Biology subjects

Du, D.

Publications and source records attributed to Du, D..

At least 19 recordsLinked to original sources

bioRxiv2026

An endodermal subpopulation generates neural and mesodermal fates in the posterior chick embryo

Embryogenesis occurs through a progressive narrowing of cell fate potential, initiating with the segregation of three distinct germ layers during gastrulation. Although classically, each germ layer contributes to distinct tissue types as development proceeds, this view has been revised with the discovery of neuromesodermal progenitors (NMPs) -- a bipotent progenitor population in the posterior embryo that gives rise to traditionally ectodermal and mesodermal tissues after gastrulation has concluded. However, until now the notion of lineage restriction of the endoderm to gastrointestinal, respiratory, and endocrine tissues has largely remained intact. Here, we describe a unique subpopulation in the chick endoderm that initially lines the ventral surface of Hensens node (the amniote organizer). As posterior regression of the node ends with termination of the primitive streak, these cells undergo an FGF-dependent epithelial-to-mesenchymal transition, erasing their endodermal identity as they invade the tailbud and subsequently differentiate into a remarkably broad range of cell types including paraxial, lateral plate, and intermediate mesoderm, and to a lesser extent, notochord and neural tube. Disrupting ingression of node endoderm reduced embryonic axis elongation -- a process attributed to mesoderm -- by 50%. Through lineage barcoding, single-cell RNA sequencing, and fate mapping experiments, we conclude that the endodermal compartment of Hensens node harbors a mixed population of fate restricted and multipotent progenitor cells that give rise to clonal populations spanning traditional germ layer boundaries. These findings illustrate a surprising example of germ layer plasticity and fate convergence across distant progenitor populations during amniote development.

developmental biology↗

bioRxiv2026

Serine Stabilizes SLC7A11 and Enhances Cystine Influx to Protect Against Acute Pancreatitis

Lethal sterile inflammatory diseases are linked to amino acid metabolism, but the role of serine remains unclear. Here, we show that dysregulated serine metabolism and reduced plasma serine levels correlate with disease severity of acute pancreatitis (AP) in patients and mouse models. Elevating serine levels via exogenous serine supplementation or pancreatic phosphoglycerate dehydrogenase (PHGDH) overexpression mitigates pancreatic injury, whereas a serine deprivation diet or pancreatic PHGDH knockdown exacerbates AP. Serine prevents cell death and oxidative stress in pancreatic acinar cells, human induced pluripotent stem cells-derived pancreatic organoids and mouse pancreatic tissue. Serine enhances cysteine and glutathione biosynthesis primarily by promoting solute carrier family 7 member 11 (SLC7A11)-dependent cystine uptake rather than by serving as a direct substrate. Mechanistically, the E3 ubiquitin ligase NEDD4 mediates ubiquitination and degradation of SLC7A11, whereas serine binds to NEDD4 and thereby inhibits SLC7A11 degradation. Similarly to serine, pharmacological inhibition of NEDD4 alleviates lipid peroxidation and pancreatic injury. These findings identify serine as a critical signaling regulator of SLC7A11 stability and oxidative stress, and provides a new therapeutic strategy for AP and associated sterile inflammatory disorders. HighlightsAcute pancreatitis (AP) is linked to abnormal serine metabolism and serine depletion. Serine prevents cell death in AP acinar cells, human pancreatic organoids and mice. Serine promotes SLC7A11-dependent cystine uptake and glutathione levels in acinar cells. Serine reduces NEDD4-mediated ubiquitination of SLC7A11. In briefSerine protects against cell death and pancreatic injury in acute pancreatitis by stabilizing SLC7A11 through disruption of NEDD4-mediated ubiquitination in acinar cells.

pharmacology and toxicology↗

bioRxiv2026

Macrophage immunosenescence prolongs intraocular inflammation in aged mice via impaired induction of regulatory T cells

Immune-mediated intraocular inflammation, called uveitis, is a leading cause of global blindness, with the highest burden of visual impairment falling on older individuals. Immunosenescence, the functional changes in immune cells with aging, impacts the age-associated immune response, but how immunosenescence and the molecular regulators of the age-associated immune response affect the clinical course of uveitis remains unclear. In the murine model of experimental autoimmune uveitis (EAU), aged mice demonstrated a delayed onset and peak of intraocular inflammation compared to young mice. In contrast to the canonical monophasic inflammation that rapidly resolves in young mice, aged mice developed persistent, chronic inflammation. Transcriptomic and flow-cytometric analyses of immune cells and the receptor-ligand interactome revealed a dominant macrophage-CD4+ T cell signature. This signaling pathway was functionally altered on both ends: macrophages from aged mice had an impaired capacity to generate peripherally induced regulatory T cells (pTreg) through an IL-6 regulated pathway, while CD4+ T cells co-cultured with aged macrophages demonstrated increased proliferation. Our study establishes aging as a key regulator of the effector immune response in uveitis. Regulatory T cells, specifically pTreg, are essential for resolving inflammation in uveitis and an impaired ability to induce pTreg led to a sustained, chronic inflammatory uveitis phenotype in old mice, thereby linking immunosenescence to persistent neuroinflammation. These findings highlight potential therapeutic avenues for vision-threatening uveitis, especially in older patients.

immunology↗

bioRxiv2025

A single-component optogenetic toolkit for programmable control of microtubule

Microtubules (MTs) form dynamic cytoskeletal scaffolds essential for intracellular transport, organelle positioning, and spatial organization of signaling. Their architecture and function are continuously remodeled through the concerted actions of microtubule-associated proteins (MAPs), post-translational modifications (PTMs), and molecular motors. To precisely interrogate these processes in living systems, we developed a genetically encoded optogenetic toolkit for spatiotemporal control of MT organization and dynamics. By replacing native multimerization motifs with a blue light-responsive oligoermization domain, we have engineered single-component probes, OptoMT and OptoTIP, that reversibly label MT polymers or track plus-ends with tunable kinetics from seconds to minutes. When coupled to enzymatic effectors, these modules enable localized tubulin acetylation or detyrosination, directly linking PTMs to MT stability. We further engineered OptoMotor, a light-activatable kinesin platform that reconstitutes tail-dependent cargo transport along MTs, and OptoSAW, a light-triggered severing actuator for controlled MT disassembly. Using these tools, we reveal how local MT integrity governs lysosomal trafficking and ER-associated signaling dynamics. Collectively, this versatile single-component toolkit bridges molecular design with cytoskeletal function, offering new avenues to illuminate how dynamic cytoskeletal architectures coordinate intracellular organization, transport, and signaling.

cell biology↗

bioRxiv2025

Human microglia in brain assembloids display region-specific diversity and respond to hyperexcitable neurons carrying SCN2A mutation

Microglia critically shape neuronal circuit development and function, yet their region-specific properties and roles in distinct circuits of the human brain remain poorly understood. In this study, we generated region-specific brain organoids (cortical, striatal, and midbrain), each integrated with human microglia, to fill this critical gap. Single-cell RNA sequencing uncovered six distinct microglial subtypes exhibiting unique regional signatures, including a subtype highly enriched for the GABAB receptor gene within striatal organoids. To investigate the contributions of microglia to neural circuitry, we created microglia-incorporated midbrain-striatal assembloids, modeling a core circuit node for many neuropsychiatric disorders including autism. Using chemogenetics to activate this midbrain-striatal circuit, we observed increased calcium signaling in microglia involving GABAB receptors. Leveraging this model, we examined microglial responses within neural circuits harboring an SCN2A nonsense (C959X) mutation associated with profound autism. Remarkably, microglia displayed heightened calcium responses to SCN2A mutation-mediated neuronal hyperactivity, and engaged in excessive synaptic pruning. These pathological effects were reversed by pharmacological inhibition of microglial GABAB receptors. Collectively, our findings establish an advanced platform to dissect human neuroimmune interactions in sub-cortical regions, highlighting the important role of microglia in shaping critical circuitry related to neuropsychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/657874v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@125b36eorg.highwire.dtl.DTLVardef@270079org.highwire.dtl.DTLVardef@903525org.highwire.dtl.DTLVardef@19145c4_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserModeling regional microglial diversity in sub-cortical regions is challenging. We generated human organoid and assembloid models containing microglia that acquire region-specific heterogeneity. Our work shows dynamic responses of microglia when exposed to hyperexcitable midbrain-striatal circuits, providing an exciting platform to study neuroimmune interactions in human brain development and neuropsychiatric disorders, including SCN2A mutation-mediated monogenic autism. HighlightsO_LI* Single-cell RNA sequencing analyses reveal six distinct microglial subtypes that spontaneously attain unique specialization in human cortical, striatal, and midbrain organoids. C_LIO_LI* Microglia facilitate axonal projections across regional organoids, promoting assembloid formation. C_LIO_LI* Microglia respond to hyperexcitable neurons via calcium signaling and exhibit excessive pruning of neuronal synapses. C_LIO_LI* Blocking microglial GABAB receptors normalizes calcium activity and reduces synaptic pruning, suggesting a potential targeting strategy for synaptic deficits. C_LI

neuroscience↗

bioRxiv2025

β-Glucan Modulates Monocyte Plasticity and Differentiation Capacity to Mitigate DSS-Induced Colitis

Trained immunity involves the reprogramming of innate immune cells after an initial exposure, resulting in heightened inflammatory responses to subsequent stimuli and enhanced bactericidal capacity during infection. However, this proinflammatory state could also exacerbate chronic conditions like inflammatory bowel disease (IBD), which is characterized by persistent inflammation and microbial imbalance. It remains unclear how trained immunity influences IBD pathogenesis and whether it can be harnessed therapeutically. In our study, pretreatment with {beta}-glucan reprogrammed bone marrow hematopoietic progenitors and peripheral monocytes, inducing a profound shift in monocyte plasticity and significantly reducing the severity of dextran sulfate sodium (DSS)-induced colitis. Adoptive transfer of bone marrow or peripheral monocytes from {beta}-glucan-trained mice into naive mice conferred robust protection against colitis, demonstrating that this protective effect is transferable. Trained mice also displayed improved clearance of intestinal bacterial infections. Single-cell RNA sequencing revealed an expansion of reparative Cx3cr1 macrophages derived from Ly6Chi monocytes, correlating with accelerated colonic epithelial regeneration. Collectively, these findings reveal how {beta}-glucan-induced trained immunity modulates monocyte differentiation to ameliorate experimental colitis, highlighting the potential of harnessing trained immunity as a therapeutic strategy to recalibrate innate immune responses and restore gut homeostasis in IBD, shedding light for future clinical applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/653036v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1b969c2org.highwire.dtl.DTLVardef@1ce603dorg.highwire.dtl.DTLVardef@10582forg.highwire.dtl.DTLVardef@10d7de6_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

CD4+ tissue resident memory Th17 cells drive IL-17A-mediated joint pathology in Spondyloarthritis

ObjectivesInterleukin (IL)-17A is a key driver of Spondyloarthritis (SpA) joint pathology. We aimed to identify its cellular source in synovial tissue from patients with two forms of SpA namely Axial SpA (AxSpA) and Psoriatic arthritis (PsA). MethodsSynovial tissue from patients with SpA was profiled using single-cell RNA sequencing (scRNA-seq: AxSpA, n=5 and PsA, n=6) or spatial RNA profiling (PsA, n=4). CellPhoneDB was used to infer cell-cell communication. Tissue resident memory Th17 (TRM17)-like cells were generated in vitro using blood memory CD4+ T cells from SpA patients. An epigenetic inhibitor library, siRNA and clustered regularly interspaced short palindromic repeats (CRISPR) were used to identify epigenetic regulator(s) for TRM17. ResultsscRNA-seq showed that CD4+CXCR6+ TRM17 cells are the predominant spontaneous IL17A producers in SpA synovium. Cell-cell communication and single-cell spatial analysis support the interaction between TRM17 and CLEC10A+ dendritic cells, which were activated in SpA. Both sublining and lining fibroblasts in SpA synovium showed evidence of IL-17A activation. In vitro-generated CD4+ TRM17-like cells phenocopied joint tissue TRM17, producing IL-17A/F upon T cell receptor (TCR) stimulation, which was further enhanced by cytokines. Perturbation of BRD1 inhibited the generation of TRM17-like cells. ConclusionsCD4+ TRM17 cells are the predominant source of IL-17A in SpA synovial tissue. TCR stimulation is essential for the secretion of IL-17A by CD4+TRM17-like cells. The epigenetic regulator BRD1 contributes to the generation of CD4+TRM17. Depleting CD4+TRM17 cells in SpA is thus a therapeutic strategy with potential to induce long-term remission. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSInterleukin (IL)-17A plays a key role in the immunopathogenesis of Spondyloarthritis (SpA), but its cellular source in joint tissue has not been determined previously. The induction and accumulation of CD4+ tissue resident memory Th17 (TRM17) cells following the clearance of pathogens has been described in skin, lung and kidney. Whether CD4+ TRM17 cells also accumulate in the joint and contribute to the pathology of SpA is not clear. What this study addsO_LICD4+ TRM17 cells are present in SpA synovial tissue and are the predominant source of IL17A C_LIO_LICD4+ TRM17 cells in SpA joints express IL17A without any in vitro exogenous stimulation C_LIO_LIT cell receptor (TCR) rather than cytokine stimulation is essential for IL-17A production by CD4+ TRM17-like cells C_LIO_LIThe epigenetic regulator BRD1 contributes to the generation of CD4+ TRM17-like cells. C_LI How this study might affect research, practice or policyOur findings identify CD4+ TRM17 cells as the primary source of IL-17A in SpA synovium, a previously unrecognized role for these cells. Key questions remain: How do CD4+ TRM17 cells relate to IL-17A producers in synovial fluid? What mechanisms induce and maintain them in the joint? How do they interact with other cells to promote arthritis? These questions warrant further investigation. In addition, our data suggest that targeting CD4+ TRM17 cells, the "factory" of IL-17A in SpA synovial tissue, has the potential to induce long-term remission, encouraging future efforts to develop new therapies to deplete CD4+ TRM17 cells in SpA.

immunology↗

bioRxiv2024

AxSpA joint tissue is characterised by HLA-DR+ tissue resident memory (TRM) and killer cell immunoglobulin-like receptor (KIR)+ CD8+ T cell subsets

ObjectiveAxial Spondyloarthritis (AxSpA) is a common inflammatory arthritis with HLA-B*27 as the major genetic risk. Recent discoveries of AxSpA-specific T cell receptor (TCR) motifs and the self and bacterial peptides that they recognize support a pathogenic role of CD8+ T cells. Despite of previous work on synovial fluid, the characteristics of CD8 cells in joint tissue are currently unknown. MethodSynovial tissues from 5 AxSpA patients were used for single cell RNA sequencing (scRNA-seq). Paired TCR sequencing was carried out for 2. The abundance of KIR+CD8+ T cells in the blood from 9 AxSpA patients and 10 healthy controls was measured using flow cytometry. The expression of naive and memory T cell markers (CCR7, CD45RA and CD45RO) were compared between KIR+ and KIR- CD8 cells. ResultsWe observed conventional, TRAV1-2+ mucosal-associated invariant T (MAIT) cell and MKI67+ proliferating cell populations in synovium. Following sub-clustering of conventional CD8+ T cells, HLA-DR+ tissue resident memory (TRM), circulating, KIR+ and FCGR3A+ (encoding CD16) cell subsets were observed. HLA-DR+ TRM and KIR+ cells were clonally expanded and exhibited distinct transcriptional features, enriched for T cell activation pathways and natural killer (NK) cell-mediated cytotoxicity pathway respectively. Lastly, KIR+CD8+ T cells were increased in AxSpA blood and enriched for CD45RA+CCR7- TEMRA cells. ConclusionHere we present the very first transcriptomic profiling of CD8+ T cells in synovium tissue and highlight potential roles of HLA-DR+ TRM and KIR+ cells in AxSpA pathology. This study adds novel insights to the disease mechanisms and offers new therapeutic opportunities.

immunology↗

bioRxiv2024

Effector T Cells under Hypoxia have an Altered Transcriptome Similar to Tumor-Stressed T Cells Found in Non-Responsive Melanoma Patients

BackgroundIn the Tumor Microenvironment (TME), hypoxia stands as a significant factor that modulates immune responses, especially those driven by T cells. As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma. MethodsTo generate detailed information on tumor oxygenation and T cell accessibility, we utilized mathematical modeling of human melanoma tissue microarrays (TMAs) that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. We created tumor maps and derived plots showing the fraction of CD4 and CD8 T cells against the distance to the nearest vessel and oxygen pressure. To assess their function and transcriptional changes caused by hypoxia, effector T cells were generated and cultured under hypoxia (0.5% oxygen) or normoxia (21% oxygen). The T cell hypoxia-transcriptional signature was compared against datasets from msigDB, iATLAS (clinical trials of melanoma patients treated with immune checkpoint inhibitors), ORIEN AVATAR (real-world melanoma patients treated with immune checkpoint inhibitors, ICIs), and a single-cell atlas of tumor-infiltrating lymphocytes (TILs). ResultsWe made three specific observations: 1) in melanoma T cells preferentially accumulated in oxygenated areas close to blood vessels (50-100 micrometers from the vasculature in the regions of high oxygen availability) but not in hypoxic areas far from blood vessels. 2) Our analysis confirmed that under hypoxia, T cell functions were significantly reduced compared to normoxic conditions and accompanied by a unique gene signature. Furthermore, this hypoxic gene signature was prevalent in resting and non-activated T cells. Notably and clinically relevant, the hypoxic T cell gene set was found to correlate with reduced Overall Survival (OS) and reduced progression-free survival (PFS) in melanoma patients, which was more pronounced in non-responder patients undergoing ICI therapy. 3) Finally, compared with a single-cell atlas of tumor-infiltrating T cells, our hypoxia signature aligned with a population of cells at a state termed stress response state (TSTR). ConclusionOur study highlights the critical role of hypoxia in shaping T cell distribution and its correlation with clinical outcomes in melanoma. We revealed a preferential accumulation of T cells in oxygenated areas. Moreover, hypoxic T cells develop a distinct hypoxic gene signature prevalent in resting, non-activated T cells and TSTR that was also associated with poorer outcomes, particularly pronounced among non-responders to ICIs. Key MessagesWhat is already known on this topic: Hypoxia significantly impairs T cell functions, including reduced proliferation and cytokine production. This impairment may contribute to immune evasion and resistance to immune therapies, such as ICIs, adoptive transfer of TILs, and Chimeric Antigen Receptor (CAR) T cells. Despite the established impact of hypoxia on T cell function, the precise spatial distribution of T cells in relation to oxygen availability within the TME and how this affects clinical outcomes in melanoma patients remains unclear. Additionally, the specific transcriptional changes in T cells induced by hypoxia and their prevalence in different T cell states, as well as the implications for resistance to ICIs, have not been thoroughly investigated. Understanding these aspects is crucial for developing targeted therapies to overcome hypoxia-induced resistance and improve immunotherapy efficacy. What this study adds: This study elucidates the profound impact of hypoxia on T cells in melanoma. Our findings reveal that T cells accumulate in well-oxygenated regions near blood vessels, whereas hypoxic conditions significantly impair their proliferation and cytokine production. By addressing the transcriptional changes induced by hypoxia, we demonstrated its prevalence in resting and non-activated T cells and TSTR. Moreover, we found that hypoxia is associated with shorter OS and PFS in melanoma patients, particularly in non-responders to ICIs. This research highlights the critical role of hypoxia in modulating T cell spatial behavior, contributing to immune evasion and poor clinical outcomes in melanoma. How this study might affect research, practice, or policy: The findings emphasizes hypoxias critical role in modulating T cell behavior and its potential as a biomarker for treatment outcomes. These insights could inform the development of therapeutic strategies aimed at improving T cell function in hypoxic TMEs, thereby enhancing the efficacy of immunotherapies for melanoma and other solid tumors. Additionally, the studys results may influence policies regarding the evaluation and implementation of combination therapies that target hypoxia to improve patient outcomes.

immunology↗

bioRxiv2024

How does the ion concentration affect the functions of kinesin BimC

BimC family proteins are bipolar motor proteins belonging to the kinesin superfamily which promote mitosis by crosslinking and sliding apart antiparallel microtubules. Understanding the binding mechanism between the kinesin and the microtubule is crucial for researchers to make advances in the treatment of cancer and other malignancies. Experimental research has shown that the ion concentration affects the function of BimC significantly. But the insights of the ion-dependent function of BimC remain unclear. By combining molecular dynamics (MD) simulations with a series of computational approaches, we studied the electrostatic interactions at the binding interfaces of BimC and the microtubule under different KCl concentrations. We found the electrostatic interaction between BimC and microtubule is stronger at 0 mM KCl compared to 150 mM KCl, which is consistent with experimental conclusions. Furthermore, important salt bridges and residues at the binding interfaces of the complex were identified, which illustrates the details of the BimC-microtubule interactions. Molecular dynamics analyses of salt bridges identified that the important residues on the binding interface of BimC are positively charged, while those residues on the binding interface of the tubulin heterodimer are negatively charged. The finding in this work reveals some important mechanisms of kinesin-microtubule binding, which helps the future drug design for cancer therapy.

biophysics↗

bioRxiv2024

Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer

Magnesium (Mg) deficiency is associated with increased risk and malignancy of colorectal cancer (CRC), yet the underlying mechanisms remain elusive. Here we used genomic, proteomic, and phosphoproteomic data to elucidate the impact of Mg deficiency on CRC. Genomic analysis identified 160 genes with higher mutation frequencies in Low-Mg tumors, including key driver genes such as KMT2C and ERBB3. Unexpectedly, initiation driver genes of CRC, such as TP53 and APC, displayed higher mutation frequencies in High-Mg tumors. Additionally, proteomics and phosphoproteomics indicated that low tumorous Mg content may activate epithelial-mesenchymal transition (EMT) by modulating inflammation or remodeling the phosphoproteome of cancer cells. Notably, we observed a negative correlation between the phosphorylation of DBN1 at S142 (DBN1S142p) and Mg content. A mutation in S142 to D (DBN1S142D) mimicking DBN1S142p upregulated MMP2 and enhanced cell migration, while treatment with MgCl2 reduced DBN1S142p, thereby reversing this phenotype. Mechanistically, Mg2+ attenuated the DBN1-ACTN4 interaction by decreasing DBN1S142p, which, in turn, enhanced the binding of ACTN4 to F-actin and promoted F-actin polymerization, ultimately reducing MMP2 expression. These findings shed new light on the crucial role of Mg deficiency in CRC progression and suggest that Mg supplementation may offer a promising preventive and therapeutic strategy for CRC.

cancer biology↗

bioRxiv2023

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Decoding high-quality human genomic sequences requires comprehensive analysis of DNA sequence functionality. Through computational and experimental approaches, researchers study the genotype-phenotype relationship and generate important datasets that help unravel complicated genetic blueprints. This study explores the use of deep learning, particularly pre-trained models like DNA_bert_6 and human_gpt2-v1, in interpreting and representing human genome sequences. We meticulously construct multiple datasets linking genotypes and phenotypes to fine-tune pre-trained models for precise DNA sequence classification. Furthermore, we specifically focused on the human endogenous retrovirus (HERV) dataset with commendable classification performance (both binary and multi-classification accuracy and F1 values above 0.935 and 0.888, respectively). We evaluate the influence of sequence length on classification results and analyze the impact of feature extraction in the models hidden layers using the HERV dataset. To further understand the phenotype-specific patterns learned by the model, we perform enrichment, pathogenicity and conservation analyzes of specific motifs in the HERV sequence with high average local representation weight (LRAW) scores. Overall, the generated datasets further provide numerous additional genotype-phenotype datasets for evaluating the performance of genomic models. The findings highlight the potential of large models in learning DNA sequence representations, particularly when utilizing the HERV dataset, and provide valuable insights for future research. This work represents an innovative strategy that combines pre-trained model representations with classical omics methods for analyzing the functionality of genome sequences, fostering cross-fertilization between genomics and advanced AI. The source code and data are available at https://github.com/GeorgeBGM/Genome_Fine-Tuning.

bioinformatics↗

bioRxiv2023

ABDS: tool suite for analyzing biologically diverse samples

MotivationAnalytics tools are essential to identify informative molecular features about different phenotypic groups. Among the most fundamental tasks are missing value imputation, signature gene detection, and expression pattern visualization. However, most commonly used analytics tools may be problematic for characterizing biologically diverse samples when either signature genes possess uneven missing rates across different groups yet involving complex missing mechanisms, or multiple biological groups are simultaneously compared and visualized. ResultsWe develop ABDS tool suite tailored specifically to analyzing biologically diverse samples. Mechanism-integrated group-wise imputation is developed to recruit signature genes involving informative missingness, cosine-based one-sample test is extended to detect enumerated signature genes, and unified heatmap is designed to comparably display complex expression patterns. We discuss the methodological principles and demonstrate the conceptual advantages of the three software tools. We also showcase the biomedical applications of these individual tools. Implemented in open-source R scripts, ABDS tool suite complements rather than replaces the existing tools and will allow biologists to more accurately detect interpretable molecular signals among diverse phenotypic samples. Availability and implementationThe R Scripts of ABDS tool suite is freely available at https://github.com/niccolodpdu/ABDS. Contactyuewang@vt.edu Supplementary informationSupplementary materials are available at Bioinformatics Advances online.

bioinformatics↗

bioRxiv2023

MRE11A: a novel negative regulator of human DNA mismatch repair

DNA mismatch repair (MMR) is a highly conserved pathway that corrects DNA replication errors. Although well characterized, MMR factors remain to be identified. As a 3-5 exonuclease and endonuclease, meiotic recombination 11 homolog A (MRE11A) is implicated in multiple DNA repair pathways. However, the role of MRE11A in MMR is unclear. Here, we show that MRE11A deficiency increased the sensitivity of HeLa cells to N-methyl-N nitro-N nitrosoguanidine (MNNG) treatment, implying a potential role of MRE11 in MMR. Moreover, we found MRE11A was largely recruited to chromatin and negatively regulated the DNA damage signals within the first cell cycle after MNNG treatment. We also showed that knockdown of MRE11A increased, while overexpressing MRE11A decreased, MMR activity in HeLa cells, suggesting that MRE11A negatively regulates MMR activity. Furthermore, we show that the recruitment of MRE11A to chromatin requires MLH1 and that MRE11A competes with PMS2 for binding to MLH1. This decreases PMS2 levels in whole cell and on chromatin, and consequently comprises MMR activity. Collectively, our findings reveal that MRE11A is a negative regulator of human MMR.

molecular biology↗

bioRxiv2022

Dynamic changes in the transcriptome of oocytes during adolescent-onset PCOS in mice

(1) Background: This study aimed to explore temporal changes in the transcriptome of oocytes in an adolescent-onset polycystic ovarian syndrome (PCOS) mouse model. (2) Methods: An adolescent-onset PCOS mouse model was established using DHEA. Genes with a similar expression trend over time were identified using trend analysis. KEGG pathway enrichment analysis and gene regulatory network diagrams were examined for signaling pathways to identify potential hub genes related to the pathogenesis of PCOS. (3) Results: Four main trends of gene expression were extracted, of which six combinations of Venn diagrams were generated. Differentially expressed genes were mainly enriched in oxidative phosphorylation, cell cycle, P53 signaling pathway. Cell cycle-related genes (Skp1, Ccnb1, Orc1 and 5, Wee2, Mapk3, Cdc20) were abnormally down-regulated in the DHEA group. Ptges3 was the top1 DEGs at the initial stage of PCOS modeling. (4) Conclusion: This study provides a novel insight into the altered transcriptome of oocytes from PCOS mice. mtDNA-related genes and Cell cycle-related genes play the most important role in the development of PCOS. Ptges3 was the one of the top DEGs which was up-regulated in DHEA group at the initial stage of modeling, which suggested it may play an important role in the early stage of PCOS.

genetics↗

bioRxiv2022

A 4-bp natural deletion of maize Na+/H+ exchanger gene alters maize salt stress tolerance

Soil salinity is a major environmental constraint severely reducing plant growth and crop productivity worldwide. Knowledge of salt tolerance-related genes can facilitate improving crop salt tolerance and alleviating the threat of increasing saline area to world food security. Here, we identified a major locus SALT TOLERANCE 1 (qST1) conferring maize salt tolerance via bulked segregant RNA-Seq (BSR-Seq). qST1 encodes a plasma membrane Na+/H+ exchanger ZmSOS1 which is the ortholog of Arabidopsis thaliana SOS1 gene. In salt-sensitive variety D9H, the natural variation of 4-bp deletion in the coding sequence of ZmSOS1 gene was the causal allele for salt sensitivity. We identified two ethyl methanesulfonate-induced mutants, zmsos1-1 and zmsos1-2, which were sensitive to salt stress and cant complement salt-sensitive variety under salt stress within an allelism test. Overexpression of ZmSOS1 enhanced maize seedling salt tolerance. ZmSOS1 can increase the salt tolerance of Arabidopsis sos1-1 mutant and can be activated by AtSOS2 and AtSOS3 in yeast cells, suggesting that ZmSOS1 confers salt tolerance through the conserved SOS signaling pathway in maize. The detrimental allele harboring the 4-bp deletion was rarely found in the natural population but appeared in an important heterotic group composed of x1132x-derived inbred lines which have been used widely for breeding dozens of hybrid varieties in China. The 4-bp deletion-based molecular marker has been successfully used to improve salt-sensitive varieties in a backcross and marker-assisted breeding program by screening and purging this deleterious allele.

plant biology↗

bioRxiv2022

RBFOX2 deregulation promotes pancreatic cancer metastasis through alternative splicing

RNA splicing is an important biological process associated with cancer initiation and progression, yet in pancreatic cancer the role and regulation of splicing is not well understood. From a forward genetic screen in a mouse model of pancreatic cancer, we identified an enrichment of RNA binding proteins (RBPs) associated with the spliceosome. Here, we link deregulation of RBFOX2, an RBP of the FOX family, to pancreatic cancer progression and liver metastasis. We show that RBFOX2 regulation in pancreatic cancer occurs at both the RNA and protein level, and that nuclear localization of RBFOX2 is significantly reduced in poorly differentiated PDAC. Deregulation of RBFOX2 in PDAC is associated with an enrichment of exon exclusion events in transcripts encoding proteins involved in cytoskeletal remodeling and invadopodia programs that potentiate metastatic potential in vivo. Using splice-switching antisense oligonucleotides (AONs) and inducible cDNA isoforms, we demonstrate that RBFOX2 mediated exon exclusion in ABI1 controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells, and that ABI1 splice-switching enhances cellular phenotypes associated with cancer cell stemness. Together, our data identify a novel role for RBFOX2 deregulation in promoting PDAC progression through alternative splicing regulation.

cancer biology↗

bioRxiv2022

CRISPR-based targeted haplotype-resolved assemblies of a megabase region

Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved de novo assemblies of targeted genomic regions with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assemblies, our targeted approach achieved comparable completeness and accuracy with greatly reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

genomics↗