Biology subjects

Ling, H.

Publications and source records attributed to Ling, H..

13 recordsLinked to original sources

bioRxiv2026

WheatPanRef: a unified linear pan-reference genome for wheat genomics

Linear reference genomes provide coordinates for read mapping, variant discovery and multi-omics data integration, yet assembly-specific coordinate systems limit data reuse, particularly in the large, repetitive and polyploid wheat genome. Here, we present WheatPanRef, a scalable linear pan-reference and coordinate framework that integrates wheat sequence diversity within a stable coordinate system. We reconciled independent Chinese Spring assemblies by resolving structural and sequences discrepancies to constructed a 14.50-Gb consensus sequences CS-NP. Using CS-NP as backbone, we incorporated 4.37 Gb of non-redundant non-CS sequences from 37 diverse wheat accessions, generating WheatPanRef (18.87 Gb). WheatPanRef improves read-alignment performance and captures putative wild-relative introgressions and sequences absent or unanchored in conventional references. Bidirectional coordinate-translation system enables accurate projection between WheatPanRef and individual assemblies without remapping, facilitating genomic resource integration and reuse. WheatPanRef provides a common sequence and coordinate foundation for population-scale wheat genomics, with potential utility for genomic resource integration in other complex crops.

genomics↗

bioRxiv2025

A Comprehensive Treatment-Induced Resistance Atlas of Glioblastoma Reveals a Fibrotic Niche Shielding the Tumor from Immunotherapy

Therapeutic resistance in IDH-wildtype glioblastoma (GBM) is driven by an intricate interplay between cellular plasticity and protective microenvironmental niches. By constructing the GRIT-Atlas--a massive transcriptomic compendium encompassing nearly one million high-quality single cells across 17 cohorts--and cross-analyzing it with 48 independent Visium spatial transcriptomics sections, we discover a recurrent "Spatial Resistance Triad" comprising mesenchymal-like (MES-like) malignant cells, myeloid-derived suppressor cells (MDSCs), and collagen-secreting cancer-associated fibroblasts (CAFs). This large-scale spatial integration reveals that the triad physically fortifies microvascular proliferation (MVP) and pseudopalisading necrosis (PAN) niches. To substantiate these findings at true single-cell resolution, we deploy high-plex spatial molecular imaging (CosMx SMI) to map over 400,000 single cells across a clinical validation cohort. This high-resolution architecture firmly validates the triads geography and, critically, provides structural gradient evidence unmasking a spatiotemporal continuum wherein PAN emerges as a direct functional consequence of MVP advancement and subsequent vascular collapse. Mechanistically, stromal CAF-derived COL6A1 engages CD44 receptors on MES-like cells to accelerate a potent neural stemness cascade within these protective domains. Utilizing a blood-brain barrier (BBB)-penetrant multi-library compound screen, we identify Lacidipine as a multi-modal stromal disruptor that successfully silences CAF activation and halts matrix secretion. Incorporating Lacidipine into the standard chemo-immunotherapy backbone (TMZ + anti-CSF1R) completely dismantles the protective desmoplastic matrix niche, forcing a profound collapse of intracranial tumor burden and dramatically extending overall survival in orthotopic models. Collectively, our study leverages unprecedented single-cell and spatial scale to provide a definitive blueprint of GBM therapeutic evasion, establishing matrix-targeted intervention as a mandatory prerequisite for successful glioblastoma eradication.

cancer biology↗

bioRxiv2025

A Generative Foundation Model for Cryo-EM Densities

Single-particle cryo-electron microscopy (cryo-EM) enables structure determination of macromolecular complexes, yet reconstructions are often degraded by noise, anisotropic sampling and reconstruction artifacts. Correcting these effects is an ill-posed inverse problem that requires strong prior knowledge in addition to experimental data. Here we introduce cryoFM, a generative foundation model for cryo-EM densities that unifies data-driven structural priors with dataset-specific constraints within a Bayesian inference framework. CryoFM is trained in an unsupervised manner on thousands of high-quality cryo-EM maps using flow matching, learning a generalizable prior over macromolecular density distributions. Combined with explicit likelihood models describing experimental degradations, cryoFM enables flow posterior sampling, an inference-only procedure that performs denoising and restoration and refinement while remaining explicitly constrained by dataset-derived statistics. We show that this framework improves density reconstruction and refinement across diverse experimental settings, including preferred-orientation datasets and cases with strong spatial heterogeneity in signal-to-noise ratio, without introducing hallucinated features. In addition, cryoFM can be fine-tuned into conditional generative models for density post-processing, yielding maps with improved interpretability and fewer artifacts compared to existing supervised approaches. Together, cryoFM establishes generative foundation models as a principled and controllable framework for cryo-EM density reconstruction and modification.

biophysics↗

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↗

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

HDAC10 blockade upregulates SPARC expression thereby repressing melanoma cell growth and BRAF inhibitor resistance

Secreted Protein Acidic and Rich in Cysteine (SPARC), a highly conserved secreted glycoprotein, is crucial for various bioprocesses. Here we demonstrate that histone deacetylase 10 (HDAC10) is a key regulator of SPARC expression. HDAC10 depletion or inhibition upregulates, while overexpression of HDAC10 downregulates, SPARC expression. Mechanistically, HDAC10 coordinates with histone acetyltransferase p300 to modulate the acetylation state of histone H3 lysine 27 (H3K27ac) at SPARC regulatory elements and the recruitment of bromodomain-containing protein 4 (BRD4) to these regions, thereby tuning SPARC transcription. HDAC10 depletion and resultant SPARC upregulation repress melanoma cell growth, primarily by induction of autophagy via activation of AMPK signaling. Moreover, SPARC upregulation due to HDAC10 depletion partly accounts for the resensitivity of resistant cells to a BRAF inhibitor. Our work reveals the role of HDAC10 in gene regulation through epigenetic modification and suggests a potential therapeutic strategy for melanoma or other cancers by targeting HDAC10 and SPARC. HighlightsO_LIHDAC10 is the primary HDAC member that tightly controls SPARC expression. C_LIO_LIHDAC10 coordinates with p300 in modulating the H3K27ac state at SPARC regulatory elements and the recruitment of BRD4 to these regions. C_LIO_LIHDAC10 depletion and resultant SPARC upregulation inhibit melanoma cell growth by inducing autophagy via activation of AMPK signaling. C_LIO_LISPARC upregulation as a result of HDAC10 depletion resensitizes resistant cells to BRAF inhibitors. C_LI

cancer biology↗

bioRxiv2023

Absolute Quantification of Microbiota in Shotgun Sequencing Using Host Cells or Spike-Ins

BackgroundAn ongoing challenge for DNA sequencing of samples containing microorganisms is the ability to meaningfully compare different samples and to connect the results back to clinically relevant disease states. The reads of DNA sequence from each sample do not, in and of themselves, give sufficient information to calculate the absolute abundances of each observed organism. Using relative abundances alone is insufficient to determine whether absolute abundances have increased or decreased in the organisms of interest from one sample to the next. This is a well-studied problem in 16S sequencing, but solutions in shotgun sequencing are lacking. Here we show how spike-ins can be used in shotgun sequencing to calculate absolute abundances of organisms present. We also propose the use of the host cells already in the sample as an alternative calculation method. Mammalian host cells are typically of sufficient size that they can be easily and cheaply counted prior to sequencing by a variety of methods and combining this with sequencing data provides sufficient information to calculate the absolute abundances of microbial organisms. ResultsMicrobial abundances in the samples calculated via this method were consistent with manufacturer-stated values of microbial communities, with qPCR, and with our method tested against itself with regard the spike-in and host-cell based options. R2 values on the log10 scale in these tests ranged from 0.85 to 0.98, and the log10-RMSE ranged from 0.1 to 0.7. ConclusionsThe proposed method can consistently calculate absolute microbial abundances to within an order of magnitude. Both versions of the method, where spike-ins are added to the samples, or where host cells in the sample are counted, are viable. Calculating absolute abundances allows for direct comparisons to be made between different samples. If disease-thresholds have been identified, absolute abundances can quantify disease states.

microbiology↗

bioRxiv2023

Effect of tuft-IL-25-ILC2 pathway on mouse small intestine stimulated by Trichinella spiralis ES antigen

ObjectiveTo explore the regulatory effect of Trichinella spiralis ES antigen on the intestinal immune function, we observed the immune response of mouse small intestine to this antigen by quantifying the changes in the related cytokines of Tuft-IL-25-ILC2 pathway. MethodsA total of 30 BALB/c female mice were randomly divided into three groups: control group, Trichinella excretion-secretion (ES) antigen stimulation group, and IL-25 blocking group. The mice in the control group were injected intraperitoneally with PBS; those in the ES antigen stimulation group were injected intraperitoneally with ES antigen once per day for 7 consecutive days; and those in the IL-25 blocking group were injected intraperitoneally, first with anti-mouse IL-25 monoclonal antibody and 3 days later with ES antigen. Alcian blue-nuclear fast red staining was employed to observe the changes in the number of small intestinal goblet cells. The number of Tuft cells was determined by immunofluorescence chemical analysis, and the expression levels of IL-25, IL-13, IL-25R, Pou2f3, and ROR mRNA were quantified by RT-PCR. Key resultsThe results of Alcian blue-nuclear fast red staining showed that, compared with the control group, the number of goblet cells in the small intestinal tissue of mice in the ES antigen stimulation group increased, and the difference was statistically significant (P<0.05). Compared with the ES antigen stimulation group, the number of goblet cells in the small intestinal tissue of the mice in the IL-25 blocking group was slightly decreased (P<0.05). Immunofluorescence analysis showed that, compared with the control group, the number of Tuft cells in the ES antigen-stimulated group increased (P<0.05), while in the IL-25 blocking group, the number of Tuft cells was decreased compared with that in the ES antigen stimulation group (P<0.05). RT-PCR analysis showed that, compared with the control group, the mRNA expression levels of IL-25, IL-13, IL- 25R, ROR and Pou2f3 in the small intestine of mice in the ES antigen stimulation group were increased (P<0.05); compared with the ES antigen stimulation group, the IL-25, IL-13, IL-25R, ROR and Pou2f3 mRNA expressions in the tissues of the mice in the IL-25 blocking group were decreased, and the difference was statistically significant (P<0.05). ConclusionThe small intestinal mucosa of mice stimulated by Trichinella ES antigen may possess an immune function via the Tuft-IL-25-ILC2 pathway.

immunology↗

bioRxiv2022

A Chromodomain Mutation Identifies Separable Roles for C. elegans MRG-1 in Germline and Somatic Development

The packaging of DNA into chromatin strongly influences gene regulation. Post-translational modifications of histones, and the proteins that bind to them, alter the accessibility of chromatin and contribute to the activation and repression of genes. The human MRG15 (MORF4- Related Gene on chromosome 15) protein is a conserved chromodomain-containing protein that binds to methylated lysine 36 on histone H3 (H3K36me) and plays important roles in development, genome integrity, and gene regulation. MRG15 affects transcriptional regulation through its interactions with both histone acetyltransferase (HAT) and histone deacetylase (HDAC) complexes. MRG-1, its C. elegans homolog, has similarly been shown to have important roles in genomic integrity and development, and has also been shown to co- purify with HDAC complexes. Like MRG15, MRG-1 is predicted to bind to H3K36me through its chromodomain, yet despite mrg-1 mutants displaying developmental and germline phenotypes that overlap with H3K36 methyltransferase mutants, the role of the MRG-1 chromodomain has never been characterized. In this study, we examined meiotic cells lacking H3K36me3 to compare to mrg-1 mutant germ cell phenotypes, and mutated key residues in the MRG-1 chromodomain (CD) to assess its function. The CD mutations cause embryonic lethality but few post-embryonic germline defects, in contrast to mrg-1 deletion mutants which are viable but sterile. The CD mutations therefore disrupt somatic development despite the apparent absence of a requirement for MRG-1 protein in embryogenesis. Furthermore, the CD mutants exhibit a dominant RNAi resistance phenotype that is not seen in other mrg-1 mutant alleles. This suggests that the function of MRG-1, and the chromatin modifying complexes with which it interacts, includes tissue-specific interactions involving different requirements for a functional chromodomain. We propose that the CD mutation disrupts proper guidance of complexes within which it acts, and this guidance defect results in improper HDAC and/or HAT regulation causing an indirect defect in RNAi machinery expression or targeting.

genetics↗

bioRxiv2021

Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

Cystic fibrosis (CF) is a severe genetic disorder that can cause multiple comorbidities affecting the lungs, the pancreas, the luminal digestive system and beyond. In our previous genome-wide association studies (GWAS), we genotyped [~]8,000 CF samples using a mixture of different genotyping platforms. More recently, the Cystic Fibrosis Genome Project (CFGP) performed deep ([~]30x) whole genome sequencing (WGS) of 5,095 samples to better understand the genetic mechanisms underlying clinical heterogeneity among CF patients. For mixtures of GWAS array and WGS data, genotype imputation has proven effective in increasing effective sample size. Therefore, we first performed imputation for the [~]8,000 CF samples with GWAS array genotype using the TOPMed freeze 8 reference panel. Our results demonstrate that TOPMed can provide high-quality imputation for CF patients, boosting genomic coverage from [~]0.3 - 4.2 million genotyped markers to [~]11 - 43 million well-imputed markers, and significantly improving Polygenic Risk Score (PRS) prediction accuracy. Furthermore, we built a CF-specific CFGP reference panel based on WGS data of CF patients. We demonstrate that despite having [~]3% the sample size of TOPMed, our CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations. We anticipate our imputed data for 4,656 samples without WGS data will benefit our subsequent genetic association studies, and the CFGP reference panel built from CF WGS samples will benefit other investigators studying CF.

genetics↗

bioRxiv2020

A membrane-associated condensate drives paternal epigenetic inheritance in C. elegans

Transgenerational epigenetic inheritance (TEI) describes the transmission of gene-regulatory information across generations without altering DNA sequences, and allows priming of offspring towards transposable elements (TEs) and changing environmental conditions. One important mechanism that acts in TEI is based on small non-coding RNAs. Whereas factors for maternal inheritance of small RNAs have been identified, paternal inheritance is poorly understood, as much of the cellular content is extruded during spermatogenesis. We identify a phase separation-based mechanism, driven by the protein PEI-1, which is characterized by a BTB-BACK domain and an intrinsically disordered region (IDR). PEI-1 specifically secures the Argonaute protein WAGO-3 within maturing sperm in C. elegans. Localization of PEI granules in mature sperm is coupled, via S-palmitoylation, to myosin-driven transport of membranous organelles. pei-1-like genes are also found in human and often expressed in testis, suggesting that the here identified mechanism may be broadly conserved.

cell biology↗

bioRxiv2020

Exploring heteroaromatic rings as a replacement for the labile amide of antiplasmodial pantothenamides

The Plasmodium parasites that cause malaria are adept at developing resistance to antimalarial drugs, necessitating the search for new antiplasmodials. Although several amide analogs of pantothenate (pantothenamides) show potent antiplasmodial activity, hydrolysis by pantetheinases (or vanins) present in blood rapidly inactivates them. We report herein the facile synthesis and biological activity of a small library of pantothenamide analogs in which the labile amide group is replaced with a variety of heteroaromatic rings. Several of the new analogs display antiplasmodial activity in the nanomolar range against P. falciparum and/or P. knowlesi in the presence of pantetheinase. A previously reported triazole and an isoxazole derivative presented here were further characterized and found to possess high selectivity indices, medium or high Caco-2 permeability, and medium or low microsomal clearance in vitro. Although we show here that the two compounds fail to suppress proliferation of P. berghei in vivo, pharmacokinetic and contact time data presented provide a benchmark for the compound profile required to achieve antiplasmodial activity in mice and should facilitate lead optimization.

pharmacology and toxicology↗

bioRxiv2019

Comparative Population Genomics of Bread Wheat (Triticum aestivum) Reveals Its Cultivation and Breeding History in China

The evolution of bread wheat (Triticum aestivum) is distinctive in that domestication, natural hybridization, and allopolyploid speciation have all had significant effects on the diversification of its genome. Wheat was spread around the world by humans and has been cultivated in China for ~4,600 years. Here, we report a comprehensive assessment of the evolution of wheat based on the genome-wide resequencing of 120 representative landraces and elite wheat accessions from China and other representative regions. We found substantially higher genetic diversity in the A and B subgenomes than in the D subgenome. Notably, the A and B subgenomes of the modern Chinese elite cultivars were mainly derived from European landraces, while Chinese landraces had a greater contribution to their D subgenomes. The duplicated copies of homoeologous genes from the A, B, and D subgenomes were commonly found to be under different levels of selection. Our genome-wide assessment of the genetic changes associated with wheat breeding in China provides new strategies and practical targets for future breeding.

plant biology↗