Biology subjects

Sun, K.

Publications and source records attributed to Sun, K..

At least 19 recordsLinked to original sources

bioRxiv2026

OPA1-dependent mitochondrial remodeling coordinates TCR signaling and metabolic adaptation during iNKT cell differentiation

Invariant natural killer T (iNKT) cells require mitochondrial metabolism for terminal effector development. We found iNKT cells express elevated levels of proteins regulating mitochondrial membrane dynamics, and identified Opa1, but not Drp1, as selectively required for iNKT cell differentiation. OPA1 deficiency disrupted mitochondrial cristae organization, reduced mitochondrial membrane potential, increased mitochondrial mass, and altered calcium homeostasis in iNKT cells. Bulk and single-cell transcriptomic analyses revealed impaired TCR-responsive gene expression, activation of mitochondrial stress adaptation and integrated stress response, enhanced glycolysis, and retention of immature differentiation features. SCENITH analysis demonstrated increased glycolytic dependence; LDHA became required in Opa1-deficient iNKT cells while dispensable for normal iNKT development, indicating compensatory glycolytic adaptation. EGTA in thymic organ culture partially restored NKT1 marker expression in Opa1-deficient cells. Co-deletion of Drp1 improved mitochondrial morphology, TCR signaling, stress and metabolic adaptation, and partially rescued iNKT cell differentiation, demonstrating that balanced mitochondrial dynamics coordinate mitochondrial function and terminal effector development.

immunology↗

bioRxiv2026

Topology-Based Query Framework for Longitudinal Omics Trajectories

1 Abstract 1.1 Background Many longitudinal omics studies contain only a small number of repeated measurements collected before, during, or after an intervention. Existing approaches, including mixed-effects models and generalized additive models, estimate temporal effects but do not generally provide a discrete representation of trajectory topology that can be queried directly across experimental groups. 1.2 Methods We developed LongOmicsTraj, an open-source R package for topology-based representation and querying of short longitudinal omics trajectories. The framework encodes the direction of change between adjacent visits as up, down, or flat, with the ordered sequence defining an Ordinal Trajectory State (OTS). LongOmicsTraj operates downstream of trajectory estimation and can therefore be applied to empirical summaries or model-derived visit-level estimates, including those from linear mixed-effects models, generalized additive models, and polynomial regression, following a maSigPro-style time-course formulation [1]. OTS labels provide a common representation for topology-based querying, cross-group comparison, and evaluation of higherlevel representations such as trajectory clusters. We evaluated the framework using controlled simulations and bronchial biopsy transcriptomic data from the GLUCOLD corticosteroid intervention study (GEO accession GSE36221), measured at baseline, 6 months, and 30 months. The biological analysis compared continued inhaled corticosteroid (ICS) treatment, ICS withdrawal after 6 months, and placebo. 1.3 Results In simulations, LongOmicsTraj recovered predefined stable, monotonic, transient, rebound, and oscillatory trajectories with high accuracy when longitudinal signal was sufficiently clear, with performance declining under high-noise conditions and depending partly on the upstream estimator. In GLUCOLD, comparator-aware topology queries reduced 20,358 measured transcripts to 168 genes showing a corticosteroid response that was maintained during continued treatment, reversed following withdrawal, and was not reproduced under placebo. The selected genes included established corticosteroid-response genes and were enriched for immune-cell migration, chemotaxis, cell adhesion, and extracellular-matrix organisation. Topology-aware evaluation of FlexMix trajectory clusters additionally revealed substantial within-cluster temporal heterogeneity, with topology purities of approximately 46% to 60%. 1.4 Conclusions LongOmicsTraj provides a compact, directly queryable representation of temporal direction and order in short longitudinal omics studies. It complements existing longitudinal estimation and clustering methods by making trajectory structure explicit, enabling structured cross-group queries and quantification of temporal heterogeneity within trajectory clusters.

bioinformatics↗

bioRxiv2026

A Time-Resolved Single-Cell Atlas Reveals Infection-Status, Age-, and Sex-Dependent Immune Responses Drive Viral Disease Severity

The majority of mortality during viral infections occurs in older males; however, underlying mechanisms by which age and sex shape antiviral immunity and pathological inflammatory responses remain incompletely understood. Here, we performed time-resolved single-cell RNA sequencing across 16 conditions spanning age, sex, and four stages of influenza infection in mice, generating a high-resolution atlas. Aged mice demonstrate delayed antiviral and inflammatory responses in multiple myeloid cells, impairing viral clearance, which delays recovery. Similarly, endothelial cells from aging mice show prolonged inflammatory and antiviral gene signatures. Altered gene signatures in immune and endothelial cells result in a shift in endothelial-immune interactions in the aged lung. Further, the infection status of the cell is a major driver of transcriptional state, with infected myeloid cells exhibiting broad upregulation of genes, including interferon-stimulated, inflammatory, complement, and oxidative stress-related genes. To assess whether these age-associated transcriptional patterns are conserved in humans, we examined BAL cells obtained from healthy individuals and COVID-19 patients, and found that immune cells from aged COVID-19 patients had elevated antiviral and pro-inflammatory gene expression compared to cells from young patients. Our analyses of sex differences identified that multiple myeloid cell types in aged male mice, but not in young male mice, show persistent inflammatory responses at later stages of infection, a likely mechanism contributing to elevated mortality in older males. These data reveal how infection status of the cell, age, and sex interact to drive persistent inflammation and impaired resolution, providing a foundational resource for designing age- and sex-specific therapeutic strategies.

immunology↗

bioRxiv2026

CAFE: A Co-folding Approach for Fragment Exploration of Allosteric and Cryptic Binding Sites

Co-folding models hold immense potential for allosteric drug discovery, but have been severely hampered by their systematic bias toward orthosteric ligand binding. While fragment screening has been proposed for allosteric binding site discovery, we show that co-folding models still suffer from memorization in which chemically simpler fragments also default to canonical orthosteric binding sites. To overcome these limitations, we introduce CAFE (Co-folding Approach for Fragment Exploration), a co-folding protocol that uses competitive orthosteric blockers to divert fragments into non-canonical sites as illustrated here with the Boltz-2 co-folding model. Using ADP as an orthosteric blocker for the kinase family, we find CAFE substantially increases the allosteric binding site exploration for fragments, with notably strong absolute binding free energies that match or exceed those of known crystallographic poses, without post-hoc refinement of the Boltz-2 prediction. We also show that CAFE identifies cryptic binding pockets undetected by conventional pocket prediction tools, some of which are more thermodynamically favorable than the allosteric or orthosteric pockets. To demonstrate generality, we apply CAFE using Type I orthosteric blockers for kinase proteins, known orthosteric ligands as blockers for non-kinase proteins in the RAS-MAPK signaling pathway, and for virtual screening campaigns using fragment libraries for new fragments that selectively engage allosteric and cryptic binding sites. CAFE establishes orthosteric blocking and fragment screening as a training-free, inference-time protocol that helps overcome some of the limitations of current co-folding models while elevating their great promise for allosteric and cryptic binding drug discovery.

molecular biology↗

bioRxiv2026

Placental invasion mismatch underlines pregnancy disorders and cancers

Mammalian placentas vary dramatically in invasiveness, parallel aggressive cancers, and are dysregulated in pregnancy disorders, yet whether they share regulatory architecture remains unclear. We investigated single-cell transcriptomes of the maternal-fetal interface across nine mammals spanning all major placental morphotypes and integrated it with thirteen cancers and five pregnancy complications. A conserved cellular framework is deployed through three discrete regulatory programs: a cancer-like program in hemochorials, endothelial-cooperation program in endotheliochorials, and collagen-rich invasion-suppressing program in epitheliochorials. Aggressive cancers selectively converge on hemochorial program, and we functionally validated share invasion regulators including the VGLL3-TEAD1 interaction and APOE. Pregnancy disorders are partially, mismatched deployments of these programs; placental APOE knockdown in mice phenocopies preeclampsia with concurrent collapse of both M1/M2 macrophage programs. These findings unify placental diversity, cancer convergence, and obstetric disorders under a regulatory-mismatch principle, whereby evolved placental invasion programs becomes pathological when deployed outside their evolutionary context.

evolutionary biology↗

bioRxiv2026

Competing effects modulate the rate of poly(A) RNA deadenylation in a biomolecular condensate

The unique solvent milieu found in biomolecular condensates can control cellular enzymatic reactions and shift reaction kinetics by modulating reactant concentrations, structural dynamics, and enzyme activities. Here we explore the interplay of multiple regulatory factors within a condensate to control poly(A) RNA deadenylation, the first and rate-limiting step in mRNA turnover. The deadenylase CNOT7, a subunit of the CCR4-NOT deadenylation complex, localizes to cytoplasmic RNA granules and shows increased degradation activity in vitro in condensates formed by the C-terminal low complexity disordered region of CAPRIN1, a component of RNA granules. We use a combination of enzymatic assays, kinetic modeling, microscopy, Nuclear Magnetic Resonance (NMR) spectroscopy, and molecular dynamics simulations to deconvolute and define the components that underlie this enhancement. We found that enzyme and RNA are concentrated in condensates relative to buffer, which increases CNOT7 activity, while the equilibrium between CNOT7s active and inactive states remains unchanged. The concentration-dependent increase in enzymatic rates is counterbalanced by a substantial decrease in the enzymes catalytic efficiency, likely due to slower diffusion of CNOT7 and RNA within the condensates, which lessens the probability of enzyme-substrate complex formation. Molecular dynamics simulations reveal CNOT7-CAPRIN1 interactions that rely on conserved CAPRIN1 sequence features, hinting at an evolutionarily conserved role for CAPRIN1 condensation. With this quantitative kinetic analysis, we describe the multifaceted mechanism behind regulation of CNOT7 deadenylation by a condensate environment. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/736149v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@51cd47org.highwire.dtl.DTLVardef@7bfccaorg.highwire.dtl.DTLVardef@114375org.highwire.dtl.DTLVardef@163f4ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Effect of CSFV on Differential Genes of Histone Lactylation at H3K18 in the PI3K-AKT Signaling Pathway

Classical swine fever (CSF) is a highly contagious disease caused by Classical swine fever virus (CSFV), posing a serious threat to the global swine industry. This study aimed to investigate the effect of CSFV on differential genes of histone lactylation at the H3K18 site in the PI3K-AKT signaling pathway. The site with the most significant change in histone lactylation antibody level was screened by Western blot. Omics analysis was performed using CUT&Tag technology to identify differential genes in the PI3K-AKT pathway between the CSFV-infected group and the mock group, followed by validation using RT-qPCR. Functional analysis of significantly differential proteins was conducted, and the protein expression level of THBS4 was detected by Western blot. The results showed that after CSFV infection of 3D4/21 cells, the H3K18la site exhibited the most significant difference in antibody level. A total of 8,859 differential genes at the H3K18la site were identified by CUT&Tag analysis, including 6,349 up-regulated genes and 2,510 down-regulated genes. Further focusing on the PI3K-AKT signaling pathway, 10 differential genes were identified, comprising 6 up-regulated genes and 4 down-regulated genes. Compared with the control group, the mRNA expression levels of CD19, LAMA1, PDGFRA, BDNF, ANGPT4, and THBS4 were up-regulated in the CSFV-infected group, while FOXO3 and NRTN were down-regulated. Western blot results showed that the protein expression level of THBS4 increased after CSFV infection. These findings lay an important foundation for understanding the molecular mechanisms regulating viral replication and immune evasion, and have significant scientific implications and potential application value.

microbiology↗

bioRxiv2026

LinkLlama: Enabling Large Language Model for Chemically Reasonable Linker Design

Fragment-based drug discovery (FBDD) relies heavily on the design of chemically viable linkers to connect fragments binding to different pocket regions into potent lead molecules. While recent generative models have advanced spatial fragment linking, they frequently produce linkers characterized by high torsional strain and non-drug-like motifs. In this work, we present LinkLlama, a fine-tuned Meta Llama 3 model that bridges the gap between text-based generation and 3D spatial awareness. By accepting natural language prompts that specify geometric constraints, such as distances and angles, alongside physicochemical targets like Lipinskis rules and rotatable bond limits, LinkLlama generates highly tailored molecules for the input fragments. Leveraging the inherent chemical grammar captured through supervised fine-tuning on a curated corpus of drug-like molecules from ChEMBL, the model prioritizes chemical validity without requiring complex reinforcement learning loops. Benchmarking on the ZINC and HiQBind datasets demonstrates that LinkLlama maintains competitive geometric fidelity compared to strictly 3D-aware models while achieving a two-fold increase in the proportion of chemically reasonable designs. This rising success rate, jumping from 35% to over 80%, is defined by strict adherence to comprehensive structural filters including PAINS, non-drug-like chemical patterns and complex ring systems. We further illustrate the models versatility through prospective case studies in novel small-molecule scaffold hopping and PROTAC linker design, validated via molecular docking and molecular dynamics simulations against known crystal poses. Ultimately, LinkLlama demonstrates that large language models can overcome the structural pitfalls of purely 3D-generative methods, offering a highly controllable and chemically robust framework to accelerate linker design and drug discovery in general.

bioinformatics↗

bioRxiv2026

KinConfBench: A Curated Benchmark for Cofolding Models on Kinase Conformational States

Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2,225 high-quality human kinase chains to evaluate the ability of three state-of-the-art cofolding models--Boltz-2, Chai-1, and Protenix--to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site does not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all three cofolding models achieve [~]65-75% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent "apo-drift" in which all three cofolding models predominately predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

biophysics↗

bioRxiv2026

DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery

Large language models (LLMs) are in the ascendancy for research in drug discovery, offering unprecedented opportunities to reshape drug research by accelerating hypothesis generation, optimizing candidate prioritization, and enabling more scalable and cost-effective drug discovery pipelines. However there is currently a lack of objective assessments of LLM performance to ascertain their advantages and limitations over traditional drug discovery platforms. To tackle this emergent problem, we have developed DrugPlayGround, a framework to evaluate and benchmark LLM performance for generating meaningful text-based descriptions of physiochemical drug characteristics, drug synergism, drug-protein interactions, and the physiological response to perturbations introduced by drug molecules. Moreover, DrugPlayGround is designed to work with domain experts to provide detailed explanations for justifying the predictions of LLMs, thereby testing LLMs for chemical and biological reasoning capabilities to push their greater use at the frontier of drug discovery at all of its stages.

bioinformatics↗

bioRxiv2026

Network Toxicology, Molecular Docking, and Molecular Dynamics Simulations Reveal the Mechanism of Tetrabromobisphenol A in Bullous Pemphigoid.

Bullous pemphigoid (BP) is an autoimmune blistering disease with a growing incidence, and environmental factors are receiving increasing attention. Tetrabromobisphenol A (TBBPA), a widely used brominated flame retardant, is a significant environmental pollutant. However, the molecular mechanisms by which TBBPA contributes to BP pathogenesis remain unclear. This study integrated network toxicology, molecular docking, and molecular dynamics (MD) simulations to systematically investigate the molecular mechanisms of TBBPA-induced BP. Using network toxicology, we identified 797 potential targets of TBBPA and 446 BP-related targets. A Venn diagram analysis revealed 48 common targets. Protein-protein interaction (PPI) network and topological analyses further identified five core hub targets: TNF, CXCL8, MMP9, ICAM1, and ITGB1. Gene enrichment analysis indicated that these targets were significantly enriched in immune-inflammatory pathways, such as leukocyte migration, inflammatory responses, and the IL-17 signaling pathway, as well as in various pathogen infection and cancer-related pathways. Molecular docking revealed that TBBPA stably binds to all five core targets with binding energies [≤] -5 kcal/mol, driven primarily by hydrophobic interactions and {pi}-{pi} stacking. Subsequent MD simulations confirmed that TBBPA complexes with TNF, CXCL8, and MMP9 remained stable throughout the 100 ns simulation. The overall protein structures remained compact, and the ligands were effectively encapsulated within the binding pockets, forming stable networks of hydrogen bonds and hydrophobic interactions. In conclusion, this study, for the first time, proposes a systematic molecular framework using integrated computational biology. Our findings suggest that the environmental pollutant TBBPA may act as a potential risk factor in BP pathogenesis by targeting core proteins (TNF, CXCL8, and MMP9). These interactions potentially disrupt critical signaling pathways related to immune inflammation, cell migration, and tissue remodeling. This study offers a novel mechanistic hypothesis regarding environmental chemical exposure in autoimmune blistering diseases, although further experimental validation is required. HighlightsO_LINetwork toxicology identified 48 common targets linking Tetrabromobisphenol A(TBBPA) exposure to Bullous Pemphigoid (BP). C_LIO_LIFive core targets (TNF, CXCL8, MMP9, ICAM1, ITGB1) were screened as potential mediators. C_LIO_LITBBPA stably binds to TNF, CXCL8, and MMP9 with binding energies [≤] -5 kcal/mol. C_LIO_LIMolecular dynamics simulations confirm stable binding and structural integrity of complexes. C_LIO_LIThis study provides a mechanistic framework for TBBPA as an environmental risk factor in BP. C_LI

pharmacology and toxicology↗

bioRxiv2026

Cost-saving, trading, and internalization of externality: three economic strategies underlying amino acid archetypes of human metabolic enzymes

Amino acid composition of proteome reflects principles of metabolic resource allocation. While amino acids with higher biosynthetic costs are used less frequently in unicellular organisms, whether this rule extends to complex multicellular life remains elusive. Here we show that amino acid composition of human metabolic enzymes does not follow a simple cost-minimizing mode but instead segregate into four distinct amino-acid composition modules each associated with specific metabolic functions, a phenomenon we term emergence of amino acid archetypes (AArchetypes). By comparing ten phylogenetically diverse species, we find that AArchetypes emerge only in multicellular organisms, indicating a fundamental shift in proteome-level economics. We further demonstrate that these AArchetypes correspond to three distinct economic strategies: cost-saving in young, fast-evolving enzymes; trading in conserved central carbon metabolic enzymes whose amino-acid compositions match that of dietary intake; and internalization of negative externalities in liquid-liquid phase separation (LLPS)-prone, intrinsically disordered proteins through elevated biosynthetic costs of LLPS-associated amino acids. Together, these results reveal that multicellular proteomes are governed not by a single cost-minimization principle, but by a multi-layered economic system that integrates production, exchange, and regulation.

systems biology↗

bioRxiv2026

TRU-PE: A Universal, Trackable Prime Editor Toolkit for Robust Single- and Multi-Locus Genome Engineering

Prime editing (PE) holds immense promise for precise genome editing, but its wider adoption is constrained by large payloads and inefficient delivery in recalcitrant cell types. Here, we present TRU-PE (Trackable, Robust, and Universal Prime Editor), a toolkit that overcomes these barriers via a split-vector architecture coupled with fluorescence-guided enrichment. This design ensures stoichiometric component expression, yielding marked improvements in editing efficiency and accelerated workflows compatible with both plasmid and viral delivery. By integrating a polycistronic hCtRNA-sgRNA/pegRNA array, the derivative TRU-MPE system enables simultaneous editing of up to ten genomic loci. Furthermore, it enhances the performance of evolved PE editors, allows flexible vector stoichiometry and inspires novel editing reporters. Leveraging these capabilities, we successfully generated a combinatorial human iPSC-based platform for GATA2 deficiency, which accurately recapitulates genotype-specific hematopoietic defects. TRU-PE thus provides a user-friendly, scalable framework for robust single- and multi-locus genome engineering, accelerating functional genomics and therapeutic development.

genetics↗

bioRxiv2026

In Vivo Surface Reconstruction of Three Signal-defined Intracortical Layers Using 5T 3D FLAIR MR Imaging

BackgroundIn vivo whole-cortex quantification of intracortical signal-defined layering on the routinely acquired structural MRI remains limited. PurposeTo develop and validate an automated framework to reconstruct three intracortical signal-defined layers from 5T three-dimensional (3D) T2-weighted fluid-attenuated inversion recovery (FLAIR) and to characterize whole-cortex morphometrics and regional organization across a prespecified cortical organizational framework. Materials and MethodsIn this retrospective study, 5T 3D FLAIR images were acquired between February and July 2024. Brain Multi-Layer Surface Reconstruction (BrainMLSR) reconstructed three intracortical signal-defined layers, and derived intracortical layer thickness and surface area measures and ratios. Performance was evaluated against manual annotations and assessed for test-retest repeatability (n=13) and cross-site feasibility (n=2). Paired two-tailed t-tests and linear mixed-effects models were used. A proof-of-concept analysis compared Heschls gyrus ratios between 19 patients with temporal lobe epilepsy (TLE) and 19 age-matched healthy controls (HC). ResultsA total of 270 healthy participants (mean age, 54.4{+/-}14.5 years; 146 men) were included. Agreement with manual hypointense-layer annotations was high (Dice, 0.960{+/-}0.003), and was similar in the cross-site dataset (Dice, 0.954{+/-}0.009). In the test-retest dataset, average symmetric surface distance was less than 0.1 mm. Across prespecified systems, thickness and surface area ratios varied by region; within an auditory-perisylvian hierarchy, banksSTS showed a localized turning point with an increased hyperintense layer thickness ratio and decreased hypointense layer thickness ratio, accompanied by inflections in surface area ratios (P < .001). In bilateral Heschls gyrus, hypointense (left: 0.619{+/-}0.262 vs 0.881{+/-}0.102; right: 0.607{+/-}0.310 vs 0.907{+/-}0.141 mm) and isointense (left: 0.406{+/-}0.225 vs 0.678{+/-}0.128; right: 0.478{+/-}0.232 vs 0.808{+/-}0.176 mm) layer thicknesses were lower in TLE than in HC (all P<.001). ConclusionBrainMLSR enabled accurate and repeatable in vivo reconstruction of three intracortical signal-defined layers from a single 5T 3D T2-weighted FLAIR acquisition and provided whole-cortex boundary-based morphometry with interpretable regional organization. Key ResultsO_LIIn this retrospective study of 270 participants, Brain Multi-Layer Surface Reconstruction (BrainMLSR) showed high agreement with hypointense-layer annotations (Dice, 0.960{+/-}0.003). C_LIO_LIWithin an auditory-perisylvian hierarchy, the hyperintense-layer thickness ratio peaked (0.620{+/-}0.003) and the hypointense-layer ratio was the lowest (0.156{+/-}0.002) in the bank of the superior temporal sulcus (P < .001). C_LIO_LIIn a proof-of-concept analysis, patients with temporal lobe epilepsy (vs healthy controls) had higher hyperintense-layer thicknesses ratio in the left hemisphere (0.523{+/-}0.085 vs 0.417{+/-}0.036, P<.001). C_LI SummaryAn automated multiple-layer surface reconstruction framework (BrainMLSR), applied to 5T 3D T2-weighted FLAIR images, produced reproducible whole-cortex, signal-defined laminar morphometry and demonstrated coherent patterns across prespecified cortical organizational framework.

neuroscience↗

bioRxiv2026

Reduced late endosome/lysosome function promotes SLE through chronic PI3k activity and SHP-1/SHIP-1 defects

Degradation of cellular waste from phagocytosis, endocytosis and autophagy occurs through hydrolases that become activated during acidification of late endosomes and lysosomes (LELs). In a cross-sectional study we show diminished LEL acidification and the accumulation of surface-bound nucleosome on monocytes, dendritic cells, and B cells from SLE patients. Diminished acidification and exocytosis of undegraded IgG-ICs is evident in active, but not inactive disease. This is supported by our murine study where LEL acidification is diminished, promoting exocytosis and the accumulation of cell surface IgG-immune complexes. Mechanistically, LEL dysfunction is induced by chronic PI3k activation in lupus-prone MRL/lpr mice. We also show that on a non-autoimmune C57BL/6 background, deficiency in SHP-1 and inhibition of SHIP-1 activity is sufficient to recapitulate LEL dysfunction found in MRL/lpr mice. Non-acidic LELs are evident in 67% of patients, and associate with SLEDAI arthritis, rash, and nephritis. The high frequency of LEL dysfunction in SLE suggests it could serve as a biomarker identifying a specific disease endotype.

immunology↗

bioRxiv2026

Site-specific integration of transposon via engineered piggyBac transposase

The precise integration of large DNA fragments into the human genome holds significant therapeutic potential. Here, we demonstrate that combining engineered piggyBac (PB) transposase with CRISPR/Cas9 enables targeted integration of PB transposons into specified genomic loci. Our engineered PB transposase (PBase) retains high excision activity while substantially reducing endogenous integration activity. In the developed Cas9-PBase fusion system, PBase excises the transposon to generate linear DNA fragments, while Cas9 introduces site-specific double-strand breaks (DSBs), facilitating insertion of the excised fragment at the target locus. The optimized tool achieves 6.1-7.3 kb transposon integration at multiple genomic sites with 10-15% efficiency, demonstrating 60-80% targeted integration specificity. As a proof of concept, we inserted a 7.1 kb transposon encoding three genes into the {beta}2M locus of human induced pluripotent stem cells (iPSCs), conferring protection against allogeneic natural killer (NK) cell-mediated cytotoxicity in derived iNK cells. These results establish Cas9-PBase as a precise and programmable platform for large DNA sequence insertion with potential clinical applications.

genetics↗

bioRxiv2026

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

In humans, the TBC1D3 gene family is thought to play a critical role in the expansion of the frontal cortex by promoting neuronal proliferation during brain development. This gene family shows some of the greatest structural heterozygosity ([~]97%) with haplotype copy numbers ranging from 3-39 among different human haplotypes. This raises the question as to how a gene so crucial in the evolutionary expansion of the human frontal cortex can be so variable in the human population. Here, we characterize the regulatory architecture that explains this paradox. We show that 45-96% of TBC1D3 expression is attributable to a single paralog located at the most telomeric position at the edge of a cluster of TBC1D3 genes. We find that its >3-fold higher expression relative to other copies is driven by a 110 kbp segmental duplication that occurred [~]8.9 million years ago, relocating a partial duplication of the puromycin-sensitive aminopeptidase gene (NPEPPS), including its promoter, adjacent to this TBC1D3 locus. Using neurospheres and comparative transcriptomics of iPSC-derived cultures, we show that expression of NPEPPSP1-TBC1D3 increases as neurons differentiate as a result of alternative splicing and differential polyadenylation usage. While the fusion exists in other ape lineages, we show subsequent deletion of the NPEPPSP1 promoter in Gorilla and a separate, lineage-specific duplication in the Pan lineage ablated the production of this fusion product, rendering this position effect of TBC1D3 specific to humans.

genomics↗

bioRxiv2026

River network connectivity and postglacial history shape pollen- and seed-mediated gene flow across riparian populations of Myricaria germanica.

River network connectivity and postglacial history jointly shape patterns of pollen-and seed-mediated gene flow in riparian plants, yet their relative contributions across spatial and temporal scales remain incompletely understood. Myricaria germanica Desv., a pioneer riparian shrub formerly widespread along European rivers but now restricted to fragmented headwaters, provides an ideal model to investigate how river systems structure genetic connectivity. We analysed genetic diversity, population structure, and migration across 2,212 individuals from 67 populations spanning 12 Central European river catchments using 20 nuclear and six chloroplast microsatellite loci. By integrating biparentally inherited nuclear markers with maternally inherited chloroplast markers, we disentangled pollen- and seed-mediated gene flow across historical and contemporary timescales. Both marker systems revealed low genetic diversity, high inbreeding, and strong population differentiation. Nuclear microsatellites showed significant isolation by distance and extensive historical connectivity, with coalescent analyses indicating high pollen-mediated gene flow among catchments and identifying the Rhine and Danube as major long-term sources of migrants. In contrast, chloroplast microsatellites exhibited stronger spatial structure, limited admixture, and highly directional historical seed dispersal, consistent with constrained hydrochorous dispersal routes. Contemporary migration analyses further showed that present-day seed-mediated gene flow is largely confined within catchments, despite widespread historical pollen connectivity. Together, these results support a two-phase postglacial history in M. germanica, involving rare, directional seed dispersal during recolonization followed by prolonged pollen-mediated gene flow. Our findings highlight catchments as biologically meaningful management units and underscore the importance of conserving river network connectivity to preserve both the evolutionary legacy and long-term adaptive potential of riparian populations.

genetics↗