Biology subjects

Xing, K.

Publications and source records attributed to Xing, K..

6 recordsLinked to original sources

bioRxiv2026

Learning from human and chemical languages to predict biological function

Understanding how molecular structure encodes biological function remains a grand challenge in drug discovery. Here, we present PubCheF-1, a deep learning model that predicts literature-derived biological function directly from chemical structure. PubCheF-1 was trained on a dataset linking molecules to labels derived from the scientific articles in which they appear, a strategy that connects disparate compounds through the language used to describe their functionalities. When tasked with identifying inhibitors of {beta}-lactamases, including enzymes considered largely refractory to inhibition, PubCheF-1 predicted structurally distinct compounds that collectively have activity against all {beta}-lactamase classes. Furthermore, hit compounds directly bind the enzyme active site, restore antibiotic efficacy in multidrug-resistant high-priority pathogens, and demonstrate potent activity in animal infection models. Together, these findings establish that machine learning-based prediction of biological function derived from the language of scientific literature allows the identification of bioactive molecules at high hit rates, thereby accelerating therapeutic discovery.

bioinformatics↗

bioRxiv2026

VASP Promotes Aortic Valve Calcification by Interacting with FBLIM1 to Activate the Focal Adhesion Pathway

BackgroundCalcific aortic valve disease (CAVD) is the most prevalent valvular heart disease, yet there is no effective pharmacological therapy to halt or reverse its progression. Focal adhesions (FAs) are dynamic structures that connect cells to the extracellular matrix (ECM), serving not only as mechanical anchors but also as critical signalling hubs that regulate cell adhesion, spreading, migration, differentiation, and mechanotransduction. However, their specific role in CAVD pathogenesis remains largely unknown. MethodsTo identify upregulated hub genes, an integrated analysis of proteomics and RNA sequencing was performed on calcified aortic valves. To investigate functional roles in vitro, we utilized genetic knockdown and overexpression of VASP in valvular interstitial cells (VICs), followed by phenotypic evaluations of osteogenic differentiation, calcification, and elastin (ELN) secretion. Downstream mechanisms were explored using RNA-seq in VASP-overexpressing VICs, alongside pharmacological inhibition of the FA pathway. Finally, protein-protein interaction assays were conducted to map and analyze the physical binding between VASP and the structural domains of FBLIM1. ResultsIntegrated omics analysis identified VASP as a significantly upregulated gene in human calcified aortic valve tissues. Functionally, VASP knockdown inhibited, whereas its overexpression promoted, the osteogenic differentiation of VICs. RNA-seq revealed that VASP overexpression activated the FA pathway, and the pharmacological blockade of this pathway successfully suppressed calcification both in vitro and vivo. Mechanistically, we demonstrated a direct physical interaction between VASP and the third LIM zinc-binding domain of FBLIM1, and knockdown of FBLIM1 effectively reversed the pro-calcific effects of VASP. Finally, VASP overexpression was found to promote the secretion of ELN, which subsequently contributed to the calcification process. ConclusionOur study reveals that the interaction between VASP and FBLIM1 drives CAVD progression by activating the FA pathway, which subsequently leads to excessive ELN secretion. These findings reveal a novel mechanistic pathway and may provide a potential therapeutic target for CAVD intervention. What are the Clinical Implications?We have identified the VASP-FBLIM1-FA-ELN axis as a novel molecular pathway involved in CAVD pathogenesis, greatly enriching our understanding of the complex process of aortic valve calcification. This pathway intricately links cytoskeletal dynamics, cell adhesion signalling, and ECM remodelling, providing a new theoretical framework for pathophysiological research in CAVD. In clinical practice, VASP and its downstream pathway components, particularly FBLIM1 and the FA pathway, may serve as potential biomarkers and therapeutic targets for the early diagnosis and treatment of CAVD. For example, the FA pathway inhibitors PF-573228 and Y15 demonstrated significant anti-calcification effects both in vitro and in vivo, suggesting that targeting this pathway may offer a new nonsurgical intervention strategy for patients with CAVD.

cell biology↗

bioRxiv2025

Decoding neuronal wiring by joint inference of cell identity and synaptic connectivity

Animal behaviors are executed by motor neurons (MNs), which receive information from complex pre-motor neuron (preMN) circuits and output commands to muscles. How motor circuits are established during development remains an important unsolved problem in neuroscience. Here we focus on the development of the motor circuits that control the movements of the adult legs in Drosophila melanogaster. After generating single-cell RNA sequencing (scRNAseq) datasets for leg MNs at multiple time points, we describe the time course of gene expression for multiple gene families. This analysis reveals that transcription factors (TFs) and cell adhesion molecules (CAMs) appear to drive the molecular diversity between individual MNs. In parallel, we introduce ConnectionMiner, a novel computational tool that integrates scRNAseq data with electron microscopy-derived connectomes. ConnectionMiner probabilistically refines ambiguous cell type annotations by leveraging neural wiring patterns, and, in turn, it identifies combinatorial gene expression signatures that correlate with synaptic connectivity strength. Applied to the Drosophila leg motor system, ConnectionMiner yields a comprehensive transcriptional annotation of both MNs and preMNs and uncovers candidate effector gene combinations that likely orchestrate the assembly of neural circuits from preMNs to MNs and ultimately to muscles.

neuroscience↗

bioRxiv2025

Global expression profile of Enterohemorrhagic Escherichia coli O157:H7 in phagosome of murine macrophages

EHEC O157:H7 is responsible for Hemolytic Uremic Syndrome (HUS) outbreaks in humans and its virulence is associated with Shiga toxin (Stx). During the pathogenesis of HUS, EHEC O157:H7 is phagocytized by the intestinal host macrophage into the phagosome. According to our study, a low percentage of phagocytized bacteria survived in the murine macrophage phagosome. To understand the initials mechanisms involved in bacterial persistence, we performed a global profile of bacterial RNAseq analysis in the early phagosome of murine macrophage and in vitro assays with more extreme stress conditions. The defense strategy of an early murine phagosome consisted on producing DNA damage, membrane damage, acid pH and nitric oxide (NO) agents. These hostile conditions triggering the bacterial SOS response, lipid biosynthesis and NO detoxification enzymes in response to DNA damage, membrane damage and nitric oxide agents, respectively. In turn, to survive, the bacterium conserves energy by downregulating flagellar biosynthesis, T3SS and T6SS virulence mechanisms. In contrast, stx2a expression is upregulated. At the same time, it increases the ribosomal levels and amino acid synthesis to react more effectively against adverse conditions. Under more extreme stress conditions, EHEC O157:H7 expressed genes related to an acidic environment (pH 4.5) upregulating the acid stress response pathways AR2-5, whereas, upon high concentrations of hydrogen peroxide, it transcribed higher levels of genes of the OxyR pathway and subsequently hydrogen peroxide oxidative stress-related genes.

microbiology↗

bioRxiv2025

A framework integrating multiscale in-silico modeling and experimental data predicts CD33 CAR-NK cytotoxicity across target cell types

Uncovering mechanisms and predicting tumor cell responses to CAR-NK cytotoxicity is essential for improving therapeutic efficacy. Currently, the complexity of these effector-target interactions and the donor-to-donor variations in NK cell receptor (NKR) repertoire require functional assays to be performed experimentally for each manufactured CAR-NK cell product and target combination. Here, we developed a computational mechanistic multiscale model which considers heterogenous expression of CARs, NKRs, adhesion receptors and their cognate ligands, signal transduction, and NK cell-target cell population kinetics. The model trained with quantitative flow cytometry and in vitro cytotoxicity data accurately predicts the short- and long- term cytotoxicity of CD33CAR-NK cells against leukemia cell lines across multiple CAR designs. Furthermore, using Pareto optimization we explored the effect of CAR proportion and NK cell signaling on the differential cytotoxicity of CD33CAR-NK cells to cancer and healthy cells. This model can be extended to predict CAR-NK cytotoxicity across many antigens and tumor targets.

cancer biology↗

bioRxiv2020

Characterization of miRNAs encoded by Autographa californica nucleopolyhedrovirus

Two Autographa californica nucleopolyhedrovirus (AcMNPV) encoded miRNAs, AcMNPV-miR-1 and -miR-3, have been reported in 2013 and 2019. Here, we present an integrated investigation of AcMNPV-encoded miRNAs. Six candidate miRNAs were predicted through small RNA deep sequencing and bioinformatics, of which, five validated by experiments. Three miRNAs perfectly matched the coding sequence of viral genes. The other two are located in coding sequences of viral genes. Targets in both virus and host were predicted and subsequently tested using dual-luciferase reporter assay. The validated targets were found mainly in AcMNPV, except for the targets of AcMNPV-miR-4, which are all host genes. Based on reporter assays, the five miRNAs predominantly function by down-regulating their targets, though individual target is slightly up-regulated. The transcription start sites of these miRNAs were analyzed. Our results suggest that AcMNPV-encoded miRNAs function as fine modulators of the interactions between host and virus by regulating viral and/or host genes. Author summaryVirus-encoded miRNAs have been widely reported as modulators participating in almost all biological processes. However, among Baculoviridae, which consists of a large family of dsDNA viruses that infect numerous beneficial insects and agricultural pests, only several have been reported encoding miRNAs. To clarify the roles of AcMNPV-encoded miRNAs in host-pathogen interactions, we employed RNA deep sequencing and series of experimental approaches identifying AcMNPV-encoded miRNAs, followed by target validation and function deduction. Among them, AcMNPV-miR-1 and AcMNPV-miR-3 have been reported in 2013 and 2019, respectively. This study reveals the sites of these miRNAs in the genome, both in coding sequences and complements, suggesting diverse functions. These miRNAs target genes in the virus itself and in the host, largely by suppressing expression, with some enhancing it. The transcription initiations of the miRNAs were analyzed. Our results provide some insight into the finely regulated process of baculovirus infection.

microbiology↗