Biology subjects

Liu, D.

Publications and source records attributed to Liu, D..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

GPX4 Promotes Optic Nerve Regeneration and RGC Neuroprotection

Preventing retinal ganglion cells (RGCs)s soma and axon degeneration and promoting optic nerve (ON) regeneration holds great promise for effective glaucoma treatment. To explore potential neural repair strategies, we focused on glutathione peroxidase 4 (GPX4), a key regulator of lipid peroxidation. GPX4 is upregulated in surviving RGCs after acute ON crush or chronic ocular hypertension insult, and also in regenerating RGCs. AAV-mediated RGC-specific overexpression of GPX4 promotes significant ON regeneration and RGC survival, along with visual functional preservation, demonstrating the detrimental role of lipid peroxidation in glaucoma and the therapeutic potential of modulating lipid peroxidation through GPX4 in optic neuropathies.

neuroscience↗

bioRxiv2025

Genome-Bench: A Scientific Reasoning Benchmark from Real-World Expert Discussions

In this short report, we present an automated pipeline tailored for the genomics domain and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learningfriendly multiple-choice questions format, supported by 3000+ high-quality questionanswer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology. The dataset is available at https://huggingface.co/datasets/Mingyin0312/Genome-Bench.

genomics↗

bioRxiv2025

BioLogical: a universal analysis framework for biosystem logical dynamic

Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical.

systems biology↗

bioRxiv2025

Alcohol Use Disorder Associated Gene FNDC4 Alters Glutamatergic and GABAergic Neurogenesis

Large-cohort genome-wide association studies (GWAS) for alcohol use disorder (AUD) and AUD-related phenotypes have identified more than one hundred genetic loci. Functional study of those GWAS-identified loci might represent an important step toward understanding AUD pathophysiology. We found that genetic loci which are splicing quantitative trait loci (sQTLs) for the fibronectin III domain containing 4 (FNDC4) gene in the brain were identified by GWAS for both AUD drug treatment outcomes and AUD risk. However, FNDC4 function in the brain and how it might contribute to AUD pathophysiology remain unknown. In the present study, we characterized GWAS locus-associated FNDC4 splice isoforms, studies which suggested that FNDC4 alternative splicing results in loss-of-function for FNDC4. We also investigated FNDC4 function using CRISPR/cas9 gene editing, and the creation of human induced pluripotent stem cell (iPSC)-derived neural organoids joined with single-nucleus RNA sequencing. We observed that knock-out (KO) of FNDC4 resulted in a striking shift in the relative proportions of glutamatergic and GABAergic neurons in iPSC-derived neural organoids, suggesting a possible important role for FNDC4 in neurogenesis. We also explored potential mechanism(s) of FNDC4-dependent neurogenesis with results that suggested a role for FNDC4 in mediating neural cell-cell interaction. In summary, this series of experiments indicates that FNDC4 plays a role in regulating cerebral cortical neurogenesis in the brain. This regulation may contribute to the response to AUD pharmacotherapy as well as the effects of alcohol on the brain.

genomics↗

bioRxiv2025

Universal Transformer-Based Tracker for Accurate Tracking of Particles and Cells in Microscopy

Accurate tracking of subcellular structures and cells under microscopy supports heavily the studies of their dynamic processes. However, the complex motion and the similar appearances of objects pose significant challenges in accurately identifying the identical object across multiple detection results without introducing ambiguities in trajectory tracking. Here we propose a Universal Transformer-Based Tracker (UTT) that achieves the accurate tracking in various biologically relevant scenarios. The self-attention of Transformer extracts features and patterns from trajectories, and the cross-attention of Transformer captures matching relations between history tracks and future hypothesis tracklets (fragments of track). Our tracker uses the Transformer to handle the tracking of particles with diverse motion dynamics, and outperforms existing tracking algorithms in terms of accuracy. Furthermore,the tracker utilizes estimated particle positions to counteract missed detections, thereby improving tracking robustness under varying ratios of missing detections. We demonstrate the flexibility and versatility of our approach by adaptively integrating motion and appearance cues in cell tracking applications.

bioinformatics↗

bioRxiv2025

Impact of maternal compensation on developmental phenotypes in a zebrafish model of severe congenital muscular dystrophy

Genetic compensation is a common phenomenon in zebrafish in response to genetic alterations. As such, differences between morphant and mutant zebrafish models of human diseases have led to significant difficulties in phenotypic interpretation and translatability. One form of compensation is the maternal deposit of mRNAs and proteins into the oocyte that supports developmental processes before zygotic genome activation. In this study, we generated a zebrafish model of severe congenital muscular dystrophy by targeting protein O-mannose N-Acetylglucosaminyltransferase 2 (pomgnt2), a maternally provided gene that maintains cell-extracellular matrix interactions through glycosylation. Zygotic knockouts (ZKOs) retain protein function in the first week post-fertilization and survive to adulthood, though they develop muscle disease later in life. In contrast, maternal-zygotic KOs (MZKOs) generated from ZKO females develop early-onset muscle disease, reduced motor function, neuronal axon guidance deficits, and retinal synapse disruptions, recapitulating features of the human presentation. While assessing transcriptional changes linked to disease progression, the availability of embryos obtained from different breeding strategies also allowed for direct comparison of ZKOs and MZKOs to define the impact of having a KO mother. We found that offspring from a ZKO mother, independently of genotype, show distinct expression patterns from animals obtained from heterozygous breeding. Some of these changes reflect an increased metabolic requirement, possibly stemming from maternal metabolic disruption. These findings will not only be applicable to other CMD models targeting maternally provided genes but also provide new insight into modeling disease using maternal-zygotic mutants.

genetics↗

bioRxiv2025

BioMedTools: a language model-powered community for biomedical computational tools

A large number of biomedical computational tools have spawned several tool registries. However, in the face of the rapid growth in the number of tools, existing tool registries, which are manually curated or community-driven, are difficult to keep up to date, resulting in inadequate tool repository data. In this paper, we show that language models (LMs) can aid in building a community of tools. We introduce BioMedTools (https://biomed.tools), a community of biomedical computational tools that mainly implements LM-based tool identification and a chat assistant. Compared with existing tool registries, BioMedTools achieves excellence in terms of the number of tools, frequency of data updates, and functionality. Meanwhile, the Model Context Protocol (MCP) servers hub in BioMedTools may promote the building of agents in the biomedical field. BioMedTools enables the efficient collection of tools and enhances their findability and accessibility.

bioinformatics↗

bioRxiv2025

Understanding Protein Language Model Scaling on Mutation Effect Prediction

Protein language models, and models that incorporate structure or homologous sequences, estimate sequence likelihood p(sequence) that reflects the protein fitness landscape and is commonly used in mutation effect prediction and protein design. It is widely believed in deep learning field that larger model performs better across tasks. However, for fitness prediction, language model performance declines beyond a certain size, raising concerns about their scalability. Here, we showed that model size, training dataset, and stochastic elements can bias the predicted p(sequence) away from real fitness. Model performance on fitness prediction depends on how well p(sequence) matches evolutionary patterns in homologs, which is best achieved at a moderate p(sequence) level for most proteins. At extreme predicted wild-type sequence likelihoods, models predict uniformly low or high likelihoods for nearly all mutations, failing to reflect the real fitness landscape. Notably, larger models tend to predict proteins with higher p(sequence), which may exceed the moderate range and thus reduce performance. Our findings clarify the scaling behavior of protein models on fitness prediction and provide practical guidelines for their application and future development.

bioinformatics↗

bioRxiv2025

A Versatile Marker-Free Genome Engineering Platform to Overcome Homologous Recombination Bias in Microbes: A Case Study in Synechococcus elongatus UTEX 2973

The single crossover occurring via homologous recombination is a common phenomenon exited among most microbes like Escherichia, Clostridium, Streptococcus, Lactobacillus, and cyanobacteria, threatening the stability of engineered strains. Among them, fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is an attractive photosynthetic chassis for CO2 bioconversion. To address the challenge of homologous recombination, we constructed two endogenous plasmid-based shuttle vectors, pSES and pSEL, enabling stable DNA delivery without reliance on homologous recombination. In parallel, two robust counter-selection systems were developed based on sepT2 and rpsL, which, in combination with positive selection markers, significantly improved the screening efficiency of double-crossover mutants. Building upon these tools, we established three marker-free platforms: (i) T4CROSS, which employs two plasmids and four rounds of single crossover; (ii) TRIPLEARM, which uses a single plasmid containing three homologous arms for three rounds of single crossover; and (iii) CRISPRARM, which integrates CRISPR/Cpf1-mediated genome editing with homologous recombination. All three methods successfully repaired mutations in the pilMNOQ pilus gene cluster in Syn2973, restoring natural competence with high efficiency and positive selection rates. As proof of concept, we employed the CRISPRARM platform for a three-step sequential engineering of the sucrose biosynthetic pathway. The final engineered strain produced 7.12 g{middle dot}L-1 of sucrose within four days.

synthetic biology↗

bioRxiv2025

Trans-ancestry Mendelian Randomization Discovers Novel Causal Genes for Autoimmune Disease Traits

Mendelian randomization (MR) using summary statistics from genome-wide association studies (GWAS) has become a powerful tool for dissecting the causal relationships between exposure and outcomes. As GWAS begins to incorporate samples of diverse ancestries, the optimal strategy to perform MR analysis integrating these GWAS results remains to be determined. To fill in this gap, we proposed a robust method that aggregates the genetic variant-risk factor association summary statistics of multiple ancestries by modelling the genetic effects of the exposure as a function of the principal components of genome-wide allele frequency. This allows borrowing information from different ancestry groups and accounting for potential between-ancestry heterogeneities. The method is general and can be used with different MR methods. We demonstrated that our method improves accuracy and power compared to the inverse-variance weighting method based on only ancestry-stratified samples, with additional benefits in correcting winners curse bias. We also illustrated the flexibility and potential of discovering novel causal genes for autoimmune disease traits of our method in practice.

genetics↗

bioRxiv2025

Modulation of viral replication, autophagy and apoptosis by induction and mutual regulation of transcription factors EB and E3 during coronavirus infection

Viral invasion of and replication in cells pose a significant impact on the structure and function of lysosomes. By sensing changes in the lysosome status, cascades of cellular responses are triggered to maintain the lysosomal homeostasis. Two key regulators, transcription factors EB (TFEB) and E3 (TFE3), play essential regulatory roles in these processes by shuttling between the cytoplasm and the nucleus. In this study, we report that infection of cells and/or chickens by gammacoronavirus infectious bronchitis virus (IBV), human betacoronavirus OC43 (HCoV-OC43), and alphacoronavirus porcine epidemic diarrhea virus (PEDV) upregulates the expression of TFEB/TFE3 as well as their downstream targets, and induces the lysosomal stress response. Knockdown of TFE3 alone or together with TFEB demonstrated a pronounced role played by TFE3 in regulating viral replication, virus-induced autophagy and apoptosis in cells infected with these viruses, and a synergistic effect of TFEB and TFE3 in regulation of these processes in cells infected with IBV and HCoV-OC43. Inhibition of the biosynthetic secretory pathway with brefeldin A (BFA) demonstrated that the release of HCoV-OC43 is mainly via the lysosomal pathway. This study provides novel insights into the functional roles of the lysosomal biogenesis and stress response in coronavirus replication and virus-host interactions. ImportanceIn recent years, more and more studies have shown that lysosomes function more than just as a recycling bin, they also play an important role as a hub for energy and signal transduction, autophagy regulation, and many physiological or pathological processes. This study showed that coronavirus infection activates lysosomal stress responses. As two transcription factors that regulate lysosomal biogenesis, TFEB and TFE3 regulate autophagy and apoptosis during the coronavirus replication cycle. In addition, it has been found that HCoV-OC43 releases viral particles through the lysosomal pathway, which may provide a new reference for the treatment of mitigating coronavirus infection.

microbiology↗

bioRxiv2025

CanASM: A comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer

Allele-specific DNA methylation (ASM) provides critical insights into the complex genetic and epigenetic mechanisms regulating gene transcription. Emerging evidence suggests that ASM is particularly enriched in gene enhancer regions, and recent studies have demonstrated that ASM is increased in cancer tissues compared with normal tissues. Despite the increasing recognition of ASM as a potential biomarker in tumorigenesis, systematic resources dedicated to identifying and annotating ASMs in cancer contexts remain limited. In this study, we developed CanASM (https://bioinfor.nefu.edu.cn/CanASM/), the first comprehensive database specifically designed to identify and annotate ASM in cancer. In CanASM, ASM sites identified from bisulfite sequencing data across 31 cancer types and their matched normal tissue samples are cataloged. Importantly, CanASM includes extensive regulatory annotations for ASMs, including associated genes, cis-regulatory elements and transcription factor binding colocalizations, transcription factor affinity changes, etc. Users can query and explore ASMs using various parameters, such as single-nucleotide variations (SNVs), chromosomal coordinates, and gene names. The current version of CanASM includes 5,003,877 unique SNV-CpG pairs, including 3,056,776 index SNVs, of which 2,634,406 are single-nucleotide polymorphisms (SNPs), and 4,157,508 CpGs. With an intuitive interface for browsing, querying, analyzing, and downloading, CanASM serves as a valuable resource for researchers investigating cancer-associated genetic variations and epigenetic regulation in cancer. Author summaryIdentifying target genes and regulatory mechanisms of cancer-associated genetic variants remains a major challenge in the post-GWAS era. Existing databases like Pancan-meQTL and ASMdb have contributed to uncovering the role of genetic variants in cancer by linking DNA variations to methylation. However, they lack comprehensive regulatory annotations for such sites and rely solely on genomic proximity for target gene prediction, overlooking distal interactions. Our analysis using 3D interaction data reveals that over 94.8% of ASMs exhibit distal regulatory relationships, emphasizing their critical role in cancer epigenetics. Furthermore, these databases cover a limited number of cancer types (Pancan-meQTL: 23, ASMdb: 8). To address these limitations, we developed CanASM, a database that provides ASMs identified from BS-seq data for 31 human cancers, along with multidimensional regulatory annotations for ASM sites. This includes target genes, cis-regulatory elements (enhancers, ATAC-seq regions, insulators, 3D interactions, CpG islands), TFBSs, and GWAS cancer trait associations. Additionally, CanASM offers three interactive tools for analyzing TF binding affinity changes, predicting ASM target genes through 3D interactions, and identifying cell marker variations. As a comprehensive resource for SNV-driven epigenetic regulation in cancer, CanASM is helpful for in-depth research in cancer genetics and epigenetics.

bioinformatics↗

bioRxiv2025

Two CENH3 paralogs in the green alga Chlamydomonas reinhardtii have a redundantly essential function and associate with ZeppL-LINE1 elements

Centromeres in eukaryotes are defined by the presence of histone H3 variant CENP-A/CENH3. Chlamydomonas encodes two predicted CENH3 paralogs, CENH3.1 and CENH3.2, that have not been previously characterized. We generated peptide antibodies to unique N-terminal epitopes for each of the two predicted Chlamydomonas CENH3 paralogs as well as an antibody against a shared CENH3 epitope. All three CENH3 antibodies recognized proteins of the expected size on immunoblots and had punctuated nuclear immunofluorescence staining patterns. These results are consistent with both paralogs being expressed and localized to centromeres. CRISPR-Cas9 mediated insertional mutagenesis was used to generate predicted null mutations in either CENH3.1 or CENH3.2. Single mutants were viable but cenh3.1 cenh3.2 double mutants were not recovered, confirming that the function of CENH3 is essential. We sequenced and assembled two chromosome-scale Chlamydomonas genomes from strains CC-400 and UL-1690 (a derivative of CC-1690) with complete centromere sequences for 17/17 and 14/17 chromosomes respectively, enabling us to compare centromere evolution across four isolates with near complete assemblies. These data revealed significant changes across isolates between homologous centromeres including mobility and degeneration of ZeppL-LINE1 (ZeppL) transposons that comprise the major centromere repeat sequence in Chlamydomonas. We used Cleavage Under Targets and Tagmentation (CUT&Tag) to purify and map CENH3-bound genomic sequences and found enrichment of CENH3-binding almost exclusively at predicted centromere regions. An interesting exception was chromosome 2 in UL-1690, which had enrichment at its genetically mapped centromere repeat region as well as a second, distal location, centered around a single recently acquired ZeppL insertion. The CENH3-bound regions of the 17 Chlamydomonas centromeres ranged from 63.5kb (average lower estimate) to 175kb (average upper estimate). The relatively small size of its centromeres suggest that Chlamydomonas may be a useful organism for testing and deploying artificial chromosome technologies. Significance statementHistone H3 variant CENP-A/CENH3 is a conserved centromere protein in eukaryotes but has not been well-characterized in green algae. Our data establish the function of CENH3 at Chlamydomonas centromeres and identify an unexpected strain-specific neocentromere candidate region in chromosome 2 likely caused by a single ZeppL-LINE1 insertion into a genic region that is distal to the native chromosome 2 centromere.

genetics↗

bioRxiv2025

A differentiated and durable allogeneic strategy applicable to cell therapies

Autologous T cell therapies have shown profound clinical responses; however, their widespread use has been limited primarily due to their individualized manufacturing requirements. To develop a persistent "off-the-shelf" allogeneic (Allo) approach, a multiplex Nme2Cas9-based cytosine base editor was deployed to knockout select HLA Class I and II alleles (HLA-A, HLA-B, and the class II transactivator (CIITA)), while retaining HLA-C to protect from NK cell rejection. Matching the residual HLA-C allele from homozygous donors to the host prevented rejection of the donor T cells by allogeneic host T and NK cells. Site-specific integration of a tumor-specific CAR or TCR into the TRAC locus using SpyCas9 nuclease and an adeno-associated virus (AAV) template allowed for high localized insertion rate while simultaneously removing the endogenous TCR and preventing GvHD. Using a lipid nanoparticle (LNP)-based delivery system of the editing components enabled a robust cell engineering process, achieving high editing rates and cell expansion. These allogeneic T cells demonstrated comparable functional activity to their autologous counterparts in preclinical assays. Moreover, this gene editing approach generated cells with minimal chromosomal aberrations. The Allo strategy has also been applied to induced pluripotent stem cells (iPSCs), suggesting potential applications in regenerative medicine applications.

bioengineering↗

bioRxiv2025

Biosynthesis and Physiological Significance of Organ-Specific Flavonol Glycosides in Solanaceae

Flavonols are subclasses of flavonoids, with hundreds of structures identified in plants. This chemical diversity primarily arises from glycosylation, where sugars are selectively added to the flavonol backbone. While flavonol profiles vary across species and organs, the evolutionary forces shaping this chemodiversity and the physiological significance of specific glycosides remain a mystery. Here, we reveal that finely tuned transcriptional regulation and the sugar selectivity of glycosyltransferases drive the formation of distinct organ specific flavonol profiles and a specific flavonol is necessary for male fertility. In Solanaceae pollen, two flavonol glycosides, K2 (kaempferol 3-O-glucosyl(1 [->] 2)galactoside) and Q2 (quercetin 3-O-glucosyl(1 [->] 2)galactoside), are exclusively accumulated. K2 is evolutionarily conserved, while Q2 was lost over time. Consistently, K2 is essential for male fertility, whereas Q2 and aglycones fail to rescue fertility defects. These findings suggest that individual flavonol glycosides have distinct physiological roles, either actively maintained or discarded through evolutionary selection.

plant biology↗

bioRxiv2025

Munc13-4 mediates tumor immune evasion by regulating the sorting and secretion of PD-L1 via exosomes

Tumor-derived extracellular vesicles primarily carry PD-L1 via exosomes, which interact with PD-1 receptors on T cells, impacting immune responses in the tumor microenvironment and beyond, leading to a more extensive immunosuppressive landscape. However, the mechanisms governing exosomal PD-L1 sorting and secretion remain elusive. In this study, we identified Munc13-4 as a crucial regulator of exosomal PD-L1 sorting and secretion. Deletion of Munc13-4 in breast tumors enhances T cell-mediated anti-tumor immunity, suppresses tumor growth, and improves the efficacy of immune checkpoint inhibitors. Our results illustrate how Munc13-4 collaborates with HRS, Rab27, and SNAREs to facilitate PD-L1 sorting and secretion via exosomes. The cryo-EM structure of the Munc13-4-Rab27a complex provide new insights into its role in exosome secretion. Importantly, we discovered that Munc13-4 has a novel role in sorting PD-L1 onto exosomes, which relies on the formation of a ternary complex with PD-L1 and HRS. In addition, IFN{gamma} stimulation modifies Munc13-4 and HRS, establishing a dynamic regulatory mechanism that enables tumor cells to adapt to immune pressure by modulating PD-L1 sorting. Using a specially designed peptide to disrupt the Munc13-4-PD-L1 interaction and impede PD-L1 sorting significantly enhances anti-tumor immunity and slows tumor growth in vivo. These results highlight the potential of targeting the Munc13-4-PD-L1 axis to suppress tumor immune evasion.

cell biology↗

bioRxiv2025

Midkine Attenuates Aβ Fibril Assembly and Amyloid Plaque Formation

Proteomic profiling of Alzheimers disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with A{beta} since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates A{beta} assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both A{beta}40 and A{beta}42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdk gene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and detergent-insoluble proteome in these mouse models indicates significant accumulation of A{beta} and A{beta}-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimers disease.

biochemistry↗

bioRxiv2025

Intratumoral Resident Microbes Directly Participate in Resistance to EGFR-TKI Targeted Drug Therapy through Metabolism in NSCLC

EGFR-TKIs targeted therapy represents a cornerstone in the treatment of non-small cell lung cancer (NSCLC). Nonetheless, a subset of patients inevitably develops acquired resistance to EGFR-TKIs, posing a significant clinical challenge. An increasing number of evidence has documented the presence of microbial communities within tumor microenvironments, but the potential interplay between tumor-resident microbiota and resistance to EGFR-TKIs remains poorly understood. Here, we report that prolonged EGFR-TKIs treatment markedly alters the diversity of tumor-resident microbiota, characterized by a notable enrichment of Bacillus mycoides and Pseudomonas veronii. In vitro experiments revealed that co-culture of gefitinib with either B. mycoides or P. veronii significantly attenuated its tumor-suppressive efficacy, both in vitro and in vivo. Mechanistically, gefitinib underwent extensive biotransformation in the presence of these bacteria, yielding redox derivatives and conjugation products, which collectively diminished its antitumor activity. Specifically, B. mycoides metabolized gefitinib into B.mPM9-C33 H45 Cl F N3 O4, while P. veronii generated P.vPM2-C24 H29 Cl N4 O3, both of which were consistently detected in in vivo and in vitro models. Furthermore, heterologous expression of maltose acetyltransferase from B. mycoides in E. coli BL21 conferred the capacity to metabolize gefitinib, underscoring the enzymatic basis of this metabolic conversion. Collectively, these findings demonstrate that B. mycoides and P. veronii drive tumor resistance to EGFR-TKIs through metabolic inactivation of the drug, unveiling a previously unrecognized role of tumor-resident microbiota in modulating therapeutic responses and providing novel insights into the mechanisms underlying EGFR-TKIs resistance in NSCLC.

microbiology↗