Biology subjects

Kong, F.

Publications and source records attributed to Kong, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Targeting the NuRD Component, CHD4, Impairs Foxp3+ Treg Cell Production and Function and Promotes Anti-Tumor Immunity

Little is known about why Foxp3 regulatory T (Treg) cells require at least three HDAC1/HDAC2-containing chromatin-remodeling complexes (NuRD, Sin3 and CoREST), or whether selective disruption of these complexes can be exploited to enhance antitumor immunity. Here, we investigated the role of chromodomain helicase DNA- binding protein 4 (CHD4), the ATP-dependent remodeling subunit of the NuRD complex, in Treg biology. Conditional deletion of Chd4 in Foxp3 Tregs resulted in severe systemic autoimmunity and early lethality, accompanied by reduced Foxp3 expression, impaired Treg suppressive function, and loss of Treg lineage stability. Transcriptomic analyses demonstrated that CHD4 deficiency closely phenocopied Hdac2 deletion, whereas quantitative proteomic analyses revealed that CHD4 assembles into highly conserved NuRD complexes in both Treg and conventional CD4 T cells. These findings indicate that the selective dependence of Tregs on CHD4 does not arise from the formation of lineage-specific protein complexes but rather from the unique epigenetic program maintained by CHD4-containing chromatin-remodeling complexes that is required for Treg differentiation and stability. Using a novel cellular target-engagement platform, we identified CH41, a potent small-molecule inhibitor of CHD4 that recapitulated the effects of genetic CHD4 ablation on Treg function. Pharmacological inhibition of CHD4 impaired intratumoral Treg accumulation and function and significantly inhibited the growth of lung and hepatocellular carcinomas in immunocompetent, but not immunodeficient, mice, without inducing systemic autoimmunity. Collectively, our findings identify CHD4 as a critical epigenetic regulator of Treg lineage stability and establish pharmacological targeting of the CHD4/NuRD axis as a promising strategy to selectively disrupt tumor-associated Tregs and enhance antitumor immunity.

cancer biology↗

bioRxiv2026

Intra-individual variation in leaf microbiota matches within-crown environmental heterogeneity and promotes tree performance

Plant-associated microbial communities exhibit pronounced specificity across biological and spatial scales. While the patterns and accompanied functions have been well documented across and within plant species, the functional importance of intra-individual variation remains underexplored. Particularly in trees that experience strong environmental gradients within single crowns, stratum-specific microbiota may significantly contribute to plant performance. We experimentally tested whether variation in microbiota within the crown of Quercus robur is related to host performance. In mesocosm experiments, we transferred microbial communities derived from sun and shade leaves to germ-reduced clonal individuals of the same species and applied UV radiation simulating conditions that matched or mismatched the origin of the microbial inoculum (environmental matching). Our results demonstrate that matching microbiota-environment combinations increased plant performance compared to mismatching combinations. We infer that pronounced intra-individual variation of leaf-associated microbial communities not only reflects environmental heterogeneity along canopy strata but is functionally relevant for the plant host.

ecology↗

bioRxiv2025

Personalized biventricular mechanics and sensitivity to model morphology

AO_SCPLOWBSTRACTC_SCPLOWWe present a computational framework for constructing patient-specific models of cardiac mechanics based on standard clinical data, including electrocardiogram (ECG), cuff blood pressure, and electrocardiography-gated computed tomography angiography (CTA) imaging. The model is coupled to a closed-loop lumped parameter network (LPN) circulatory model and incorporates rule-based fiber architecture, as well as spatially varying epicardial boundary conditions to approximate surrounding tissue support. Model parameters are personalized through a multistep procedure that sequentially tunes circulatory dynamics, passive mechanics, and active contraction. The resulting personalized BiV model closely matches clinical pressure and volume measurements and reasonably agrees with image-based myocardial deformation. To assess the impact of anatomical model choice, we compare the BiV model to two commonly-used simplifications: a truncated BiV (t-BiV) model cut at the basal plane and a left ventricle-only (LV) model. For these models, we also evaluate their sensitivity to plausible variations in boundary conditions and contractile strength. With all other inputs held fixed, the LV model exhibits similar global pressure/volume behavior, despite moderate differences in regional deformation. In contrast, the t-BiV model produces substantial differences in both global function and local myocardial mechanics. These results suggest that while LV-only models may be sufficient for biomechanical studies, truncation at the basal plane strongly impacts model outputs and should be used with caution.

bioengineering↗

bioRxiv2025

MFAP5 Drives Elastic Fiber Disorganization to Promote Pulmonary Fibrosis

BACKGROUNDElastic fibers (EF) disorganization contributes to increased tissue stiffness and impaired lung function in pulmonary fibrosis (PF). However, the complex structural features of EF are difficult to capture using conventional histology. Moreover, the molecular mechanisms governing EF homeostasis during fibrosis remain poorly understood. METHODSA high-dimensional Elastic Fiber Algorithm (EFA) was developed to digitally quantify EF structural features in PF. Gene variation-rate analysis was performed to identify candidate regulators of EF homeostasis. Fibroblast-specific and pathological fibroblast-specific MFAP5 knockout mice were generated to assess the role of MFAP5 in PF rodent models. Bulk RNA sequencing was employed to investigate MFAP5-mediated fibroblast activation and signaling pathways. RESULTSEFA revealed profound EF disorganization in fibrotic lungs, capturing various architectural alterations. Gene variation-rate analysis identified MFAP5 as a candidate regulator of EF homeostasis, with upregulated expression in PF patients and mouse models. Fibroblast-specific deletion of MFAP5 significantly attenuated fibrosis, restored EF architecture, reduced collagen deposition, and improved pulmonary function in PF mouse models. MFAP5-positive fibroblasts displayed a dynamic shift toward pathological states during PF progression. Mechanistically, MFAP5 promoted fibroblast activation and ECM production via v{beta}3 integrin-mediated TGF{beta} signaling. CONCLUSIONSMFAP5 is a key orchestrator of EF remodeling and fibroblast activation in PF. Targeting MFAP5 restores EF homeostasis, reduces fibrotic severity, and represents a potential therapeutic strategy for PF.

molecular biology↗

bioRxiv2025

TXNDC5 Governs Extracellular Matrix Homeostasis in Pulmonary Hypertension

BACKGROUNDPulmonary hypertension (PH) is characterized by vascular remodeling without effective treatments. Thioredoxin domain containing 5 (TXNDC5), a member of the protein disulfide isomerases (PDI) family, regulates protein folding and vascular homeostasis, yet its role in PH remains unknown. METHODSLabel-free proteomics profiled protein expression in lungs from PH patients. TXNDC5 was analyzed by single-cell RNA sequencing, immunofluorescence, and Western blot. Endothelial gain- and loss-of-function approaches were applied in Sugen5416/hypoxia (SuHx)-induced rodent PH models. RNA sequencing and protein-protein interaction analysis were used to investigate underlying mechanisms. RESULTSTXNDC5 was significantly upregulated in the lungs of patients with PH and in experimental PH models, with predominant localization in endothelial cells (ECs) of remodeled distal pulmonary arteries. Endothelial TXNDC5 overexpression exacerbated pulmonary vascular remodeling, elevated right ventricular systolic pressure, and promoted right ventricular hypertrophy, whereas global or endothelial-specific TXNDC5 deficiency conferred protection against SuHx-induced PH. Hypoxia-induced factor (HIF)-2 transcriptionally activated TXNDC5 to drive PH development. Single-cell RNA sequencing identified a distinct subpopulation characterized by TXNDC5high extracellular matrix (ECM)-producing ECs. Bulk RNA sequencing combined with protein-protein interaction analysis revealed that TXNDC5 regulated ECM homeostasis through biglycan (BGN). Pharmacological inhibition of TXNDC5 with E64FC26 and endothelial-targeted TXNDC5 gene therapy significantly attenuated PH severity in rats. CONCLUSIONSOur study reveals that TXNDC5 is a main modulator to regulate ECM homeostasis and may serve as a promising target for the treatment of PH.

molecular biology↗

bioRxiv2025

Proline transporters balance the salicylic acid-mediated trade-off between regeneration and immunity in plants

A robust immune response and regenerative capacity are both essential for survival after injury. In plants, salicylic acid (SA) is essential for activating immunity but simultaneously suppresses regenerative capacity. The mechanisms coordinating the trade-off between immunity and regeneration remain poorly understood. Here, we identify proline transporters as key regulators of this balance. Mutations in two wound-induced proline transporters, ProT2 and ProT3, rescued exogenous proline-induced suppression of de novo root regeneration (DNRR) and enhanced DNRR. ProTs are required for SA-mediated suppression of regeneration, without affecting SA-dependent defense responses. Mechanistically, a ProT3-CPK1 complex modulates the dynamics of wound-induced reactive oxygen species (ROS), sustaining a ROS level that restricts DNRR after wounding. Notably, pharmacological inhibition of proline transport rescued SA-mediated suppression of regeneration and enhanced regeneration across multiple plant species. These findings establish proline transporter as a regulatory hub integrating stress-induced proline metabolism, SA signaling, and ROS homeostasis to balance immunity and regeneration, and highlight chemical inhibition of proline transport as a strategy to improve crop regeneration under biotic stresses without compromising disease resistance.

plant biology↗

bioRxiv2025

The AltR transcription factor responds to plant thiosulfinates to regulate gene expression in a bacterial pathogen of onion.

Pantoea ananatis, the causative agent of onion center rot, encounters potent antimicrobial thiosulfinates, volatile organosulfur compounds released from damaged Allium tissues. The allicin tolerance (alt) gene cluster allows P. ananatis to overcome this chemical barrier. We demonstrate that AltR, a TetR-family transcriptional repressor, specifically regulates expression of the alt cluster and thus thiosulfinate tolerance in vitro and fitness in vivo. We identified a putative AltR binding box both in the altR promoter and elsewhere in the alt cluster, show that AltR-mediated repression is relieved in response to thiosulfinates. Using cysteine to serine substitutions, we demonstrate that AltR Cys100 is essential for thiosulfinate-responsive de-repression, while other AltR cysteine residues tune responsivity. Strains expressing AltR alleles with reduced thiosulfinate responsivity have reduced fitness in planta. Our findings uncover a regulatory mechanism by which a plant antimicrobial secondary metabolite acts as an environmental cue to modulate bacterial gene expression, enabling pathogen survival and virulence.

microbiology↗

bioRxiv2025

BioinAI: a general bioinformatic framework for multi-level transcriptomic data analysis using multiple semi-agents

Clinical and biological insights from large-scale transcriptomic data are often limited by technical variability and analytical complexity. Here, we introduce BioinAI, a general bioinformatic framework designed for multi-level transcriptomic data analysis. As part of the BioinAI framework, two algorithms named DeepAdvancer and stNiche were developed to improve data integration and analytical efficiency. DeepAdvancer leverages a class-aware adversarial autoencoder to reconstruct gene-expression profiles from 49,738 samples across 131 skin conditions. These profiles revealed a conserved inflammatory axis and a transcriptomic continuum which link diverse diseases through shared immune responses and structural programs. stNiche leverages spatial graph networks and symmetry-aware matching to identify functional cellular niches and reveals microstructural alterations across development, homeostasis, and disease. For instance, it identified a fibroblast-immune niche surrounding hair follicles in healthy skin, which disappears in pathological states. In addition, BioinAI provides a user-friendly online analysis platform powered by multiple semi-agents (www.bioinai.com), significantly facilitating the extraction of biological insights to advance scientific research.

bioinformatics↗

bioRxiv2025

Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1

Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin-resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). Here we present cryo-EM structures of Arabidopsis thaliana AUX1 in the IAA-free and IAA-bound states. AUX1 exists as a monomer that contains 11 transmembrane helixes (TMs). TMs 1-5 and 6-10 constitute the two halves of a classic LeuT-fold, and TM11 interacts with both halves at the interface. In the IAA-bound state, IAA is specifically recognized in a central pocket formed by TM1, TM3, TM6, and TM8. In the presence of IAA, TM1 and TM6 undergo marked conformational changes that are critical for IAA transport. His249 stands out to be a key residue for substrate uptake and release. Our structures reveal the molecular basis for AUX1-mediated IAA binding and transport. SignificanceAuxin-resistant 1 (AUX1) is a major auxin influx transporter, playing critical regulatory roles in callus growth, vascular patterning, leaf phyllotactic patterning, root aerial development, and apical hook formation. However, its working mechanism remains unclear. In this study, we report two structures of IAA-bound and IAA-free AUX1, elucidating its substrate recognition mechanism and proposing a potential substrate release model for AUX1. These findings offer important insights into the molecular mechanisms of AUX1-mediated IAA binding and transport, and lay the foundation for future structure-based functional studies of the AUX1/LAX family and the application of auxin analogs in agriculture.

molecular biology↗

bioRxiv2025

A pan-positive allosteric modulator that mediates sustainable GPCR activation

Approximately 1/3 of all clinical drugs exert their therapeutic effects by modulating the activity of G protein-coupled receptors (GPCRs). Thus, there is a constant interest in finding novel ways to modulate GPCR activity. In this work, through a newly established Survival Pressure Selection (SPS) method for high-throughput screening of GPCR agonists, we discover that atazanavir functions as an agonist for GPR119. Further studies suggest that atazanavir is capable of activating a number of Family A GPCRs, including the {beta}1 adrenergic receptor ({beta}1AR), the {beta}2 adrenergic receptor ({beta}2AR) and the opoioid receptor (OR). Cryo-EM structures reveal that atazanavir binds to an allosteric pocket near TM6/7 in both GPR119 and the {beta}1AR. Pharmacological studies suggest that atazanavir mediates non-canonical signaling of Family A GPCRs. During this process, G protein and {beta}-arrestin are spatially close, but {beta}-arrestin forms a complex with the receptor and G protein instead of desensitizing G protein signaling, thus resulting in sustained G protein signaling. The work expands the signal transduction modes and pharmacological properties of allosteric modulators for GPCRs and provides a general starting point for developing therapeutics targeting this allosteric site.

biochemistry↗

bioRxiv2025

A GPCR-G protein-β-arrestin megacomplex induced by an allosteric modulator

GPCRs signal through both G protein pathways and {beta}-arrestin pathways. Previous work suggests that {beta}-arrestins bind to GPCRs through different modes, including core engagement and tail engagement. Core engagement competes with G proteins and terminates G protein signaling, while tail engagement can coexist with G proteins, mediating sustained intracellular activation of the receptor - a process dependent on the high affinity between {beta}-arrestin and the phosphorylated C-terminus of the receptor. In this study, we determined the structure of a GPCR - G protein - {beta}-arrestin-1 complex stabilized by an allosteric modulator. The compound, atazanavir, acts like molecular glue to anchor {beta}-arrestin-1 to the receptors TM6 and TM7 regions. This pendulum binding mode is structurally compatible with simultaneous G protein binding. We further demonstrate that the atazanavir-mediated {beta}-arrestin recruitment does not require the receptors C-terminal region. This work illustrates a novel paradigm of GPCR-G protein-{beta}-arrestin1 megacomplex assembly and opens up new avenues for modulating GPCR function.

biochemistry↗

bioRxiv2025

The Proteomics Landscape of Pattern Triggered Immunity in the Arabidopsis Leaf Apoplast

The apoplast is a critical interface in plant-pathogen interactions particularly in the context of pattern-triggered immunity (PTI), which is initiated by recognition of microbe-associated molecular patterns (PAMPs). Our study characterizes the proteomic profile of the Arabidopsis apoplast during PTI induced by flg22, a 22 amino acid bacterial flagellin epitope, to elucidate the output of PTI. Apoplastic washing fluid (AWF) was extracted with minimal cytoplasmic contamination for LC-MS/MS analysis. We observed consistent identification of PTI enriched and depleted peptides across replicates with limited correlation between total protein abundance and transcript abundance. We observed topological bias in peptide recovery of receptor-like kinases with peptides predominantly recovered from their ectodomains. Notably, tetraspanin 8, an exosome marker, was enriched in PTI samples. We additionally confirmed increased concentrations of exosomes during PTI. This study enhances our understanding of the proteomic changes in the apoplast during plant immune responses and lays the groundwork for future investigations into the molecular mechanisms of plant defense under recognition of pathogen molecular patterns.

plant biology↗

bioRxiv2025

IQI: Individualized Quantitative trait loci (QTL) Index

There is currently no standard efficient method to precisely detecting and characterizing the difference of quantitative trait loci (QTL) effect among groups and/or populations at individual level. The main reason is that the traditional global regression based QTL analyses can only derive an overall effect of genetic variants on the quantitative trait in a specific group. It is a big challenge to obtain the individual-level QTL effect, which is necessary for accurate testing and precise characterization. Here, we first proposed an individualized QTL index (IQI) that represents the degree of regulation between genetic variants and the trait for each individual. Based on IQI, Differential QTL (DQ) analysis framework was presented to accurately detect the case-control differences in more detail. In addition, IQI can be a new feature/biomarker applied to various accurate bioinformatics analysis, such as differential analysis, disease prediction, and survival analysis. Overall, IQI affords a new perspective on pathogenic mechanisms and will facilitate the study of genetic regulation more detailedly and precisely.

bioinformatics↗

bioRxiv2024

The effects of L-carnitine and fructose in improved Ham's F10 on sperm culture in idiopathic severe asthenospermia within 24h

Trial designTo study the effects of L-carnitine and fructose on semen parameters of severe asthenospermia patients by sperm culturing in vitro within 24h. We optimized the energy composition and antioxidant substances of sperm culture medium in vitro (based on Hams F10 culture medium) by orthogonal test for preparing high quality culture medium. Sperms of 60 patients with idiopathic severe asthenospermia were collected, and cultured in vitro within 24h, by Hams F10 culture medium added to different concentrations of L-carnitine and fructose and culture temperature, whose effects on sperm motility were observed to determine which is the most appropriate concentration and temperature. MethodsFor determining the appropriate concentration of L-carnitine and fructose and the suitable culture temperature in Hams F10 culture medium, the orthogonal experiments were carried out to optimize above three factors, which had great influence on sperm viability, survival rate, deformity rate and DNA fragmentation index (DFI). ResultsThe final concentration of L-carnitine and fructose was determined in terms of initial tests to assess the effects of different concentrations (4, 8, 12, and 16 mg/ml L-carnitine and 0.125, 0.250, 0.375, and 0.50 mg/ml fructose) on sperm viability and motility in culture. During the operation of processing and culturing sperms in vitro within 24h, orthogonal test showed that sperm viability was better at the final concentration of 8 mg/ml L-carnitine and 0.375 mg/mL fructose in improved Hams F10 culture medium at 36.5 . ConclusionIdiopathic severe asthenospermia sperm can be effectively improved by the modified Hams F10 culture medium of the final concentration of 8 mg/ml L- carnitine and 0.375 mg/mL fructose in at 36.5 within 24h, which has shown better culture effect and is superior to Hams F10 basic medium.

biochemistry↗

bioRxiv2024

Post-flowering photoperiod sensitivity of soybean in pod-setting responses

The development of soybean (Glycine max) is regulated by photoperiod, with genes related to photoperiod sensitivity primarily focused on flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to photoperiod. Long-day (LD) conditions tend to extend the time from flowering to pod formation (R1 to R3 stage), and the first wave of flowers tends to fall off. Additionally, photoperiod affects pistil morphology; under short-day (SD) conditions, the stigma has a curved hook-like structure that facilitates better interaction with the filaments when pollen is released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex genes, showed no difference in pod formation time under LD or SD conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, ROS signals, and the application of sucrose solution in vitro might influence floral organ abscission. HighlightPhotoperiod sensitivity after flowering affects the pod-setting time in soybean.

plant biology↗

bioRxiv2024

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

In wheat (Triticum aestivum L.), yield component traits (YCTs) are the most important yield traits. Only several genes for YCTs have been originally cloned. The efficient cloning of genes for YCTs directly from wheat remains a challenge. Here, we proposed a strategy for cloning genes from quantitative trait loci (QTLs) by sequencing of recombinant inbred lines (RILs) (QTL-Seq-RIL). Using the TN18 x LM6 RIL population as an example, we identified 138 candidate unigenes (CUGs) for YCTs from 77 stable QTLs. The average of CUGs per QTL was 1.8, which enabled us to confirm the CUGs directly. We have confirmed seven CUGs, TaIFABPL, TaDdRp, TaRLK, TaTD, TaTFC3, TaKMT and TaSPL17, via the CRISPR/Cas9 system. Of these, six genes were found firstly to regulate YCTs in crops except for TaSPL17. Five CUGs (include TaSPL17) for which orthologous genes have been cloned previously with the same or similar agronomic functions. It is to say, 11 CUGs were preliminarily validated using a single RIL population. QTL-Seq-RIL provides an efficient method for rapid gene cloning using existing RIL populations.

plant biology↗

bioRxiv2023

Digital twinning of cardiac electrophysiology for congenital heart disease

In recent years, blending mechanistic knowledge with machine learning has had a major impact in digital healthcare. In this work, we introduce a computational pipeline to build certified digital replicas of cardiac electrophysiology in pediatric patients with congenital heart disease. We construct the patient-specific geometry by means of semi-automatic segmentation and meshing tools. We generate a dataset of electrophysiology simulations covering cell-to-organ level model parameters and utilizing rigorous mathematical models based on differential equations. We previously proposed Branched Latent Neural Maps (BLNMs) as an accurate and efficient means to recapitulate complex physical processes in a neural network. Here, we employ BLNMs to encode the parametrized temporal dynamics of in silico 12-lead electrocardiograms (ECGs). BLNMs act as a geometry-specific surrogate model of cardiac function for fast and robust parameter estimation to match clinical ECGs in pediatric patients. Identifiability and trustworthiness of calibrated model parameters are assessed by sensitivity analysis and uncertainty quantification.

bioengineering↗

bioRxiv2023

Isolating Small Extracellular Vesicles from Small Volumes of Blood Plasma using size exclusion chromatography and density gradient ultracentrifugation: A Comparative Study

Small extracellular vesicles (sEVs) are heterogeneous biological vesicles released by cells under both physiological and pathological conditions. Due to their potential as valuable diagnostic and prognostic biomarkers in human blood, there is a pressing need to develop effective methods for isolating high-purity sEVs from the complex milieu of blood plasma, which contains abundant plasma proteins and lipoproteins. Size exclusion chromatography (SEC) and density gradient ultracentrifugation (DGUC) are two commonly employed isolation techniques that have shown promise in addressing this challenge. In this study, we aimed to determine the optimal combination and sequence of SEC and DGUC for isolating sEVs from small plasma volumes, in order to enhance both the efficiency and purity of the resulting isolates. To achieve this, we compared sEV isolation using two combinations: SEC-DGUC and DGUC-SEC, from unit volumes of 500 l plasma. Both protocols successfully isolated high-purity sEVs; however, the SEC-DGUC combination yielded higher sEV protein and RNA content. We further characterized the isolated sEVs obtained from the SEC-DGUC protocol using flow cytometry and mass spectrometry to assess their quality and purity. In conclusion, the optimized SEC-DGUC protocol is efficient, highly reproducible, and well-suited for isolating high-purity sEVs from small blood volumes.

bioengineering↗