Biology subjects

Li, G.

Publications and source records attributed to Li, G..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Expanding KitBase: Genome and Phenotype Integration of 3,268 Fast-Neutron Rice Mutants

Fast-neutron mutagenesis creates diverse genome-wide mutations, providing a powerful tool for crop functional genomics. Here, we present an expanded genomic and phenotypic analysis of 3,268 fast-neutron (FN)-induced mutant rice lines (Oryza sativa L. cv. Kitaake). All FN lines were whole-genome sequenced, and mutations were identified by alignment in the Nipponbare and KitaakeX reference genomes. We cataloged over 428,000 mutations affecting 78.49% of Nipponbare genes and 70.38% of KitaakeX genes. In silico expression analysis indicates that 575 non-mutated Nipponbare genes are highly expressed and likely essential for viability. Each mutant carries, on average, 68.5 mutations in the Nipponbare alignments or 63.2 mutations for KitaakeX alignments, distributed randomly across all 12 chromosomes with no evident hotspots. FN lines have approximately 8.5% fewer mutations when using the KitaakeX alignment, underscoring the unique contributions of each reference genome and the importance of utilizing both for comprehensive mutation discovery. The majority of mutations are small deletions and single-base substitutions, with deletions predominating in their effect on genes. We found that 74.4% of all transcription factor Nipponbare genes were mutated at least once. Phenotypic characterization of over 2,700 lines revealed a broad spectrum of variation in core agronomic traits (heading date, tiller number, plant height, panicle weight, seed yield components) and other morphological variants of interest. The integration of genomic and phenotypic data through the KitBase platform enabled the identification of candidate genes for several traits of interest. The KitBase website (https://kitbase.ucdavis.edu) has been updated to provide open access to all mutation data and seed stocks, as well as an intuitive query interface, facilitating forward and reverse genetic analyses in rice. This expanded resource enriches the rice functional genomics toolkit and highlights the value of coupling high-density mutation mapping with phenotypic data for rapid gene discovery and crop improvement.

plant biology↗

bioRxiv2026

Crystal structure of E. coli Nissle 1917 flagellin reveals novel features that modulate bacterial motility but not TLR5 recognition

The probiotic E. coli Nissle 1917 (EcN) strain is known to promote intestinal homeostasis via flagellin, the protomer of its motility apparatus, the flagellum. The flagellin of EcN shows atypical features, namely a hypervariable region (HVR), whose structure and significance have remained elusive. We therefore determined the crystal structure of the E. coli Nissle 1917 flagellin FliC at a resolution of 1.2 [A] which revealed an unusual domain architecture: the canonical D1 domain was found connected by an extended linker to an extensive HVR whose D2, D3 and D4 domains form an outer domain (OD) which surrounds the filament core comprised of conserved domains D0-D1. Using both recombinant proteins and gene-edited EcN strains expressing mutant flagellins, the functional requirement for these unique features was subsequently studied for effects on immune recognition on intestinal epithelial and immune cells, as well as on flagellar protein expression, assembly and bacterial motility. While human and mouse TLR5 immune recognition of flagellar proteins or intact bacteria was only moderately affected by removal of linker or D4, especially linker removal reduced protein stability and bacterial motility in both soft agar and liquid media swimming assays. Interestingly, depending on the environment, D4 or HVR removal had different effects on motility and surface structure. Finally, a site-directed mutagenesis approach highlighted that loss of TLR5 recognition strictly entails loss of motility but not vice versa. Our data indicate that specific HVRs/OD might be relevant for motility of E. coli Nissle 1917 in specialized environments, but not for immune recognition. Moreover, we find mutational tolerance is greater for immune recognition than for motility, providing new insights into bacterial adaptation to the host environment.

microbiology↗

bioRxiv2026

An oxytocin-gated circuit from the hypothalamus silences olfactory tubercle neurons to drive prosocial grooming

Spontaneous helping behaviors such as allogrooming are vital for survival in social species, yet their underlying neural mechanisms remain largely unknown. Although oxytocin (OXT) is known to modulate allogrooming, the precise neural circuits, molecular pathways, and sensory drivers remain unclear. Here, using a social emergency paradigm in mice, we show that observer mice selectively allogroom distressed, anesthetized conspecifics, a behavior that is guided by main olfactory system cues and mitigates the demonstrators anxiety. We identify an oxytocinergic circuit from the paraventricular hypothalamus to the medial olfactory tubercle (PVNOXT[->]mOT) that is necessary and sufficient for this helping behavior. In vivo fiber photometry reveals that PVNOXT[->]mOT activity and OXT release are temporally locked to allogrooming initiation. This behavioral effect requires oxytocin receptor (OXTR) signaling specifically on mOT dopamine D1 receptor-expressing neurons, where OXTRs suppress neuronal excitability via G protein-gated inwardly rectifying K+ (GIRK) channels. Disruption of this inhibitory mechanism induces neuronal hyperexcitability and impairs allogrooming, a deficit rescued by restoring GIRK function. These findings define a PVNOXT-mOT circuit for prosocial helping, revealing an oxytocinergic pathway with potential therapeutic relevance for neuropsychiatric disorders characterized by social deficits.

neuroscience↗

bioRxiv2026

Coronavirus envelope protein drives iron sensing disorder by hijacking the TAp73-FDXR axis

Iron overload is increasingly recognized as a critical contributor to coronavirus pathogenesis1, yet the underlying induction mechanisms remain unclear. Here, we uncover a fundamental pathway by which coronavirus drives IRP1 RNA-binding activity to induce iron accumulation2 via targeting the TAp73-FDXR axis. Specifically, coronavirus infection represses transcription of FDXR (encoding the key rate-limiting enzyme in host iron-sulfur cluster synthesis3), thereby impairing host iron-sulfur cluster generation to trigger the functional conversion of the cytosolic aconitase 1 (ACO1) into iron-regulatory protein 1 (IRP1)4, ultimately leading to the hosts persistently false perception of iron deficiency. We identify TAp73 as the primary transcription factor governing FDXR expression, and demonstrate that the coronavirus envelope protein (CoV-E) orchestrates TAp73 nuclear export. Subsequently, CoV-E binds TAp73 through a critical valine residue within its C-terminal PBM domain, inducing the K48-linked ubiquitination and proteasomal degradation of TAp73. Furthermore, we developed a CoV-E-targeting molecule, DPTP-FC, which blocks CoV-E-TAp73 interaction via forming steric hindrance and effectively alleviates iron accumulation and tissue damage caused by PEDV, PDCoV, and SARS-CoV-2 infection. Our study reveals the central role of the TAp73-FDXR axis in CoV-induced iron accumulation, highlighting CoV-E as an attractive antiviral target and DPTP-FC as a promising therapeutic candidate.

microbiology↗

bioRxiv2026

Single-cell Landscape of T Cell Heterogeneity in Kawasaki Disease: STAT3/JAK Axis Regulates the Lineage Differentiation Bias of Th17 Cells

BackgroundKawasaki disease (KD) is a pediatric systemic vasculitis in which T-cell-mediated immune responses play a pivotal role. However, the precise dynamic evolution of T-cell subsets during disease progression remains poorly understood. MethodsSingle-cell RNA sequencing (scRNA-seq) was employed to perform high-resolution annotation of peripheral blood mononuclear cells (PBMCs) from healthy controls and KD patients, both pre- and post- IVIG treatment. T-cell developmental trajectories were reconstructed via Monocle3-based pseudotime analysis. Furthermore, the functional significance of the significant pathway was validated in a CAWS-induced KD murine model. ResultsA high-resolution single-cell landscape identified 13 distinct T-cell subtypes. Pseudotime analysis revealed a significant lineage commitment of CD4+ T cells toward a Th17 phenotype during the acute phase of KD, synchronized with the transcriptional upregulation of the STAT3/JAK signaling axis. Animal experiments further demonstrated that pharmacological inhibition of this pathway substantially attenuated inflammatory infiltration in the cardiac vasculature of KD mice. ConclusionThis study identifies the STAT3/JAK-mediated Th17 differentiation bias as a potential regulatory program associated with acute inflammation in Kawasaki disease, thereby highlighting the STAT3/JAK axis as a potential therapeutic target.

bioinformatics↗

bioRxiv2026

Microfluidic low-input profiling reveals lncRNA roles in disease

Long noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in diseases. Existing approaches for profiling lncRNA-chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging especially when examination of a specific cell type is desired. Here we demonstrate a low-input microfluidic technology based on Chromatin Isolation by RNA Purification (ChIRP) for mapping lncRNA-chromatin interactions using as few as 50,000 cells. We validate our technology, muChIRP-seq, on two lncRNAs of different sizes (GOMAFU and TERC) in human and mouse cell lines and in brain tissues. Furthermore, we profile neuronal nuclei from postmortem human brain tissues of schizophrenia and control subjects. Our profiling data reveal distinct roles and levels of involvement for the two lncRNAs in contribution to schizophrenia. Our multimodal integrative analysis suggests coordination between lncRNA binding and other epigenomic mechanisms such as histone modifications in schizophrenia pathogenesis. Our technology enables lncRNA studies in tissue samples and in a cell-type-specific fashion, unlocking new opportunities to screen and understand lncRNA involvement in diseases.

genomics↗

bioRxiv2026

Italia: A PARP-Directed Auger Electron-Emitting Agent for Targeted Radionuclide Therapy of Cancer

Poly(ADP-ribose) polymerase 1 (PARP1) is a central mediator of DNA damage repair and an established therapeutic target in homologous recombination-deficient cancers. Radiolabelled PARP inhibitors provide a strategy to deliver cytotoxic radiation directly to tumour DNA by exploiting PARP overexpression and trapping at sites of DNA damage. Here, we describe the design, radiosynthesis, and in vitro evaluation of [123I]Italia, a talazoparib-derived Auger electron-emitting agent for PARP-targeted radionuclide therapy. Stereochemically pure [123I]Italia, (8S,9R)-5-fluoro-8-(4-(iodo-123I)phenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one was synthesised in one step via copper-mediated iodo-deboronation, achieving activity yields >80% and molar activities >6.2 {+/-} 3.1 GBq/{micro}mol (n=8). UPLC analysis confirmed radiochemical purity >97%. Italia exhibited potent PARP1 inhibition (IC50 0.48 nM) and in silico predicted binding affinity comparable to talazoparib. In a panel of PARP-expressing cancer cell lines, [123I]Italia demonstrated highest uptake at 60 min, PARP-selective uptake, predominant nuclear localisation (up to 60% of added activity) and chromatin association consistent with PARP trapping (up to 15% of total activity recorded). Uptake was reduced more than 50-fold by addition of an excess of any PARP inhibitor (e.g. olaparib, talazoparib, and rucaparib) and in PARP1 knockout cells, confirming target specificity. Clonogenic assays showed a marked, added activity-dependent reduction in survival of PARP-expressing cells following a brief one-hour exposure, whereas PARP1-deficient cells were resistant. Collectively, these findings identify [123I]Italia as a promising PARP-targeted Auger electron-emitting theranostic candidate that warrants further in vivo evaluation.

cancer biology↗

bioRxiv2026

Programming Biomolecular Interactions with All-Atom Generative Model

Biomolecular interactions lie at the core of cellular life, spanning diverse molecular modalities from small molecules to nucleic acids and proteins. Nevertheless, design strategies remain separated despite shared physicochemical principles of molecular recognition. Here we present AnewOmni, a unified generative framework trained on more than 5 million biomolecular complexes, that enables transferable molecular design across molecular scales by assembling chemically meaningful building blocks at atomic resolution. We further introduce programmable graph prompts to support user-defined chemical, topological, and geometric steering during generation, exploring hybrid and unconventional chemistries beyond canonical structures. We demonstrate that transferable learning of interaction patterns and physical constraints across molecular modalities is possible, via an atom-to-block latent space capturing both atomic details and structural priors. The framework successfully designed small molecules, peptides, and nanobodies targeting the challenging KRAS G12D switch II pocket, as well as orthosteric peptides and allosteric small-molecule inhibitors for PCSK9 in the absence of known binding site, achieving 23%-75% success with only low-throughput validation, bypassing modality-specific high-throughput screening. AnewOmni is the first to succeed in functional molecular design across all scales, from small chemical entities to large biologics, and represents a stepstone towards general molecular reasoning engines, advocating a generative foundation model for biomolecular interactions to enter regimes where data and human intuition remain limited.

bioengineering↗

bioRxiv2026

Efficient Reprogramming of the Epiblast Enables the Generation of Cloned Mice

Somatic cell nuclear transfer (SCNT) can generate viable mammals despite pervasive epigenetic abnormalities in cloned embryos, yet the mechanism underlying this paradox remains unclear. Here we show, using single-cell transcriptomics, that efficient reprogramming occurs exclusively in the epiblast (EPI), but the not primitive endoderm (PrE) of late mouse SCNT blastocysts. Integrating this with previous findings of trophectoderm (TE) aberration, we propose the EPI as the sole effectively reprogrammed lineage. By innovatively employing a Lego-like multi-lineage embryonic aggregation approach, where the extra-embryonic lineages were replaced with fertilization-derived counterparts, we demonstrated that SCNT-derived EPI inherently possesses full-term developmental potential nearly identical to that of fertilized EPI (20.5% vs. 21.8% birth rate), functionally confirming its effective reprogramming. Our study uncovers a lineage-specific asymmetric reprogramming mode where the EPI specifically achieves effective reprogramming, thereby constituting the deterministic basis for cloned animal generation. This work also provides a versatile strategy for investigating lineage potency and function.

developmental biology↗

bioRxiv2026

NLRP3 acts as a direct sensor of intracellular potassium ions

The NLRP3 inflammasome is a sentinel of cellular homeostasis, and its activation triggers the assembly of a molecular machinery that drives inflammation in infection, cardiovascular, metabolic, and neurodegenerative diseases. The majority of the many triggers known to activate NLRP3 are believed to induce potassium ion (K+) efflux from the cell as a fundamental danger signal for compromised cellular integrity. However, it has remained unclear how a reduction in intracellular K+ concentration is mechanistically translated into conformational changes in NLRP3 that promote inflammasome assembly, interleukin (IL)-1 release, and cell death. Here, we provide evidence that alterations in K+ levels directly regulate the conformation of the NLRP3 protein. In cell-free lysates derived from cell lines and primary blood immune cells high K+ concentrations stabilized a compact, protease-resistant structure resembling inhibitor-bound NLRP3, whereas low K+ conditions or the presence of a K+ chelator favored an open, more flexible and protease-accessible conformation. Notably, human NLRP3 remained responsive to K+ even when exogenously expressed in macrophage-like Drosophila cells or purified as recombinant protein. This indicates that K+ sensing occurs independently of cellular co-factors and is consistent with direct ion coordination. Of note, stimulation with the K+-independent NLRP3 agonist CL097 failed to recapitulate the conformational transition caused by K+ efflux inducer, nigericin. Moreover, pathogenic gain-of-function mutant variants of NLRP3 constitutively resembled the open and flexible protease-accessible conformation. Mapping K+-interactions by high-performance computation suggested that K+ ions populate the nucleotide binding pocket of the FISNA-NACHT module of individual NLRP3 chains but also stabilize face-to-face interactions within inactive oligomeric cage assemblies via the NACHT-adjacent acidic loop. Collectively, our findings enable us to propose a mechanistic model of how intracellular K+ ions preclude NLRP3 activation prior to efflux and thus how NLRP3 responds to cellular danger as a direct K+ sensing protein.

immunology↗

bioRxiv2026

Synergy Feedback Control Predicts Walking Across Multiple Cycles

Neural feedback is important for the control of movement, and multiple neurological disorders (e.g., stroke, cerebral palsy, Parkinsons disease, incomplete spinal cord injury) are characterized by altered neural feedback. Researchers have created numerous computational neuromusculoskeletal models controlled by simulated neural feedback mechanisms, but these models rarely represent actual human subjects and thus have not found practical clinical application. As a step toward designing patient-specific treatments for individuals with neurological disorders, this study used the Neuromusculoskeletal Modeling Pipeline to develop and evaluate a novel synergy-based feedforward (FF)+feedback (FB) control model using a personalized three-dimensional neuromusculoskeletal walking model of an actual human subject post-stroke. Experimental walking data collected from the subject were used to create the subjects personalized walking model. Then for 5 calibration walking cycles, personalized synergy-based FF+FB control models were created. First, the personalized model was used to estimate lower body muscle activations consistent with the subjects electromyographic, joint motion, and joint moment data. Second, five synergy activations per leg with associated synergy vectors were calculated that closely reconstructed the subjects muscle activations and joint moments simultaneously. Third, nominal FF synergy activation controls were calculated by averaging the synergy activations for each leg. Fourth, the nominal FF synergy controls were scaled by 0, 25, 50, 75, 100, and 125%, and the gap in reproducing the subjects muscle activations was filled by fitting FB synergy activation controls as a function of joint positions, velocities, and moments as surrogates for muscle lengths, muscle velocities, and tendon forces. Next for 3 testing walking cycles, the six synergy-based FF+FB models were used to control the subjects personalized walking model in predictive simulations. The 100% FF model (which still had minimal FB) reproduced the testing walking cycles the most closely, and only the 75%, 100%, and 125% FF models predicted near-periodic walking motions using initial conditions consistent with experimental values. The 0, 25, and 50% FF models could generate near-periodic walking motions only when the initial conditions were allowed to diverge substantially from experimental values. Our findings suggest that predictive simulations of walking may require substantial feedforward control when modeling an actual human subject.

bioengineering↗

bioRxiv2026

Reproducible Research: Computational Design of PersonalizedClinical Treatments for Walking Impairments Using the Neuromusculoskeletal Modeling Pipeline

Background: Personalized computational neuromusculoskeletal models have great potential for optimizing the design of clinical treatments for movement impairments. While many software tools address specific parts of the model personalization and treatment optimization processes, they typically require significant programming experience to use and do not cover the full breadth of these two processes. Furthermore, published neuromusculoskeletal modeling studies typically do not provide all the methodological details needed for others to reproduce the work. Consequently, researchers seeking to develop skills in the model personalization and treatment optimization processes face a steep learning curve due to the lack of detailed training materials that demonstrate both processes for real-life clinical problems using real-life subject movement data. Methods: This article presents detailed training tutorials for the model personalization and treatment optimization processes using two real-life clinical problems and the Neuromusculoskeletal Modeling (NMSM) Pipeline. The first clinical problem involves the design of personalized gait modifications and high tibial osteotomy surgery for an individual with bilateral medial knee osteoarthritis, where the goal is to reduce the peak adduction moment in both knees to a specified target level. The second clinical problem involves the design of a synergy-based functional electrical stimulation prescription for an individual post-stroke with impaired walking function, where the goal is to equalize the propulsive and braking impulses between the two legs. Both tutorials were implemented as course projects given to novice users in a combined undergraduate/graduate mechanical engineering course. Results: Both tutorials produced personalized neuromusculoskeletal models and associated dynamically consistent tracking optimizations that closely reproduced subject-specific experimental joint angles, joint moments, ground reaction forces and moments, and (if applicable) muscle activations measured during walking. Subsequent design optimizations predicted personalized treatments that achieved target values of peak knee adduction moments or propulsive and braking impulses. Conclusions: The detailed step-by-step tutorials presented with this article are the first to walk users through the entire process of creating personalized neuromusculoskeletal models and then using them to design personalized treatments for two subjects with two different clinical problems. These tutorials can be used to introduce new users to the NMSM Pipeline and as projects in neuromusculoskeletal modeling courses.

bioengineering↗

bioRxiv2026

Type 2 diabetes amplifies environmental Pb toxicity and intergenerational risk

Type 2 diabetes (T2D) and environmental lead (Pb) exposure intersect as prevalent global health challenges. Prior studies report elevated blood Pb in T2D, but the underlying mechanism and directionality remain unresolved. Here we show that T2D fundamentally alters Pb toxicokinetics, converting otherwise modest exposure into progressive organ injury and heritable risk. In a human cohort, elevated blood Pb in T2D specifically associated with impaired renal function rather than glycaemic control or adiposity. In db/db mice, diabetes increased oral Pb absorption through delayed gastrointestinal transit and epithelial barrier dysfunction, leading to enhanced systemic retention. With sustained exposure, renal Pb accumulation induced tubular stress that reduced effective clearance, creating a feed-forward loop in which diabetes promotes Pb retention and retained Pb accelerates kidney injury. Chronic Pb exposure exacerbated diabetic kidney injury without inducing hyperglycaemia, and short-course chelation attenuated renal stress markers. Beyond somatic toxicity, combined paternal T2D and Pb exposure programmed renal and neurobehavioral phenotypes across generations via sperm RNA. These findings redefine Pb from a passive environmental exposure to a context-dependent driver of disease, identify T2D as a vulnerability state that reshapes toxicant handling, and establish a mechanistic link between metabolic disease, environmental exposure and intergenerational risk. This work highlights the need for vulnerability-informed clinical management and environmental regulation in populations burdened by T2D.

genetics↗

bioRxiv2026

Efficient derivation and transcriptional characterization of mouse extra-embryonic endoderm stem cell lines generated by somatic cell nuclear transfer

Somatic cell nuclear transfer (SCNT) holds great promise for regenerative medicine and agriculture, but its application is severely hampered by low efficiency, primarily attributable to aberrant epigenetic reprogramming. Although embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) have been successfully derived from cloned embryos, an in vitro counterpart of the primitive endoderm (PrE) lineage has remained unavailable. To address this gap, this study reports the first successful establishment of extra-embryonic endoderm stem cell lines (XENs) from mouse SCNT-derived blastocysts (NT-XENs). Under conventional culture conditions, NT-XENs were generated from hybrid B6D2F1 blastocysts at a high efficiency of 55%, comparable to that of fertilization-derived XEN lines (FD-XENs, 50%), whereas derivation from inbred C57BL/6J SCNT-derived blastocysts was markedly lower (12.5%). Immunofluorescence and NanoString multiplex gene expression profiling confirmed that NT-XENs robustly expressed specific marker genes for PrE/XENs (e.g., Gata4, Gata6, Sox17), while exhibiting negligible or absent expression of pluripotency and trophoblast markers. Based on NanoString assay data, NT-XENs and FD-XENs shared highly similar global gene expression patterns, yet also exhibited some nonnegligible differences, exemplified by the differentially expressed genes (DEGs) Pecam1, Gtl2, Thbd and Xlr3b, which may suggest that the NT-XENs resided in a more differentiated state (potentially biased toward parietal endoderm (PE)) and retained SCNT-specific epigenetic imprinting errors, including aberrant X-chromosome inactivation and dysregulation of imprinted domains. In summary, this study successfully establishes NT-XEN cell lines, providing a valuable in vitro model for investigating the reprogramming scenarios of PrE lineage in SCNT and offering novel insights into the mechanisms underlying developmental failure of cloned embryos.

developmental biology↗

bioRxiv2026

Weckle is a molecular switch that diverts Toll signalling from innate immunity towards growth by engaging Yki

The mechanisms underlying how the brain can switch from a plastic to a degenerative state are unknown. Tolls and Toll-Like receptors (TLRs) could be involved since they underlie both neuroinflammation and structural brain plasticity. Here, we show that the Toll signalling adaptor Weckle (Wek) - a ZAD-Zinc-finger transcription factor - can switch the response from promoting innate immunity or cell death, to inducing growth instead. Myristoylated Wek binds Tolls at the membrane, and concerted PI3K and Toll signalling drive its nuclear translocation. Wek interacts with Yorkie (Yki) - the key regulator of growth restrained by Hippo - enabling its nuclear shuttling. Remarkably, Wek blocks innate immunity. Instead, Wek and Yki together drive glial cell proliferation and growth. Through this mechanism, Toll signalling could promote structural brain plasticity via Wek and Yki downstream. As Tolls and Yki are widespread, these findings could have important implications for understanding also regeneration and cancer.

developmental biology↗

bioRxiv2026

Super-resolution single-cell spatial atlas of plant de novo regeneration

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com.

cell biology↗

bioRxiv2026

Single-nucleus RNA sequencing reveals cell type-specific responses to heat stress in bovine mammary gland

BackgroundHeat stress (HS) poses a major challenge to the dairy industry by reducing milk production, yet its cell type-specific effects in the bovine mammary gland remain incompletely defined. In this study, we recorded production traits and collected mammary biopsies from cows under thermoneutral (TN), HS, and pair-fed (PF) conditions. ResultsClinical measurements confirmed HS-induced physiological alterations. Compared with TN cows, HS cows exhibited reduced dry matter intake (DMI), milk yield, and yields of fat, protein, and lactose, along with increased water intake and milk urea nitrogen. The use of PF controls indicated that decreased DMI accounted for 45% of the milk-yield reduction, whereas direct HS effects accounted for the remaining reduction. We applied single-nucleus RNA-seq (snRNA-seq) on mammary biopsies to generate cell-resolved HS responses. We identified 14 distinct cell clusters, including epithelial, immune, and stromal populations. Under the TN condition, casein genes (e.g., CSN1S1, CSN2) were broadly expressed across luminal cells but were attenuated under HS, whereas luminal alveolar cells showed relative upregulation. Heat shock protein genes were strongly induced by HS, primarily in epithelial clusters. Gene-set enrichment analyses revealed increased ribosomal activities across HS-responsive clusters and enrichment of protein folding and metabolic pathways in luminal alveolar cells, suggesting elevated proteostasis demands under stress. Pseudotime analysis positioned luminal cells along a progenitor-to-secretory trajectory under TN, accompanied by increased casein gene expression, whereas under HS, mature luminal cells shifted toward a homeostasis regulatory state. Cell-cell communication analysis demonstrated HS-induced remodeling of interepithelial signaling, including altered ERBB4-mediated signaling from luminal hormone-sensing to alveolar lineages. Finally, transcription factor activity profiling highlighted cell type-specific HS-activated regulators and their downstream target genes. ConclusionsTogether, this cell type-resolved atlas delineates how HS alters bovine mammary epithelial function, developmental state, and intercellular crosstalk. These findings point to proteostasis pressure, disrupted signaling pathways, and rewired regulatory networks as mechanistic contributors to reduced lactational performance under HS, offering insights for improving heat resilience in dairy cattle.

genomics↗

bioRxiv2026

Non-enzymatic ABHD6 interacts with Akt-FoxO1 axis to regulate selective hepatic insulin resistance

The enzymatic function of ABHD6 on insulin secretion and insulin resistance is well documented. However, its non-enzymatic function, especially its effects on selective hepatic insulin resistance and metabolic dysfunction-associated steatotic liver disease (MASLD) is completely unexplored. ABHD6 is elevated under conditions of diet-induced obesity and aging. To define the role of ABHD6 in liver physiology, we generated liver-specific ABHD6 knockout mice, as well as liver specific overexpression of native and enzymatic inactive mutant ABHD6 mouse models. We demonstrated that ABHD6 is an unidentified regulator of selective hepatic insulin resistance and contributes to MASLD and liver fibrosis. Furthermore, we found that non-enzymatic ABHD6, rather than its enzymatic form, contributes to this regulation. Mechanistically, we found that ABHD6 translocated into the nucleus and interacted with Akt/FoxO1 axis to regulate its function. In addition, knockdown of FoxO1 in primary hepatocytes or overexpression of constitutively active mutant FoxO1 by AAV approach could completely abolish the effects of ABHD6 on glucose tolerance and gluconeogenesis. Our study reveals an entirely different mechanism underlying selective hepatic insulin resistance that involves a previously unknown non-enzymatic function of ABHD6. This study opens an avenue for the development of a novel class of ABHD6 inhibitors to treat MASLD and liver fibrosis. HighlightsO_LIABHD6 expression in the liver is increased with obesity and aging. C_LIO_LIABHD6 manipulation affects selective hepatic insulin resistance, MASLD and liver fibrosis. C_LIO_LINon-enzymatic ABHD6 interacts with Akt/FoxO1 axis to regulate FoxO1 transcriptional activity. C_LIO_LIThe effects of ABHD6 on glucose tolerance and hepatic gluconeogenesis are completely dependent on FoxO1 activity. C_LI

physiology↗