Biology subjects

Dong, X.

Publications and source records attributed to Dong, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Three-hinge gyri link individualized folding topology to cortical and superficial white-matter diffusion organization

Individual differences in cortical folding are a hallmark of human brain anatomy, but what this variability reflects in the underlying tissue remains unclear. Three-hinge gyri (3HGs), where three gyral crests converge, provide an individualized higher-order folding landmark for probing this relationship. Using 7T diffusion MRI in six postmortem hemispheres, we found lower mean, axial, and radial diffusivity and higher fractional anisotropy at 3HGs than at matched gyral crowns, with the principal tensor pattern replicated in 414 age-matched in vivo adults. Diffusivity differences extended across the cortical ribbon, whereas anisotropy- and fiber-related differences strengthened toward and beneath the white surface. Ex vivo, diffusion measures also varied with gyral-skeleton degree, and streamlines sampled beneath 3HGs preferentially reached other 3HGs. These findings link individualized folding topology to cortical and superficial white-matter diffusion-inferred tissue properties, providing tissue-level context for understanding the microstructural correlates of individual folding variation.

neuroscience↗

bioRxiv2026

Biologically inspired alignment reveals distributed and directionally asymmetric correspondence between rat and human cortices

Rodent models enable causal interrogation of brain circuits, but translating their systems-level organization to humans requires correspondence beyond one-to-one anatomical homology. Guided by the view that cortical areas are characterized by their relationships within distributed functional networks, we developed BrainMapping, a biologically inspired framework for aligning rat and human cortex using resting-state functional MRI. The framework combined a shared representation with optimal transport to derive probabilistic, bidirectional maps. These alignments revealed distributed, many-to-many correspondences that generalized to held-out subjects and preserved functional connectivity architecture, cortical gradients, and graph topology. Organizational preservation was directionally asymmetric. Human-to-rat mapping preserved organization more uniformly across rat cortical systems, whereas rat-to-human mapping showed stronger preservation in human association-related networks than in primary sensory and motor networks. The maps recovered literature-consistent default-mode and salience-system correspondences and generated testable non-canonical predictions. These findings provide a framework for expressing rat functional organization in human functional-network coordinates.

neuroscience↗

bioRxiv2026

Linoleic Acid-Lyso PG Axis promoting lipid droplet-mitochondria tethering by stabilizing Noncanonically Mitochondrial PPAR β/δ to Ameliorate Microglial Dysfunction in subarachnoid hemorrhage

Background Microglial lipid handling and mitochondrial failure contribute to brain injury after subarachnoid hemorrhage (SAH), but the lipid signals coupling these processes remain unclear. We investigated whether linoleic acid (LA) restores microglial homeostasis through lysophosphatidylglycerol 16:0 (LPG[16:0]) and peroxisome proliferator-activated receptor-{delta} (PPAR{delta}). Methods Cerebrospinal fluid metabolomics included 30 patients with aneurysmal SAH and 10 control participants. Mechanisms were examined in a blood-injection mouse model and hemoglobin-exposed primary mouse microglia using targeted lipidomics, RNA sequencing, mitochondrial and phagocytosis assays, pharmacological perturbation, fractionation, coimmunoprecipitation, thermal shift analysis, and structural modeling. Behavioral outcomes were evaluated by open-field, Y-maze, and Morris water-maze testing. Results; CSF LA was higher in SAH and discriminated the groups within this cohort (area under the curve, 0.9967 [95% CI, 0.9859-1.000]; P<0.001). LA attenuated inflammatory activation and restored phagocytosis, mitochondrial membrane potential, respiration, and ATP production in hemoglobin-exposed microglia. LA restored PLA2G15-associated LPG(16:0), which phenocopied these effects. Transcriptomic and inhibitor analyses identified PPAR{delta} as a downstream effector. LPG(16:0) increased PPAR{delta} stability, and fractionation and protease protection identified a PPAR{delta} pool on the cytosolic face of the outer mitochondrial membrane. PPAR{delta} associated with PLIN2 and CPT1A, promoted lipid droplet-mitochondria apposition, and supported fatty acid oxidation. In mice, LA reduced neuroinflammatory injury and partially improved anxiety-related behavior and spatial memory.

neuroscience↗

bioRxiv2026

Ion-Pair-Free Capillary HILIC-MS for Sensitive Nucleic Acid Analysis and RNA Modification Mapping

Mass spectrometry (MS)-based nucleic acid analysis provides direct chemical evidence for oligonucleotide sequence, composition, and modifications. However, oligonucleotide LC-MS analysis commonly relies on ion-pairing reversed-phase liquid chromatography (IP-RPLC). Although IP-RPLC provides strong retention and high-resolution separation of highly charged nucleic acids, ion-pairing reagents can contaminate LC-MS systems, suppress electrospray ionization, require extensive system cleaning, and limit the use of high-end MS platforms that are primarily dedicated to proteomics or metabolomics. Here, we developed and evaluated an ion-pair-free capillary hydrophilic interaction liquid chromatography mass spectrometry (capillary HILIC-MS) workflow for RNA modification mapping. To enable robust analysis of biologically relevant samples, we optimized sample preparation, high-organic loading conditions, chromatographic parameters, and MS source settings to overcome key challenges associated with capillary HILIC, including limited sample volume, solvent compatibility, and solvent breakthrough during injection. The optimized capillary HILIC-MS method provided effective separation of oligonucleotides below 30 nt and enabled sensitive detection of RNA modifications in the populations of tRNAs and rRNAs in biological samples. Importantly, the ion-pair-free workflow also allowed switching between nucleic acid analysis and proteomics on the same LC-MS platform without the need for extensive system decontamination. Together, this workflow provides a sensitive, robust, and MS-compatible approach for nucleic acid analysis, expanding the utility of high-end LC-MS systems for both therapeutic oligonucleotide characterization and biological RNA modification profiling.

biochemistry↗

bioRxiv2026

Glioblastoma Invasion Remodels Neural Circuits and Drives Persistent GABAergic Dysfunction in Human Brain Organoids

BackgroundGlioblastoma (GBM) is characterized by neurological dysfunction caused by tumor cells that interact with and alter neuronal circuits. However, the specific neuronal populations and molecular mechanisms most susceptible to GBM invasion remain poorly understood. MethodsWe created a human tumor-brain organoid model by combining U87 glioblastoma cells with iPSC-derived neural organoids. This system enabled us to study tumor-neural interactions over an extended period under standard temozolomide (TMZ) treatment. We used single-cell transcriptomics to monitor cell-type-specific responses. ResultsOur model recapitulated the diffuse infiltration observed in patients, leading to extensive structural remodeling and a profound loss of neuronal and glial populations. Single-cell analysis revealed that TMZ suppressed proliferative and biosynthetic programs but enriched for stress-responsive, mesenchymal-like, and therapy-adapted tumor states. Notably, GABAergic neurons exhibited the greatest transcriptional vulnerability, with [~]36% (7,499 of 20,659) of genes differentially expressed. Invasion triggered endoplasmic reticulum stress and shut down metabolic, respiratory, synaptic, and ion-homeostatic pathways. Crucially, SLC12A5-expressing GABAergic neurons plummeted from 31% to 12%, accompanied by a sharp decline in KCC2 protein expression. While TMZ partially rescued neuronal metabolic and electron transport chain function, it failed to restore SLC12A5/KCC2 expression or inhibitory signaling. ConclusionsGBM invasion leads to a continued imbalance of chloride in GABAergic networks, and this disruption remains even after undergoing tumor-targeted chemotherapy. This human iPSC-derived tumor-brain organoid platform provides a reliable and scalable system for studying complex tumor-neural interactions and exploring therapeutic approaches that aim to eliminate the tumor while preserving neural function.

cancer biology↗

bioRxiv2026

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

The liver is organized into tightly regulated zones with distinct metabolic functions but zonation erodes with age. Cellular senescence contributes to aging and liver diseases, however, its impact on aging biology is ill-defined. As part of The Cellular Senescence Network Consortium, we used multiple spatial transcriptomics approaches (GeoMx, Visium, CosMx) with snRNA-seq to profile senescence signatures, zonation markers, and metabolic pathways in livers from wild-type (WT) mice of multiple ages. We observed a loss of canonical zone signatures in aged mouse livers characterized by "expansion" of midlobular (zone 2) marker gene expression, accompanied by diminished expression of zone 3 marker genes by middle-age (18 months), indicative of loss of cell identity. Multiple analytic approaches identified distinct age-, zone- and sex-specific senescence signatures, which were significantly associated with zonation markers changes. This was recapitulated in Ercc1 mutant models of accelerated senescence, supporting a causal role of senescent cells in liver aging. A "no-zone" hepatocyte-like cluster expanded with age and with the strongest Senescence-Associated Secretory Phenotype (SASP) profile. Gene expression profiles from senescent hepatocytes implicate decreased WNT signaling and increased BMP as contributing to age-related loss of zonation. Together, these data elucidate the role of senescent cells in driving aging biology in non-diseased liver through disruption of cell:cell signaling and the loss of metabolic and cell identity gene expression necessary for hepatocyte function.

cell biology↗

bioRxiv2026

Genomic repeats for single-cell molecular recording

Genomic recording enables transient biological signals to be indelibly captured through DNA alterations, creating a permanent record of cellular history retrievable by sequencing. However, current methods are limited by scarce writing space, typically targeting only one or a few amenable genomic sites and requiring large cell populations for signal reconstruction. Here, we establish Repeats for Genomic Recording (RGRs): sequences with up to 400 copies targetable by a single CRISPR guide RNA, readable with a common primer pair, and predicted to have minimal functional impact. We demonstrate that RGRs enable both signal deconvolution in single cells and high-resolution recording in cell populations. Individual RGR sites exhibit distinct response kinetics; thus, combining them improves recording resolution beyond what redundancy alone provides, analogous to diversity reception in wireless communication. We develop a computational pipeline for systematic RGR identification, revealing 15,000 to 25,000 candidates per species across human, mouse, and zebrafish, thereby markedly expanding recording capacity and enabling cell-type-specific applications. Finally, we validate RGRs in live mice by recording long-term immediate early gene activity across the brain following epilepsy induction. This work establishes genomic repeats as a high-capacity platform for single-cell molecular recording in vivo.

synthetic biology↗

bioRxiv2026

Pathogen context reshapes antimicrobial peptide generation

Antimicrobial peptides are a promising source of new anti-infective agents, but their discovery is limited by a practical bottleneck: selecting a small set of candidates to synthesize and test for a specific pathogen. Existing peptide generators can expand antimicrobial-like sequence space, but most leave pathogen specificity to predictors or filters after generation. Here, we use AMPHORA, a pathogen-conditioned sequence-structure generator, to build antimicrobial peptide libraries shaped by target context. AMPHORA couples a short-peptide representation model to latent-flow generation conditioned on target class, genome-derived features and strain-description text. In matched, partial and shuffled controls, pathogen context redirected generated peptide pools beyond broad activity labels, with the strongest effects when genome and text conditions were combined. Counterfactual generation from the same initial noise showed that strain descriptions primarily changed amino-acid choices, whereas genome-derived features contributed more strongly to predicted structural properties. Across species, AMPHORA produced target-dependent enrichment, and matched bacterial context shifted APEX-predicted potency-score distributions compared with class-only generation. The generated peptides remained diverse, novel and peptide-like by sequence and predicted-structure analyses. Collectively, our results establish pathogen context as an active design signal for antimicrobial peptide generation and provide a target-aware route to pre-synthesis library design.

bioinformatics↗

bioRxiv2026

An engineered IdeS variant with enhanced activity and performance for IgG degradation

IgG-degrading enzymes have emerged as innovative therapeutic agents for treating conditions driven by pathogenic antibodies. Here, we used structure-guided rational design to engineer IdeSM33, a double mutant (K167R/D226E) of the IgG-specific bacterial protease IdeS from Streptococcus pyogenes, with improved catalytic efficiency. Biolayer interferometry revealed a fourfold increase in binding affinity relative to wild-type IdeS (IdeSWT). This enhancement is likely attributable to mutations that strengthen hydrogen bonding at the enzyme-IgG Fc interface. In vitro, IdeSM33 has higher performance than IdeSWT in cleaving serum IgG. In vivo studies in rabbits demonstrated that IdeSM33 effectively depleted circulating IgG and showed better performance at a dose of 0.005 mg/kg than the IdeSWT. Although doses greater than 0.2 mg/kg demonstrated higher plasma concentrations of IdeS and a larger AUClast, they did not show a significant enhancement in the pharmacodynamics of IgG degradation. Importantly, a single dose of IdeSM33 (0.2 mg/kg) potently degraded binding and neutralizing antibodies against AAV9 within 1-2 days and restored hepatic AAV9 transduction in pre-immunized animals. Together, these findings highlight IdeSM33 as a potent and safe engineered enzyme with therapeutic potential for autoimmune disorders, transplant rejection, and overcoming pre-existing humoral immunity in gene therapy.

bioengineering↗

bioRxiv2026

Defining Pseudo-Haplotype Analysis Reveals Multi-Gene Genetic Pattern Across BAF Chromatin Remodeling Complexes

BRG1-associated factor (BAF) is a crucial chromatin remodeling complex. Variants in genes encoding BAF complex components cause human diseases, including cancers and developmental disorders. However, the genetic diversity and variant co-occurrence patterns within BAF genes remain incompletely understood. It is feasible, though largely untested, that rare patterns of common variations could alter function similarly to rare deleterious variants. Further, there is no modern census of how often individual people simultaneously carry multiple rare and common variations, nor means for genomics practitioners to assess their combined effects. Approaches are needed to characterize complete sequences from individual samples. In this study, we introduce a pseudo-haplotype analysis (PHA) framework, combining multiple protein-coding sequence variants, observed concurrently within individual samples, into discrete BAF patterns. In this cohort, 78.44% of pseudo-haplotype (PH) copies carry at least one BAF coding variation. Among these, 56.18% contain at least two distinct variants, and 32.39% contain three or more, indicating a substantial burden of multi-variant configurations across individuals. Notably, 25.30% of unique PHs are observed only once, highlighting a considerable proportion of people who are affected by rare or private combinations of genetic variations. We identify multiple significant (FDR < 0.05) co-occurrence combinations across global populations. These findings underscore the importance of considering population-specific genetic structures, and complete individual variant configurations when investigating disease associations and genetic mechanisms. Our approach provides a generalizable framework for characterizing multi-variant architectures within chromatin remodeling genes at a population scale, with potential applications in elucidating disease etiology and advancing precision medicine.

bioinformatics↗

bioRxiv2026

Defining the molecular tolerance-to-damage landscape of SMARCA4 helicase genetic alterations

Evaluating the impact of genomic variation is essential for identifying underlying mechanistic causes of human diseases. The spectrum of neurodevelopmental disorders is driven by diverse genetic alterations with genes like SMARCA4 being prototypical examples. There have been significant hurdles to implementing the protein-specific and mechanism-informed variation effect predictors that are anticipated to have the highest yield of mechanistic information. Yet, there is a pressing need, for example, within SMARCA4 where 98% of the 2780 reported variants lack a disposition and remain of uncertain significance (VUS). Further, the field has yet to identify each variants specific molecular mechanism, which will inform targeted therapeutic development strategies. In this study we developed a mechanistic structure-informed helicase-specific variant effect predictor by leveraging diverse information with state-specific calculations. Our approach has 100% recall of pathogenic variants while classifying 87.23% of VUS into damaging (55.74%, n=262) versus tolerated effects (31.49%, n=148), including those with conflicting interpretations. This analysis reveals significant enrichment of integrated functional metrics, such as conservation and solvent exposure, that parallel allele frequences in health populations, and emphasizes the robustness of the method. Thus, we have demonstrated a novel approach for the development of mechanism-informed protein-specific interpretation of human genetic information.

genetics↗

bioRxiv2026

ARID1B damaging variants from more than one million genomes, cause human diseases by impairing protein-protein interactions, stability, and regulation

ARID1B is the most frequently de novo altered gene across a spectrum of human neurodevelopmental disorders and cancers. We found 1,456 missense variants in ARID1Bs C-terminal domains, 94% of which are clinically uninterpreted and 59% of which are observed in human disorders and cancers. Using integrative modeling of ARID1B cBAF and DNA bound structures, we calculate how these variants impact key functional sites, structural stability, and topological features, finding that 617 variants clearly impair ARID1Bs interactions within BAF, interactions with DNA, fold stability, or post-translational regulation. Our study enables scalable and precise variant interpretation by illuminating the molecular mechanisms by which missense variants damage ARID1B function, with commonalities across malignancies and congenital anomalies mutually informing therapeutic developments.

genetics↗

bioRxiv2026

Spatiotemporal Patterns and Structural Substrates of Individual Functional Variability in Youth

Youth is a period of emerging individuality and extensive neural remodeling, yet how functional brain individuality is organized across development remains unclear. Prior work has often conflated variability in functional topography with variability in functional connectivity, highlighting the need to examine them separately to better understand how functional individuality relates to brain structure and cognition. Here, using individualized functional parcellation in two large multimodal developmental cohorts (total N = 1211), we separately quantified variability in individualized functional parcellation (vIFP) and in functional connectivity (vFC). Both forms of variability were organized along the sensorimotor-association axis and were greatest in the association cortex. During development, vIFP increased significantly with age at both regional and whole-brain level, whereas vFC showed regionally specific age effects but no significant whole-brain increase. Both trajectories exhibited a common mid-adolescent inflection (14-16 years), marking a window of accelerated functional individualization. Despite shared spatial and temporal organization, vIFP and vFC showed dissociable associations with brain structure and cognition. vIFP was more strongly coupled to structural variability, whereas vFC was more strongly associated with cognitive variability. These findings reveal convergent and divergent developmental principles of topographic and connectional functional variability, highlighting their complementary roles in structural constraints and cognitive specialization.

neuroscience↗

bioRxiv2026

The role of the neutrophil receptor Mrgpra2 in the formation of itch in atopic dermatitis

Atopic dermatitis (AD), or eczema, is estimated to affect more than 30 million people in the United States, with over 6 million have moderate or severe disease. Chronic pruritus is a common symptom and is one of most difficult to manage. Even though itch is a major component in the pathology of AD, the biological underpinnings are not fully understood. In the present manuscript we identify a role for the neutrophil receptor, Mrgpra2, in the development of AD hyperplasia and chronic itch in the mouse. The role of Mrgprs in the context of itch have provided a huge step in our understanding of pruritus and have led to the development of novel therapeutics. Here we provide new evidence for the involvement of Mrgpra2 in the development of AD. Here we show that genetic deletion of Mrgpra2 significantly reduces scratching behaviors, transepidermal water loss, epidermal thickening, and Tslp expression in AD.

immunology↗

bioRxiv2026

Ca2+-activated CKL3 phosphorylates nucleoporin 58 to reprogram nuclear transport and execute effector-triggered immunity

Recognition of pathogen effectors by nucleotide-binding leucine-rich repeat receptors (NLRs) activates effector-triggered immunity (ETI) in plants through resistosome formation, which generates a sustained cytosolic Ca2+ influx and ultimately leads to programmed cell death (PCD) at infection sites and resistance. However, the mechanisms linking Ca2+ influx to ETI execution remains a major knowledge gap. Using TurboID proximity labeling with the central transport channel nucleoporin 58 (Nup58) as a probe, we show that, instead of deregulation, ETI induction restricts general nuclear trafficking while selectively enhancing nuclear import of defense-related proteins. This switch is driven by elevated cytosolic Ca2+, which binds to the conserved Asp-149 in CASEIN KINASE 1-LIKE 3 (CKL3), promoting its interaction with and phosphorylation of Nup58 at Ser-149, thereby altering nuclear pore selectivity. This study identifies CKL3 and Nup58 as key regulators of ETI by establishing a mechanistic link from resistosome-mediated Ca2+ influx to nuclear transport reprogramming and immune execution.

plant biology↗

bioRxiv2026

An Itch Receptor Drives Melanoma

Mas-Related GPCR X4 (MRGPRX4) is a sensory neuron-restricted receptor for cholestatic itch. Here, we identify MRGPRX4 as an unexpected melanoma driver. MRGPRX4 is upregulated in melanoma and is confined to invasive, neural-crest-like and pre-EMT states associated with dedifferentiation and therapy resistance. Ectopic MRGPRX4 expression in mouse melanocytes drives 100% penetrant, highly metastatic melanoma, demonstrating oncogenic behavior. MRGPRX4 promotes melanoma cell proliferation and invasion through basal, ligand-independent, PI3K-AKT-MAPK activation. Multi-omics links MRGPRX4 expression to a mesenchymal/neural-crest-like program that defines a distinct invasive MRGPRX4? niche. Comparing transcptomics of MRGPRX4-driven tumors shows a broad overlap with BRAF/NRAS-driven tumors; however, the MRGPRX4 model also enriches an ECM-rich, invasive neural crest-like melanoma state. MRGPRX4 further remodels the tumor microenvironment toward an immunosuppressive, checkpoint-high state enriched in suppressive myeloid cells. Pharmacologic MRGPRX4 inhibition suppresses basal signaling and limits melanoma growth and invasion. In sum, melanoma exploits MRGPRX4 to acquire an invasive and immunosuppressive phenotype, nominating this somatosensory GPCR as a promising therapeutic target.

cancer biology↗

bioRxiv2026

A red-emitting, genetically encoded indicator for two-photon voltage recording in vivo

Genetically encoded voltage indicators (GEVIs) enable minimally invasive, cell-type-specific optical measurements of neuronal membrane potential with millisecond temporal resolution. Red-shifted GEVIs are especially advantageous because they permit spectral multiplexing with complementary sensors and enable all-optical circuit interrogation in combination with blue-light-activated opsins. Despite these advantages, existing red GEVIs remain poorly suited for in vivo use due to limited performance under two-photon (2P) excitation, the predominant modality for deep-tissue imaging. Here, we introduce VADER1, a red GEVI that overcomes this limitation and enables reliable spike detection in vivo under 2P illumination. Under 2P excitation, VADER1 supports extended voltage imaging with both random-access and resonant-scanning microscopy, enables recordings from neurons as deep as cortical layer 5, and allows dual-color imaging with calcium indicators. By filling a critical spectral gap, VADER1 enables integrated optical measurements of fast electrical activity alongside other neural signals and establishes a foundation for two-photon all-optical electrophysiology.

neuroscience↗

bioRxiv2026

Integrated physiological markers of drought tolerance and yield stability in cotton under deficit irrigation

The selection of drought-resistant cotton genotypes with high productivity and improved water-use efficiency is an increasingly pressing challenge in arid and semi-arid cotton-growing regions, where climate variability is intensifying water scarcity. This study evaluated two widely cultivated cotton varieties in Texas, NG 4190 B3XF and ST 4990 B3XF, under full and moderate deficit irrigation to identify physiological markers associated with contrasting yield responses under water limitation. A comprehensive set of physiological traits was assessed, including plant water status, leaf gas exchange, carbon isotope composition ({delta}13C), total nitrogen and C/N ratio, chlorophyll fluorescence, light and CO{square} response curves, and canopy temperature. While no yield differences were observed under full irrigation, moderate water deficit resulted in stable seed and fiber yield in NG 4190, but significant yield reduction in ST 4990. Yield differences were not explained by instantaneous gas exchange or direct biochemical limitations of photosynthesis, but rather by integrated physiological behavior over time. Key discriminating traits included midday relative water content (RWC), photosynthetic light-response parameters ( and Pm), stomatal optimization parameter (g{square}), and {delta}13C. NG 4190 exhibited higher RWC, more negative {delta}13C, and higher g{square} values, indicating a less conservative stomatal regulation strategy that supported sustained carbon assimilation under water stress. These findings provide insight into the physiological mechanisms underlying cotton performance under drought and support the use of integrated physiological markers for the selection of resilient genotypes in water-limited environments.

plant biology↗