Biology subjects

Lin, X.

Publications and source records attributed to Lin, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

ViFIT-assisted Histopathology: From H&E Style Standardization to Virtual Fiber Image Transformation

Deep learning-based virtual fiber staining provides a promising complement to routine H&E pathology. However, the reliance on predefined staining style inputs and manual intervention limits the clinical applicability of existing methods. To address these challenges, we introduce ViFIT-assisted histopathology, a two-stage diagnostic approach that integrates our proposed unsupervised deep learning-based virtual fiber transformation model (ViFIT). This approach enables the conversion of H&E-stained images with diverse styles into pathologist-preferred H&E images, while simultaneously generating content-consistent virtual fiber images containing label-free collagen fibers and stained reticular and elastic fibers. ViFIT-assisted histopathology reveals tumor-associated fibers and provides quantitative metrics across multiple intraoperative and postoperative cases. Experimental results demonstrate that ViFIT significantly outperforms state-of-the-art unsupervised methods in both style standardization and virtual staining, across various downstream tasks and cancer types. By eliminating the need for staining variation and manual annotation, ViFIT-assisted histopathology streamlines histopathology workflows, making it well-suited for multi-center consultations and differential diagnosis.

pathology↗

bioRxiv2025

Decoding cellular transcriptional regulatory networks governing wheat inflorescence development

Wheat inflorescence architecture, particularly spikelet and floret development, is critical for grain yield. To decode the cellular transcriptional regulatory network (cTRN) underlying wheat inflorescence development, we integrated multiple single-cell omics technologies to construct a spatiotemporal atlas of transcriptional and chromatin accessibility dynamics. This comprehensive analysis identified 20 cell types, 7,211 cell type-specific genes and 152,333 cell type-specific accessible chromatin regions (csACRs) in the wheat inflorescence. Trajectory analysis identified two sub-clusters of proliferating cells as the origins of spikelet and floret formation, deviating from the traditional developmental model. Key transcription factors and hormone-related genes in the cTRN, along with the csACRs, providing new targets for modulating wheat inflorescence architecture. Our findings provide a high-resolution resource for crop inflorescence research and establish a paradigm for applying spatiotemporal single-cell omics analysis to plant biology.

plant biology↗

bioRxiv2025

The Role Of Fzd8 For Bone Development And Homeostasis In A Mouse Model Generated By CRISPR/Cas9 Genome Editing

BackgroundFZD8 could be a promising therapeutic target in osteoporosis (OP), although the signal transduction mechanism in OP regarding FZD8 has not been completely elucidated. AimsWe used the CRISPR/Cas9 technique to develop an Fzd8-knockout mouse model to study whether Fzd8 inactivation results in genetic changes with potential correlations to OP. Materials and MethodsGenotypes of distinguished classified knockout mice, i.e., heterozygous, homozygous, and wild-type were identified through PCR. Applying the murine model, third generation mice were used for the downstream experiments. We investigated the potential relevance of differentially expressed genes (DEGs) in OP. ResultsWe found that osteoclasts significantly increased in Fzd8-knockout homozygous mice, compared to wild-type mice, while osteoblasts reduced significantly. Before transcription, heterozygous and homozygous mice possessed DEGs related to exons SNP, which are associated with exons CNV. After transcription, DEGs related to exons SNP in heterozygous and homozygous mice were observed, some of which are potentially associated with OP based on pathway and gene set enrichment analyses. ConclusionsOur Fzd8-knockout murine model showed that there were significant alternations in Fzd10 and Lta gene expressions and Itgb3 and RANK protein expressions among the wild-type and homozygous mice, which are significantly associated with bone remodeling. Our results revealed that FZD8 could be a therapeutic target in OP. This study elucidates the molecular mechanisms in OP, providing evidence-based data for OP drug development and treatment.

bioengineering↗

bioRxiv2025

A comprehensive benchmark and guide for sequence-function interpretable deep learning models in genomics

The development of sequence-based deep learning methods has greatly increased our understanding of how sequence determines function. In parallel, numerous interpretable algorithms have been developed to address complex tasks, such as elucidating sequence regulatory syntax and analyzing non-coding variants from trained models. However, few studies have systematically compared and evaluated the performance and interpretability of these algorithms. Here, we introduce a comprehensive benchmark framework for evaluating sequence-to-function models. We systematically evaluated multiple models and DNA language foundation models using 369 ATAC-seq datasets, employing diverse training strategies and evaluation metrics to uncover their critical strengths and limitations. Our benchmark study highlights that different model architectures and interpretability methods are better suited to specific scenarios. Negative samples derived from naturally inactive regions outperform synthetic sequences, whereas single-cell tasks require specialized models. Additionally, we demonstrate that interpretable sequence-function models can complement traditional sequence alignment methods in studying cross-species enhancer regulatory logic. We also provide a pipeline to help researchers select the optimal sequence-function prediction and interpretability algorithms.

bioinformatics↗

bioRxiv2025

The ift140-Deficient Zebrafish: A Model for Renal Cystogenesis and an F0-Based Screen to Identify Genetic Modifiers of Kidney Cysts

Genetic modifiers are believed to play an important role in the onset and severity of polycystic kidney disease (PKD), but identifying these modifiers has been challenging due to the lack of effective methodologies. In this study, we investigated zebrafish mutants of IFT140, a newly identified ADPKD gene, and observed phenotypes similar to those seen in mammalian models, including kidney cysts and bone defects. Using efficient microhomology-mediated end joining (MMEJ)-based genome editing technology, we demonstrated that ift140 CRISPRants recapitulate mutant phenotypes while bypassing the early lethality of the mutants to allow for renal cyst analysis in adult fish. In addition to cilia defects, non-cilia phenotypes, such as disrupted cell polarity and aberrant microtubule stabilization in kidney epithelial cells, may also contribute to ift140-associated cystogenesis. Importantly, the ability to detect ift140-associated renal cysts with ease allowed us to develop an F0-based genetic screen to identify potential protective modifiers. A pilot screen of sixteen genes previously linked to dysregulated signaling pathways in ADPKD revealed both known and novel modifiers, including mtor and ulk1a. Inhibition of mtor and ulk1a reversed both cilia-related and non-cilia-related abnormalities. In summary, our study underscores the potential of using zebrafish as a model for the efficient discovery of genetic modifiers of kidney cysts.

genetics↗

bioRxiv2024

Single-cell RNA sequencing analysis reveals new insights for intersex gonad initiation and early sex differentiation of goats

Polled intersex syndrome in goats severely impacts productivity and economic benefits, serving as a potential model for human reproductive defects. However, its specific molecular and cellular regulatory mechanisms remain unclear. This study combined single-cell RNA-sequencing (scRNA-seq) with tissue morphology and immunofluorescence detection to investigate the cellular heterogeneity, pseudo-time differentiation trajectory, differentially expressed genes, and regulatory networks of female, intersex, and male gonads during the 55-65 days embryonic stage of goats. The results indicated significant heterogeneity and cell fate transition in the somatic and germ cells of female, intersex, and male gonads at different developmental stages. Stromal cells may initiate female and intersexual gonad development, and epithelial cells may be the source of gonad cells in male fetuses. The abnormal expression of FOXL2, SOX9, AMH, DMRT1, RSPO1, INSL3, TCF21 and CSF1R may cause female-to-male sex reversal. The new candidate genes like PHLDB2, ZNRF3 and TEAD1 may contribute to the gender differentiation. Additionally, TREM2+ macrophages analogous to those in humans were identified in male gonads, while genes such as CSF1R and TYROBP potentially regulate macrophage immune privilege mechanisms. Early gonadal development in goats may also be regulated by circadian rhythm mechanisms similar to humans, with genes such as NR1D1, LGR4, and ATG5 involved in granulosa cell development, while genes such as ATG5, NRIP1, and FBXW11 may affect intersex trait development. In general, this study provided an important reference for exploring molecular and cellular mechanisms of intersex initiation during early embryonic development in goats and also for modelling human reproductive defects. Author summaryIn this study, we investigated the cell fate trajectory and key gene expression profile of goat fetus gonads using scRNA-seq. The analysis revealed cellular heterogeneity among normal male, normal female, and intersex gonadal somatic and germ cells, alongside their dynamic fate transitions across various developmental states. Pseudo-time trajectory analysis suggested that stromal cells might act as the initiation signal for female and intersexual gonad development, while epithelial cells could serve as the primary source of gonadal cells in male fetal goats. GO functional enrichment and KEGG analyses confirmed that abnormal expression of FOXL2, SOX9, AMH, DMRT1 and RSPO1 was linked to the emergence of intersexual gonads. Newly identified candidate genes including LRP2, PITX2, ARX, LHX9, PHLDB2, ZNRF3 and TEAD1 may contribute to sex-specific differences, while INSL3 and TCF21 could be linked to intersexual gonads. We identified TREM2+ macrophages analogous to those in humans, which could regulate immune privilege mechanisms. Circadian rhythmic changes were observed during early goat gonadal development.

developmental biology↗

bioRxiv2024

Reshaping epigenomic landscapes in facilitating the speciation of bread wheat

Polyploidization is a driving force of wheat evolution and speciation, yet its impact on epigenetic regulation and gene expression remains unclear. Here, we constructed a high-resolution epigenetic landscape across leaves, spikes, and roots of hexaploidy wheat and its tetraploid and diploid relatives. Inter-species stable-expression genes exhibited conserved amino acid sequences under strong purifying selection, while dynamic-expression genes were linked to species-specific adaptation. During hexaploidization, dominant D-subgenome homoeolog expression was suppressed via reduced activating epigenetic signals, converging expression with the A and B subgenomes. Proximal chromatin regions near genes were more stable, whereas distal regions, particularly enhancer-like elements mediated by H3K27ac and H3K4me3, exhibit higher dynamism. Sequence variations in these enhancers lead to differential gene regulation, influencing traits such as spike development. For instance, the two haplotypes of dCRE region of TaDEP-B1 resulted in significant differences in its expression and spikelet numbers. We also observed a coevolution of transcription factors and their binding sites, particularly within the expanded ERF family, which regulates spike morphology. This study highlights the interplay between sequence variation and epigenetic modifications in shaping transcriptional regulation during wheat speciation, offering valuable insights for genetic improvement.

plant biology↗

bioRxiv2024

Integrative Omics reveals genetic basis and TaMYB7-A1's function in wheat WUE and drought resilience

Improving water use efficiency (WUE) and drought resistance in wheat is critical for ensuring global food security under changing climate conditions. Here, we integrated multi-omic data, including population-scale phenotyping, transcriptomics, and genomics, to dissect the genetic and molecular mechanisms underlying WUE and drought resilience in wheat. Genome-wide association studies (GWAS) revealed 8,135 SNPs associated with WUE-related traits, identifying 258 conditional and non-conditional QTLs, many of which co-localized with known drought-resistance genes. Pan-transcriptome analysis uncovered tissue-specific expression patterns, core and unique gene functions, and dynamic sub-genomic biases in response to drought. eQTL mapping pinpointed 146,966 regulatory loci, including condition-specific hotspots enriched for genes involved in water regulation, osmoregulation, and photosynthesis. Integration of Weighted gene co-expression network analysis (WGCNA), Summary-data-based Mendelian Randomization (SMR) and GWAS, eQTLs identified 207 candidate causal genes as key regulators for WUE-related traits in wheat, such as TaMYB7-A1. Functional analyses found that TaMYB7-A1 enhances drought tolerance by promoting root growth, reducing oxidative stress, and improving osmotic regulation, enabling better water access and survival under stress. It also increases photosynthesis efficiency and WUE, boosting yield under drought without compromising performance in well-watered conditions, making it ideal target for breeding. Our findings provide a comprehensive omic framework for understanding the genetic architecture of WUE and drought resistance, offering valuable targets for breeding resilient wheat varieties.

plant biology↗

bioRxiv2024

Interfamily co-transfer of sensor and helper NLRs extends immune receptor functionality between angiosperms

Plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors recognize pathogen effectors and activate defense. NLR genes can be non-functional in distantly related plants (restricted taxonomic functionality, RTF). Here, we enable Solanaceae NLR gene function in rice, soybean and Arabidopsis by co-delivering sensor NLR genes with their cognate NRC-type helper NLRs. In soybean protoplasts and in Arabidopsis plants, Solanum americanum Rpi-amr1, Rpi-amr3 and pepper Bs2 sensor NLRs confer cognate effector responsiveness if co-expressed with NRC helper NLRs. Rice carrying pepper Bs2 and NRCs recognizes the conserved effector, AvrBs2, and resists an important pathogen, Xanthomonas oryzae pv. oryzicola for which no resistance gene is available in rice. Rice lines carrying sensor and helper NLR genes otherwise resemble wild-type, with unaltered basal resistance or field fitness. Thus, interfamily co-transfer of sensor and helper NLRs can broaden utility of sensor NLRs, extending the tools available to control diseases of rice, soybean, Brassicas and other crops.

plant biology↗

bioRxiv2024

SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI

Water molecules play a significant role in maintaining protein structural stability and facilitating molecular interactions. Accurate prediction of water molecule positions around protein structures is essential for understanding their biological roles and has significant implications for protein engineering and drug discovery. Here, we introduce SuperWater, a novel generative AI framework that integrates a score-based diffusion model with equivariant graph neural networks to predict water molecule placements around proteins with high accuracy. SuperWater surpasses existing methods, delivering state-of-the-art performance in both crystal water coverage and prediction precision, achieving water localization within 0.3 {+/-} 0.06 {degrees}A of experimentally validated positions. We demonstrate the capabilities of SuperWater through case studies involving protein hydration, protein-ligand binding, and protein-protein binding sites. This framework can be adapted for various applications, including structural biology, binding site prediction, multi-body docking, and water-mediated drug design.

bioinformatics↗

bioRxiv2024

Natural variations of TaMYB7-A1 regulate PHS resistance and specify wheat geographic adaptation

Crop domestication tended to select against seed dormancy for uniform germination--raising risks of undesirable pre-harvest sprouting (PHS) -- but regulation of seed dormancy and PHS in wheat are grossly under-characterized. Here, we identified wheat PHS resistance loci by GWAS. TaMYB7-A1 confers PHS resistance by elevating ABA signaling and seed dormancy in grains. Three TaMYB7-A1 haplotypes (Hap-1/2/3) contrast in PHS resistance, with Gly23 and Gly92 crucial for binding to and activating TaABI5 in Hap-1/3. A MITE transposon in the TaMYB7-A1Hap-1 promoter likely recruited the TaAZF1-TaABI4 module to boost expression, resulting in strong PHS resistance. TaMYB7-A1Hap-1 originated from wild einkorn and was integrated into hexaploid wheat through introgression into wild emmer. Different haplotypes of TaMYB7-A1, in conjunction with alleles of other major PHS resistance genes, is pivotal in shaping wheats adaptability to rainfall conditions in China, US and Europe during the harvest season. Introduction of TaMYB7-A1Hap-1 into elite cultivars confers PHS resistance without yield defects. Thus, artificial and natural selection across diverse climates regions have collectively shaped wheat adaptation and enabled rational delivery of improved lines tailored to local cropping needs.

plant biology↗

bioRxiv2024

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Chromatin organization is essential for DNA packaging and gene regulation in eukaryotic genomes. While significant progresses have been made, the exact atomistic arrangement of nucleosomes remains controversial. Using a well-calibrated residue-level coarse-grained model and advanced dynamics modeling techniques, particularly the non-Markovian dynamics model, we map the free energy landscape of tetra-nucleosome systems, identify both metastable conformations and intermediate states in folding pathways, and quantify the folding kinetics. Our findings show that chromatin with 10n base pairs (bp) DNA linker lengths favor zigzag fibril structures. However, longer linker lengths destabilize this conformation. When the linker length is 10n + 5 bp, chromatin loses unique conformations, favoring a dynamic ensemble of structures resembling folding intermediates. Embedding the tetra-nucleosome in a nucleosome condensate similarly shifts stability towards folding intermediates as a result of the competition of inter-nucleosomal contacts. These results suggest that chromatin organization observed in vivo arises from the unfolding of fibril structures due to nucleosome crowding and linker length variation. This perspective aids in unifying experimental studies to develop atomistic models for chromatin. SignificanceAtomic structures of chromatin have become increasingly accessible, largely through cryo-EM techniques. Nonetheless, these approaches often face limitations in addressing how intrinsic in vivo factors influence chromatin organization. We present a structural characterization of chromatin under the combined effects of nucleosome condensate crowding and linker DNA length variation--two critical in vivo features that have remained challenging to capture experimentally. This work leverages a novel application of non-Markovian dynamical modeling, providing accurate mapping of chromatin folding kinetics and pathways. Our findings support a hypothesis that in vivo chromatin organization arises from folding intermediates advancing toward a stable fibril configuration, potentially resolving longstanding questions surrounding chromatin atomic structure.

biophysics↗

bioRxiv2024

Disease-linked mutations dysregulate neuronal condensate physical properties, composition, and RNA translation

Local RNA translation is essential for development. In neurons, deficient local translation linked with mutations in scaffold proteins results in dysregulated dendrite and dendritic spine growth. However, mechanisms by which these proteins control translation and how disease-linked mutations induce aberrant translation were unclear. We use biochemical reconstitution and neuronal assays to show that mutations to the neuronal condensate scaffold shank2 cause physical hardening and altered composition of condensates; a key RNA translation-modulator FMRP is excluded from mutant condensates. Functionally, shank2 condensates repress translation while condensates composed of shank2 with intrinsically disordered region-localized missense mutations promote translation. These results demonstrate that disease-linked dysregulation of condensate physical properties and composition is an underlying mechanism of aberrant RNA translation often observed in disease. One Sentence SummaryDisease-linked missense mutations in the postsynaptic density scaffold protein shank2 dysregulate phase separated biomolecular condensate physical properties and composition resulting in aberrant RNA translation.

biophysics↗

bioRxiv2024

An mTOR-Tfeb-Fabp7a signaling axis can be harnessed to ameliorate bag3 cardiomyopathy in adult zebrafish

Dysregulated proteostasis in cardiomyocytes is an important pathological event in BAG3 cardiomyopathy, which can be repaired by inhibiting mechanistic target of rapamycin (mTOR) for cardioprotective effects. Here, we aimed to uncover additional pathological events and therapeutic target genes via leveraging zebrafish genetics. We first assessed transcription factor EB (tfeb), a candidate gene that encodes a direct downstream phosphorylation target of mTOR signaling. We found that cardiomyocyte-specific transgenic overexpression of tfeb (Tg[cmlc2:tfeb]) is sufficient to repair defective proteostasis, attenuate accelerated cardiac senescence, a previously unrecognized phenotype in the bag3 cardiomyopathy model, and rescue cardiac dysfunction. Next, we compared cardiac transcriptomes between the Tg(cmlc2:tfeb) transgenic fish and the mtorxu015/+ mutant, and tested 4 commonly downregulated lipodystrophy genes using an F0-based genetic assay. We found that inhibition of the fatty acid binding protein a (fabp7a) gene, but not the other 3 genes, exerts therapeutic effects on bag3 cardiomyopathy. Conversely, fabp7a expression is elevated in bag3 cardiomyopathy model and cardiomyocyte-specific overexpression of fabp7a resulted in dysregulated proteostasis, accelerated cardiac senescence, as well as cardiac dysfunction. Together, these genetic studies in zebrafish uncovered Fabp7a activation and accelerated cardiac senescence as important pathological events in bag3 cardiomyopathy. The mTOR-Tfeb-Fabp7a signaling axis can be harnessed to repair these pathological changes and exert cardioprotective effects.

genetics↗

bioRxiv2024

BBATProt: A Framework Predicting Biological Function with Enhanced Feature Extraction via Explainable Deep Learning

Accurately predicting the functions of peptides and proteins from their amino acid sequences is essential for understanding life processes and advancing biomolecule engineering. Due to the time-consuming and resource-intensive nature of experimental procedures, computational approaches, especially those based on machine learning frameworks, have garnered significant interest. However, many existing machine learning tools are limited to specific tasks and lack adaptability across different predictions. Here we propose a versatile framework BBATProt for the prediction of various protein and peptide functions. BBATProt employs transfer learning with a pre-trained Bidirectional Encoder Representations from Transformers (BERT) model, to effectively capture high-dimensional features from amino acid sequences. The whole custom-designed network, integrating Bidirectional Long Short-Term Memory (Bi-LSTM) and Temporal Convolutional Networks (TCN), can align with the spatial characteristics of proteins. It combines local and global feature extraction through attention mechanisms for precise functional prediction. This approach ensures that key features are adaptively extracted and balanced across diverse tasks. Comprehensive evaluations show BBATProt outperforms state-of-the-art models in predicting functions like hydrolytic catalysis, activity of peptides, and post-translational modification sites. Visualizations of feature evolution and refinement via attention mechanisms validate the frameworks interpretability, providing transparency into the evolutional process and offering deeper insights into function prediction.

bioinformatics↗

bioRxiv2024

SPLENDID incorporates continuous genetic ancestry in biobank-scale data to improve polygenic risk prediction across diverse populations

Polygenic risk scores are widely used in disease risk stratification, but their accuracy varies across diverse populations. Recent methods large-scale leverage multi-ancestry data to improve accuracy in under-represented populations but require labelling individuals by ancestry for prediction. This poses challenges for practical use, as clinical practices are typically not based on ancestry. We propose SPLENDID, a novel penalized regression framework for diverse biobank-scale data. Our method utilizes ancestry principal component interactions to model genetic ancestry as a continuum within a single prediction model for all ancestries, eliminating the need for discrete labels. In extensive simulations and analyses of 9 traits from the All of Us Research Program (N=224,364) and UK Biobank (N=340,140), SPLENDID significantly outperformed existing methods in prediction accuracy and model sparsity. By directly incorporating continuous genetic ancestry in model training, SPLENDID stands as a valuable tool for robust risk prediction across diverse populations and fairer clinical implementation.

genetics↗

bioRxiv2024

Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions

Histone acetylation is a key regulatory post-translational modification closely as-sociated with gene transcription. In particular, H4K16 acetylation (H4K16ac) is a crucial gene activation marker that induces an open chromatin configuration. While previous studies have explored the effects of H4K16ac on nucleosome interactions, how this local modification affects higher-order chromatin organization remains un-clear. To bridge the chemical modifications of these histone tail lysine residues to global chromatin structure, we utilized a residue-resolution coarse-grained chromatin model and enhanced sampling techniques to simulate charge-neutralization effects of histone acetylation on nucleosome stability, inter-nucleosome interactions, and higher-order chromatin structure. Our simulations reveal that H4K16ac stabilizes a single nucleosome due to the reduced entropic contribution of histone tails during DNA unwrapping. In addition, acetylation modestly weakens inter-nucleosome interactions by diminishing contacts between histone tails, DNA, and nucleosome acidic patches. These weakened interactions are amplified when nucleosomes are connected by linker DNA, whose fluctuation causes significant chromatin destacking and decompaction, exposing nucleosomes for transcriptional activity. Our findings suggest that the geometric constraint imposed by chromatin DNA plays a critical role in driving chromatin structural reorganization upon post-translational modifications.

biophysics↗

bioRxiv2024

Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis

BackgroundCell type-specific transcriptional heterogeneity in embryonic mouse skin is well-documented, but few studies have investigated the regulatory mechanisms. ResultsHere, we present high throughput single-cell chromatin accessibility and transcriptome sequencing (HT-scCAT-seq), a method that simultaneously profiles transcriptome and chromatin accessibility. We utilized HT-scCAT-seq to dissect the gene regulatory mechanism governing epidermal stratification, periderm terminal differentiation, and fibroblast specification. ConclusionsBy linking chromatin accessibility to gene expression, we identified candidate cis-regulatory elements (cCREs) and target genes crucial for dermal and epidermal development. We described cells with similar gene expression profiles that exhibit distinct chromatin accessibility statuses during periderm terminal differentiation. Finally, we characterized the underlying lineage-determining transcription factors (TFs), and demonstrated that ALX4 and RUNX2 were candidate TF regulators of the dermal papilla lineage development through in silico perturbation analysis.

developmental biology↗