limiting diversification and later checkpoints constraining persistence.

immunology↗

bioRxiv2026

The Magnaporthe oryzae Effector AvrPii Attenuates Rice Immunity by Targeting the Calcium-Associated ANK Protein AVIN8

Rice blast, caused by the fungus Magnaporthe oryzae, poses a severe threat to global rice production. Although numerous M. oryzae effectors have been identified, the molecular mechanisms remain poorly understood. The effector AvrPii triggers ETI upon recognition by NLR receptor Pii and has been shown to target host exocytosis and oxidative metabolic pathways to suppress immunity. Here, we identify AVIN8 (AvrPii-interacting protein 8) as a new target of AvrPii. AVIN8 is an ankyrin-repeat (ANK) protein localized to the plasma membrane and nuclear envelope, with sequence similarity to known ANK calcium channels. AVIN8 expression is induced during early M. oryzae infection. Overexpression of AVIN8 enhances blast resistance, whereas its silencing increases susceptibility. AVIN8 promotes chitin-triggered ROS production in a Ca2+-dependent manner. In contrast, AvrPii impairs Ca2+ influx and chitin-triggered ROS burst. Our findings reveal a virulence strategy in which M. oryzae effector AvrPii hijacks the Ca2+ influx-associated ANK protein AVIN8 to suppress early calcium and PTI signaling in rice.

plant biology↗

bioRxiv2026

Calmodulin requires calcium to be a constitutive component of the spindle pole bodies in fission yeast

Although calmodulin is best known as a calcium sensor, it also possesses Ca2+-independent functions, exemplified by the surprising finding that the budding yeast cells remain viable using a calmodulin mutant that cant bind Ca2+ (Geiser et al., 1991). It remains unclear why Ca2+-calmodulin is required in other yeasts or vertebrates. Here, we determined whether such holo-calmodulin is an essential cytoskeletal protein in fission yeast. The S. pombe calmodulin Cam1 was an integral part of both the spindle pole body (SPB) and many actin structures at the equatorial division plane. Two mutants Cam1-2V and -3V, which bound Ca2+ poorly, reduced their localization at the SPBs by 90%. However, their presence in the actin structures remained unchanged. Replacing the endogenous cam1 with cam1-2V cut the number of the Cam1-interacting protein Pcp1 in the SPB by [~]70% and delayed mitosis. In contrast, the assembly and constriction of the cytokinetic ring, which depends on the Cam1-interacting myosins Myo1, Myo51 and Myo52, accelerated. The temperature-sensitive cam1-2V mutant was rescued by either over-expression of pcp1 or deletion of myo1. Thus, Cam1 depends on Ca2+ to promote the SPB assembly and to modulate the actomyosin ring constriction, suggesting holo-calmodulin as an essential cytoskeletal protein.

cell biology↗

bioRxiv2026

miR-128 Regulates Hypertensive Vascular Remodeling via PPAR-γ

OBJECTIVEThis study aimed to explore the role and underlying mechanism of microRNA-128 (miR-128) in regulating vascular remodeling in spontaneously hypertensive rats (SHRs), focusing on its targeting of peroxisome proliferator-activated receptor {gamma} (PPAR-{gamma}) and modulation of the Toll-like receptor 4/nuclear factor-{kappa}B (TLR4/NF-{kappa}B) inflammatory pathway. METHODSAll experimental procedures were approved by the Animal Care and Use Committee of Fujian Medical University. In vivo, ten-week-old male SHRs were randomly assigned to three groups: renal denervation (RDN, n=6), sacubitril/valsartan (Sac/Val, n=6), and Sham (n=6). Age-matched Wistar-Kyoto (WKY) rats served as normotensive controls (n=6).Eight weeks after intervention, mesenteric arteries were harvested for histological, functional, and molecular analyses. Serum miR-128 levels were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The expression levels of key proteins in the vascular wall were assessed via immunofluorescence (IF), immunohistochemistry (IHC), and Western blotting (WB). Bioinformatics analysis and RNA sequencing (RNA-seq) were employed to identify core genes and signaling pathways associated with hypertension-induced pathological inflammation. RESULTSIn vivo, in the SHR sham-operated group, elevated blood pressure, severe vascular remodeling, and impaired vasodilatory function were observed, accompanied by downregulated miR-128 expression and upregulated TLR4/NF-{kappa}B signaling activity (all p < 0.0001).RDN postoperative, miR-128 expression was significantly restored, which in turn inhibited the TLR4/NF-{kappa}B pathway, reduced the production of pro-inflammatory cytokines (including IL-1{beta}, IL-6, and TNF-), and ameliorated vascular dilation dysfunction in SHRs (all p < 0.0001). Mechanistically, miR-128 negatively regulated the TLR4/NF-{kappa}B signaling pathway while upregulating the expression of PPAR-{gamma} (p < 0.05). CONCLUSIONRDN not only exerts a hypotensive effect but also improves hypertensive vascular remodeling. miR-128 inhibits excessive inflammation in vascular smooth muscle cells and alleviates vascular remodeling in SHRs via the PPAR-{gamma}/TLR4/NF-{kappa}B axis. These findings identify miR-128 as a potential therapeutic target for RDN in the treatment of hypertension, providing a novel regulatory strategy for the precision management of cardiovascular diseases.

bioinformatics↗

bioRxiv2026

Molecular and genetic heterogeneity in iPSCs derived from an outbred laboratory mouse population

Genetically diverse panels of human pluripotent stem cells enable genetic dissection of cellular phenotypes, but comparable induced pluripotent stem cell (iPSC) resources in model organisms remain limited. We generated a panel of iPSCs from the Diversity Outbred (DO) mouse population and established 288 genetically unique lines that retain the allele frequency distribution, heterozygosity, and low population structure of the source population. The lines exhibit consistent growth, pluripotent gene expression profiles, and capacity to form embryoid bodies. Transcriptomic profiling of the lines revealed significant variation in gene expression driven in part by genetic background. We used expression quantitative trait locus (eQTL) mapping to identify over 10,000 regulatory loci that influence gene expression variation, including multiple distal eQTL hotspots that are key gene regulatory hubs and are shared with DO embryonic stem cells (ESCs). The largest hotspot, mediated by Lifr, showed a shift in founder allele effects relative to ESCs, consistent with differences in cellular state and culture conditions. These results establish the DO iPSC panel as a genetically diverse, publicly accessible platform derived from a laboratory mouse genetic reference population, enabling integration of in vitro cellular phenotypes with in vivo traits within a closed, outbred population.

genetics↗

bioRxiv2026

Physics-inspired computational methods for spatial transcriptomics reveal a dysplasia-restricted premalignant basin and a density-asymmetric autocrine niche in oral mucosal carcinogenesis

Spatial transcriptomics is often interpreted with tools that do not explicitly encode tissue-scale physical priors such as finite ligand diffusion, density-based state stability, or self-exciting spatial recruitment. We introduce three compact computational methods and apply them to a 326,554-cell spatial atlas of human oral mucosal carcinogenesis spanning normal mucosa, hyperplasia, oral lichen planus, and dysplasia. DC3 (Diffusion-Constrained Cell Communication) replaces distance-blind ligand-receptor co-expression with a ligand-specific exponential distance kernel. It down-weights short-range ECM-class interactions by three to four orders of magnitude relative to traditional scoring, remains rank-stable under diffusion-length perturbation and dys2 removal (Spearman rho >= 0.93), and better matches COMMOT than traditional co-expression on the dys2 benchmark. A within-section label-permutation null indicates that only 0.5-6.6% of the top MRB-autocrine DC3 signal is attributable to spatial clustering alone. A log-density landscape, reported in nats rather than thermodynamic units, places the Malignant_risk_basal (MRB) cluster in a high-density epithelial region with a reverse barrier of 2.43 nats from stress-proliferative basal cells on the full atlas, 1.93 nats after dys2 removal, and 1.0-1.9 nats under Silverman/Scott bandwidth rules. MRB local neighborhood entropy is stable at 0.67-0.68 bits across bandwidth and PCA-dimension choices. A spatial Hawkes model separates immune-cell background density from self-excitation; apparent dysplasia-level adaptive-immune attenuation is not significant by 10,000 label permutations (all FDR q = 1.00) and is retained only as a section-level observation. External checks in CELLxGENE Census and Puram 2017 reposition the MRB signature as a dysplasia-restricted aberrant-basal-differentiation phenotype rather than a marker preserved in fully malignant OSCC. The methods are presented as lightweight, interpretable tools, and the biological findings as hypotheses requiring independent validation. Author summarySpatial transcriptomics records both gene expression and tissue position, but common analysis pipelines often treat signaling and cell-state structure as if distance and tissue architecture were secondary details. We developed three simple methods that make these assumptions explicit: DC3 scores cell-cell communication with ligand-specific diffusion distances, a log-density landscape summarizes where epithelial states are densely populated in expression space, and a spatial Hawkes model separates baseline immune density from local self-excitation. Applied to an oral mucosal carcinogenesis atlas, these methods highlight a dysplasia-enriched Malignant_risk_basal (MRB) population with short-range autocrine signaling and mixed epithelial neighborhoods. We also stress-test each claim by removing the MRB-rich section, varying model parameters, running permutation tests, benchmarking against COMMOT, and checking public external datasets. These tests narrow the biological interpretation: MRB is best viewed here as a dysplasia-restricted aberrant-basal-differentiation phenotype, not as a proven step toward fully malignant oral squamous cell carcinoma, and the apparent dysplasia-level immune-cascade attenuation is not statistically supported. The study therefore offers both a reusable computational toolkit and a deliberately constrained biological hypothesis for future validation.

bioinformatics↗

bioRxiv2026

Hypermorphic TaARF4 shapes wheat architecture by repressing SPL-mediated developmental timing

Integrating spatial morphogens with temporal developmental clocks is fundamental to optimizing plant architecture and crop yield, yet their molecular interface remains elusive. Here, we characterize Branched shoot 1 (Bsh1), a semi-dominant wheat mutant exhibiting non-canonical upper-aerial branching and aberrant spike development, caused by a T265I substitution in the DNA-binding domain of the auxin response factor TaARF4-A2. Unlike flanking mutations governing protein stability in basal land plants, this central substitution uniquely converts TaARF4-A2 into an auxin-insensitive hypermorphic repressor. The mutant protein disrupts auxin-cytokinin homeostasis and markedly enhances the native repression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, the core timers of developmental phase transitions. This spatial and temporal uncoupling unleashes upper axillary buds from dormancy, promoting aerial branching and diverting resources from reproductive development. Our findings demonstrate how a conserved spatial morphogen effector was evolutionarily rewired in polyploid wheat to dictate the temporal SPL clock, orchestrating species-specific shoot architectural innovation.

plant biology↗