Biology subjects

Xing, G.

Publications and source records attributed to Xing, G..

14 recordsLinked to original sources

bioRxiv2026

Dietary Non-protein Amino Acid AZE as an Environmental Trigger Activating Latent Genetic Susceptibility in C9orf72-ALS Pathogenesis

In human disease, clinical manifestations are not always tightly correlated with genetic etiology. While the GGGGCC (G4C2) hexanucleotide repeat expansion in the C9orf72 gene is the most prevalent genetic cause of ALS, a subset of mutation carriers stays asymptomatic. The molecular mechanisms underlying this incomplete penetrance remain elusive. Here, we identify L-azetidine-2-carboxylic acid (AZE), a dietary non-protein amino acid, as a critical environmental risk factor capable of unmasking latent genetic susceptibility in C9orf72-ALS pathogenesis. Specifically, AZE disrupts the proteasome-mediated clearance of toxic poly-GA dipeptide repeats derived from G4C2 repeats, triggering pronounced neuroinflammation and motor defects in a C9orf72-ALS mouse model that otherwise exhibits minimal phenotypes. Notably, AZE is widely present in the food chain (particularly in sugar beet) and consistently detectable in the postmortem human brains. A significant positive correlation was observed between sugar beet consumption and the incidence of sporadic C9-ALS cases in European nations. Critically, dietary intake of sugar beet juice is sufficient to activate subclinical genetic susceptibility in C9orf72-ALS mice. These findings reveal a direct diet-gene interplay in governing C9orf72-ALS penetrance, and propose dietary restriction of AZE-rich foods as a tangible strategy for genetically susceptible individuals to potentially delay or mitigate this currently incurable disorder.

neuroscience↗

bioRxiv2025

The trimeric Shu complex in C. elegans is an ATPase that remodels RAD51 filaments in the homologous recombination-associated DNA damage response.

Homologous recombination (HR) is critical to error-free lesion bypass in the DNA damage response. This error-free lesion tolerance pathway is initiated by the RAD51 recombinase, which forms nucleoprotein filaments on single-stranded DNA (ssDNA) to facilitate template-directed repair using homologous sister chromatids. RAD51 filaments are tightly regulated by RAD51 mediator proteins. Among these, the Shu complexes facilitate HR-directed DNA damage tolerance and are evolutionarily conserved from yeast to humans. The Caenorhabditis elegans Shu complex is a heterotrimer consisting of three protein subunits: RFS1, RIP1, and SWS1. However, the biochemical properties of this trimeric complex remain unclear. Here, we report the biochemical characterization of the C. elegans Shu complex and interactions with DNA, ATP, and Rad51 filaments. We first revealed that the Shu trimer preferentially binds DNA with an exposed 5' end, particularly favoring a fork-shaped double-stranded DNA (dsDNA). Then, we found that the trimer binds to ATP and exhibits DNA-dependent ATPase activity. Through site-specific mutagenesis, we identified the catalytic residues in the RFS1 domain and validated the ATPase activity. Using fluorescence-based assays, we further demonstrated that the Shu trimer remodels RAD51 filaments in an ATP-hydrolysis-dependent manner and stabilizes the filaments in an ATP-binding-dependent manner. These findings provide key mechanistic insights into how the C. elegans Shu complex regulates RAD51 filaments, priming them for downstream HR-mediated DNA repair processes.

biochemistry↗

bioRxiv2025

Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome

BackgroundThe relationship between the gut mycobiome and non-alcoholic fatty liver disease (NAFLD) is largely unexplored. MethodsIn this study, we used a publicly available shotgun metagenomic sequencing dataset of fecal samples to compare the gut fungal communities of 90 NAFLD patients with those of 90 healthy controls. We examined their correlations with gut bacterial communities, host serum metabolite s, and the interactions of key taxa within these networks. ResultsOur results revealed a remarked dysbiosis in the gut mycobiome of NAFLD patients, cha racterized by a significant increase in four fungal taxa, including Pseudopithomyces sp. c174, Muc or sp. c176, Aspergillus sp. c25, and uncultured Ascochyta c213. Multi-omics analysis showed that the gut mycobiome significantly contributes to the host serum metabolome. Pseudopithomyces s p. c174 was notably associated with some beneficial blood metabolites, such as glycoursodeoxycholic acid and alpha-linolenic acid, whereas the NAFLD-enriched pro-inflammatory phenylacetic acid was linked to Aureobasidium sp. c170 and Basipetospora sp. c193. Network analysis revealed significant alterations in the gut microbiome of NAFLD patients, highlighting the potential roles of Alternaria alternata c42, Penicillium sp. c5, and uncultured Malassezia c303. Moreover, predictive models that integrated both bacterial and fungal taxa improved prediction accuracy, emphasizing the crucial role of gut fungi in NAFLD. ImportanceNon-alcoholic fatty liver disease (NAFLD) is a widespread liver condition with limited treatments. While gut bacteria have been extensively studied in NAFLD, the role of gut fungi (the mycobiome) remains poorly understood. This study fills that gap by characterizing gut fungal communities in NAFLD patients and linking these changes to their blood metabolite profiles. We found that NAFLD patients show distinct fungal imbalances, which correlate with key metabolic alterations in the host. These findings expand our understanding of NAFLD by spotlighting gut fungi as important contributors to disease progression. This insight opens new avenues for potential biomarkers and therapies targeting the gut-liver axis. ConclusionsOur findings provide a comprehensive understanding of the link between the gut mycobiome and NAFLD progression, which is essential for guiding future therapeutic research.

microbiology↗

bioRxiv2024

The enzyme glutamate-cysteine ligase (GCL) is a target for ferroptosis induction in cancer

Despite glutathiones long-recognized role as a major cellular antioxidant and its central role in ferroptosis defense, inhibition of glutathione biosynthetic enzymes has received little attention as a target for the therapeutic induction of ferroptosis. Here, we report that small-molecule inhibition of glutamate-cysteine ligase (GCL), the rate-limiting enzyme of glutathione biosynthesis, selectively and potently kills cancer cells by ferroptosis. We further describe novel GCL inhibitors including KOJ-1 and KOJ-2, compounds with excellent cellular potency and pharmacological properties, representing valuable tools to study the biology of ferroptosis and glutathione.

cancer biology↗

bioRxiv2024

Validation of ferroptosis in canine cancer cells to enable comparative oncology and translational medicine

Ferroptosis is a cell death mechanism that has attracted significant attention as a potential basis for the development of new cancer therapies. Validation of ferroptosis biology in species commonly used in translation and pre-clinical development is a necessary foundation for enabling the advancement of such ferroptosis modulating drugs. Here, we demonstrate that canine cancer cells exhibit sensitivity to a wide range of ferroptosis-inducing perturbations in a manner indistinguishable from human cancer cells, and recapitulate characteristic patterns of ferroptotic response across tumor types seen in the human setting. The foundation provided herein establishes the dog as a relevant efficacy and toxicology model for ferroptosis and creates new opportunities to leverage the canine comparative oncology paradigm to accelerate the development of ferroptosis-inducing drugs for human cancer patients.

cancer biology↗

bioRxiv2024

Shu complex is an ATPase that regulates Rad51 filaments in homologous recombination-directed DNA damage response.

Rad51 filaments are Rad51-coated single-stranded DNA and essential intermediates in homologous recombination (HR) and the HR-associated DNA damage response. The yeast Shu complex (Shu) is a conserved regulator of HR, working through its modulation of Rad51 filaments. However, the biochemical properties of Shu remain unclear, which hinders molecular insight into Shus role in HR and the DNA damage response. In this work, we biochemically characterized Shu and analyzed its molecular actions on single-stranded DNA and Rad51 filaments. First, we revealed that Shu preferentially binds DNA with ssDNA components and ssDNA/double-stranded DNA junctions. Then, we identified and validated, through site-specific mutagenesis, that Shu is an ATPase and hydrolyzes ATP in a DNA-dependent manner. Furthermore, we showed that Shu interacts with ssDNA and Rad51 filaments at the 5 end preferentially, altering the conformations of ssDNA and the filaments. The alterations depend on the ATP hydrolysis of Shu, suggesting that the ATPase activity of Shu is important in regulating its functions in HR. The preference of Shu for acting on the 5 end of Rad51 filaments aligns with the observation that Shu promotes lesion bypass at the lagging strand of a replication fork. Our work on Shu, a prototype modulator of Rad51 filaments in eukaryotes, provides a general molecular mechanism for Rad51-mediated error-free DNA lesion bypass.

biochemistry↗

bioRxiv2023

Consensus prediction of cell type labels with popV

Cell-type classification is a crucial step in single-cell analysis. To facilitate this, several methods have been proposed for the task of transferring a cell-type label from an annotated reference atlas to unannotated query data sets. Existing methods for transferring cell-type labels lack proper uncertainty estimation for the resulting annotations, limiting interpretability and usefulness. To address this, we propose popular Vote (popV, https://github.com/YosefLab/popV), an ensemble of prediction models with an ontology-based voting scheme. PopV achieves accurate cell-type labeling and provides effective uncertainty scores. In multiple case studies, popV confidently annotates the majority of cells while highlighting cell populations that are challenging to annotate. This additional step helps to reduce the load of manual inspection, which is often a necessary component of the annotation process, and enables one to focus on the most problematic parts of the annotation, streamlining the overall annotation process.

bioinformatics↗

bioRxiv2023

Telomere-to-Telomere Assembly Improves Host Reads Removal in Metagenomic High-Throughput Sequencing of Human Samples

Metagenomic high-throughput sequencing brings revolution to the study of human microbiome, clinical pathogen detection, discovery and infection diagnosis, but clinical samples often contain abundant human nucleic acids, leading to a high proportion of host reads. A high-quality human reference genome is essential for removing host reads to make downstream analyses faster and more accurate. The recently published complete human genome, Telomere-to-Telomere CHM13 assembly (T2T), though achieved great success immediately, has yet to be tested for metagenomic sequencing. In this study, we demonstrated the innovation that T2T brings to the field, using a diverse set of samples containing 4.97 billion reads sequenced from 165 libraries, on short- and long-read platforms. To exclude the effect of algorithms in comparison of the genomes, we benchmarked the per-read performance of state-of-the-art algorithms. For short reads, bwa mem was the best-performing algorithm, with positive median of differences (MD) and adjusted p-values <0.001 for all comparisons, while no consistent difference in overall performance was found for long reads algorithms. T2T, when compared to current reference genomes hg38 and YH, significantly improved the per-read sensitivity (MD: 0.1443 to 0.7238 percentage point, all adjusted p-values < 0.001) in removing host reads for all sequencers, and the per-read Mathews correlation coefficient (MCC) with T2T was also higher (MD: 1.063 to 16.41 percentage point, all adjusted p-values <0.001). Genomic location of reads exclusively mappable to T2T concentrated mainly in newly added regions. Misclassified reads generally resulted from low complexity sequences, contaminations in reference genomes and sequencing abnormalities. In downstream microbe detection procedures, T2T did not affect true positive calls but greatly reduced false positive calls. The improvement in the ability to correctly remove host reads foretells the success of T2T to serve as the next prevailing reference genome in metagenomic sequencing of samples containing human nucleic acids.

bioinformatics↗

bioRxiv2022

Genome-wide signatures of geographic expansion and breeding process in soybean

The clarification of genomic signatures left during evolutionary histories of crops is crucial for breeding varieties adapting to changing climate. Soybean, a leguminous crop, provides both plant oil and protein. Here, we analyzed genome sequences of 2,214 soybeans and proposed its evolutionary route, which includes four geographic paths, expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from Southern China, domestication in Central China, expansion of landrace (G. max (L.) Merr.), and local breeding. We observed that local adaptation of the wild and cultivated soybeans was largely independent, and that genetic introgression was mostly derived from sympatric rather than allopatric wild populations during the range expansion of soybean landraces. Range expansion and breeding processes were accompanied with positive selection of flowering-time genes including GmSPA3c as validated by knock-out mutants. Our study shed lights on the evolutionary history of soybean and provides valuable genetic resources for future breeding. TeaserThe expansion and selection history of soybean

genomics↗

bioRxiv2021

Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens

Game animals are wildlife species often traded and consumed as exotic food, and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1725 game animals, representing 16 species and five mammalian orders, sampled across China. From this we identified 71 mammalian viruses, with 45 described for the first time. Eighteen viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high risk viruses. We identified the transmission of Bat coronavirus HKU8 from a bat to a civet, as well as cross-species jumps of coronaviruses from bats to hedgehogs and from birds to porcupines. We similarly identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence. HighlightsO_LI1725 game animals from five mammalian orders were surveyed for viruses C_LIO_LI71 mammalian viruses were discovered, 18 with a potential risk to humans C_LIO_LICivets harbored the highest number of potential high risk viruses C_LIO_LIA species jump of an alphacoronavirus from bats to a civet was identified C_LIO_LIH9N2 influenza virus was detected in a civet and an Asian badger C_LIO_LIHumans viruses were also identified in game animals C_LI

zoology↗

bioRxiv2021

Serine catabolism generates NADPH to support hepatic lipogenesis

Carbohydrate can be converted into fat by de novo lipogenesis1,2. This process is known to occur in adipose and liver, and its activity is upregulated in fatty liver disease3. Chemically, de novo lipogenesis involves polymerization and reduction of acetyl-CoA, using NADPH as the electron donor1. While regulation of the responsible enzymes has been extensively studied, the feedstocks used to generate acetyl-CoA and NADPH remain unclear. Here we show that, while de novo lipogenesis in adipose is supported by glucose and its catabolism via the pentose phosphate pathway to make NADPH, liver makes fat without relying on glucose. Instead, liver derives acetyl-CoA from acetate and lactate, and NADPH from folate-mediated serine catabolism. Such NADPH generation involves the cytosolic serine pathway running in liver in the opposite direction observed in most tissues and tumors4,5, with NADPH made by the SHMT1-MTHFD1-ALDH1L1 reaction sequence. Thus, specifically in liver, folate metabolism is wired to support cytosolic NADPH production for lipogenesis. More generally, while the same enzymes are involved in fat synthesis in liver and adipose, different substrates are utilized, opening the door to tissue-specific pharmacological interventions.

biochemistry↗

bioRxiv2021

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

AO_SCPLOWBSTRACTC_SCPLOWProbabilistic models have provided the underpinnings for state-of-the-art performance in many single-cell omics data analysis tasks, including dimensionality reduction, clustering, differential expression, annotation, removal of unwanted variation, and integration across modalities. Many of the models being deployed are amenable to scalable stochastic inference techniques, and accordingly they are able to process single-cell datasets of realistic and growing sizes. However, the community-wide adoption of probabilistic approaches is hindered by a fractured software ecosystem resulting in an array of packages with distinct, and often complex interfaces. To address this issue, we developed scvi-tools (https://scvi-tools.org), a Python package that implements a variety of leading probabilistic methods. These methods, which cover many fundamental analysis tasks, are accessible through a standardized, easy-to-use interface with direct links to Scanpy, Seurat, and Bioconductor workflows. By standardizing the implementations, we were able to develop and reuse novel functionalities across different models, such as support for complex study designs through nonlinear removal of unwanted variation due to multiple covariates and reference-query integration via scArches. The extensible software building blocks that underlie scvi-tools also enable a developer environment in which new probabilistic models for single cell omics can be efficiently developed, benchmarked, and deployed. We demonstrate this through a code-efficient reimplementation of Stereoscope for deconvolution of spatial transcriptomics profiles. By catering to both the end user and developer audiences, we expect scvi-tools to become an essential software dependency and serve to formulate a community standard for probabilistic modeling of single cell omics.

bioinformatics↗

bioRxiv2021

Genetic Diversity of Dianthus Plants Revealed by SRAP Markers

Dianthus is a valuable genetic resource for flower breeding. However, study on the genetic similarity of Dianthus plants is rare. In this work, 20 pairs of SRAP markers were used to analyze genetic diversity of 44 Dianthus plants, including 13 lines of wild Dianthus chinensis L., 7 lines of wild Dianthus superbus L. and 24 commercial varieties including Dianthus caryophyllus L., Dianthus plumarius L. and Dianthus barbatus L.. Results showed that precise interspecific and intraspecific genetic diversity was provided in Dianthus plants by using 20 pairs of SRAP molecular markers. The interspecific genetic diversity of Dianthus plants was much abundant and the intraspecific genetic difference of wild Dianthus species was related to their geographical distribution and habitats. In this work, theoretical basis and technical support were provided for crossbreeding and molecular mechanism research of Dianthus plants.

genetics↗

bioRxiv2020

Qualitative and quantitative bioanalytical methods validation of aristolochic acid DNA adducts and application in human formalin-fixed paraffin-embedded hepatocellular carcinoma tissues

Mutation signature of aristolochic acid (AA) found in urothelial or hepatocellular carcinoma causes public concern about the cancer risk of AA. In contrast, direct evidence based on the reliable bioanalytical method for the exposure of AA is still lacking and not universal. Here, we strictly complied with the qualitative and quantitative guidance for forensic toxicological analysis: In the sample preprocessing, DNA from formalin-fixed and paraffin-embedded (FFPE) tissues was digested to single nucleotide by a series of enzymes with 70% enzymatic digestion efficiency. After protein precipitation, the samples were submitted to an ABI6500+ mass spectrometer for LC-MS/MS analysis. Ion pairs 543.2/427.2 and 543.2/395.2 of dA-AAI were selected from 5 ion pairs due to their higher LC-MS/MS response. Both these ion pairs have excellent selectivity and specificity in rat liver DNA matrix, and a linear regression range from 5 pg/mL to 200 pg/mL with the best fit and determination coefficient (r) greater than 0.99. The intra and inter batch accuracy and precision of these two ion pairs are also acceptable with less than 15% variation. The total recovery for ion pair 543.2/427.2 and 543.2/395.2 of dA-AAI was 90.06% and 90.76%, respectively. Our method has a minor matrix effect and good stability under different temperature and time conditions. With signal to noise ratio [≥] 3, 2 ion pairs (< 50 % relative abundance variation), the lower limit of quantification (LLOQ) of our method is set to 5 pg/mL([~]3.6 AAI-DNA adducts per 108 DNA bases). By using this validated bioanalytical method of dA-AAI, 165 human HCC FFPE tissues were analyzed, the total ratio of samples with peak543.2/427.2 is 17.0% (28/165), with peak543.2/395.2 is 9.09% (15/165) which yields the total ratio of samples combined peak543.2/427.2 and peak543.2/395.2 is 7.27% (12/165). Two samples are higher than 5 pg/mL under the qualitative requirements. In conclusion, we first reported a fully validated methods to analyze the DNA adducts level of aristolochic acid, which could be qualitatively and quantitatively applied to the investigation of AA exposure in the human and other species.

pharmacology and toxicology↗