Biology subjects

Yang, W.

Publications and source records attributed to Yang, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

The future burden of congenital Toxoplasmosis in Africa under demographic and climate change

The impact of climate change on environmental pathogens is a question whose importance will amplify in coming years. The protozoan parasite and global zoonosis Toxoplasma gondii is one such: empirical evidence indicates that oocyst survival is reduced at high temperatures. Paradoxically, a decline in incidence of T. gondii infections could amplify the burden of this disease, as the most damaging outcome occurs subsequent to first infection during pregnancy, and reductions in the incidence of the infection will increase the average age of first infection. We blend models of infection dynamics rooted in occurrence across the African continent with models of human demography to bound expectations for the future burden of this pathogen, accounting for the effects of changing temperatures. We discuss targeting efforts and approaches for mitigation.

ecology↗

bioRxiv2025

JARID2 Inhibition Reprograms Human Hematopoietic Progenitor Cells To Enhance Bone Marrow Transplantation

Hematopoietic stem cell transplantation is a common treatment for many blood disorders and can be a life-saving therapy for patients with leukemias, lymphomas and multiple myeloma. Umbilical cord blood (UCB) serves as a valuable source of hematopoietic stem and progenitor cells (HSPCs) for transplantation, particularly for patients lacking a matched donor. However, the limited number of repopulating cells in UCB units restricts its clinical utility. Our prior studies showed that genetic deletion of the polycomb repressive complex 2 (PRC2) co-factor Jarid2 in mouse multipotent progenitors (MPPs) conveyed ectopic self-renewal capacity. Here, we hypothesized that the function of human HSPCs could be enhanced through JARID2 inhibition. In this study, we demonstrate that both constitutive and transient knockdown of JARID2 increases the number and enhances the functionality of human HSPCs both in vitro and in vivo. This phenotype was distinct from inhibition of EZH2 in UCB cells, suggesting the mechanism was independent of PRC2 co-factor activity of JARID2. Mechanistically, JARID2 knockdown promotes a quiescent, long-term self-renewal gene expression program governed by upregulating STAT1 and characterized by an MHC class II immunophenotype. Analogous to mice, these mechanisms conferred HSC-like potential to human MPPs in vivo. Taken together, these findings highlight JARID2 inhibition as a novel and reversible approach to expand functional UCB-derived HSPCs ex vivo, potentially improving access to stem cell transplantation for a wider patient population. One Sentence SummaryGenetic inhibition of JARID2 enhances repopulating activity of human hematopoietic stem and progenitor cells in vivo via STAT1 upregulation.

developmental biology↗

bioRxiv2025

Proteome profiling reveals HES1-driven mitotic catastrophe in ovarian serous carcinoma

Ovarian high-grade serous cancer (HGSC) is an aggressive subtype of epithelial ovarian cancer. Here, we identify BX-912, a phosphoinositide-dependent kinase 1 (PDPK1) inhibitor, as a promising therapeutic agent for HGSC. BX-912 suppressed HGSC growth as a single agent and synergized with olaparib independently of BRCA status. Unexpectedly, BX-912 treatment induced multinucleation, a phenotype not observed with other PDPK1 inhibitors. Proteome Integral Solubility Alteration (PISA) profiling revealed the transcription factor HES1 as a functional target of BX-912. Structural modeling showed that BX-912 binds the Orange domain of HES1, while its WRPW motif mediates interactions with protein partners, including the AP2 endocytic protein complex, coordinating their nuclear accumulation that leads to a mitotic catastrophe. Furthermore, cell cycle analyses showed that BX-912 combined with olaparib synergistically enhanced DNA damage and G2-M arrest. Our study demonstrates the value of proteomics for revealing hidden drug activities. It also identifies potential inhibition strategies for HES1, which is commonly overexpressed in HGSC. Additionally, this study proposes a novel strategy of targeting consecutive cell cycle phases to enhance treatment efficacy in HGSC.

cancer biology↗

bioRxiv2025

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

Deciphering the regulatory syntax of the genome is essential to understand the genetic and molecular architecture of complex traits, as most trait-associated variants lie in non-coding regions. Yet, functional annotation of the bovine genome remains limited, hindering our ability to unravel the mechanisms underpinning complex traits of economic and ecological importance in cattle. Here, we present a comprehensive epigenetic atlas comprising 1,138 genome-wide epigenetic profiles, including chromatin accessibility, six histone modifications, CCCTC-binding factor (CTCF) transcription factor binding, DNA methylation, chromatin conformation, and transcriptomes across 53 adult tissues, five fetal tissues, and seven primary cell types. This atlas-level data enables us to annotate around 45% of the genome as putative regulatory elements exhibiting tissue- or cell-specific regulatory activity. Leveraging sequence-to-function deep learning models, we discovered 301 sequence motifs and predicted the functional impact of genetic variants through in silico mutagenesis, thereby facilitating the decoding of the regulatory syntax of the cattle genome and fine-mapping of GWAS loci for 22 complex traits. Cross-species analysis further revealed evolutionarily conserved features of regulatory architecture and provided evolutionary insights into complex traits and diseases in humans. Together, this atlas offers a foundational resource for advancing cattle functional genomics, sustainable breeding, and studies of regulatory evolution.

genomics↗

bioRxiv2025

Oncolytic peptide NF27 effectively inhibits tumor growth and eradicates tumors in multiple cancer types

Oncolytic peptides are amphipathic peptides that specifically induce cell death in cancer cells by rupturing the cell membrane. Despite their therapeutic potential, few have advanced to clinical trials, and none have been approved for cancer treatment, highlighting the need for more potent and safe candidates. Moreover, the structure-activity relationship (SAR) of oncolytic peptides remains poorly understood. To address these challenges, we designed a series of peptides based on the previously reported oncolytic peptide CKS1 and evaluated their activity to induce cancer cell death. By comparing the structures and the activities of these peptides, we discovered novel insights in the SAR of oncolytic peptides. Among the peptides, we identified NF27 as the most potent peptide. NF27 showed broad cytotoxicity across multiple cancer types but displayed minimal toxicity against healthy cells and low hemolysis. Cell death induced by NF27 was immunogenic and promoted infiltration of immune cells in murine tumors. In murine tumor models, NF27 effectively suppressed tumor growth and achieved complete eradication in some cases, with no observable side effects. These findings highlight NF27 as a promising lead peptide for the development of safe and effective oncolytic therapies. One Sentence SummaryWe identified NF27, a novel oncolytic peptide that induces immunogenic cancer cell death and eradicates tumors with low toxicity via SAR study.

pharmacology and toxicology↗

bioRxiv2025

RIG-I-dependent tumor-intrinsic type I interferon signaling restricts growth in breast cancer 3D culture

Discovery of key growth drivers that can be targeted for therapy is a central goal in cancer research. While high-throughput CRISPR screens have revolutionized our ability to identify gene dependencies in cancer, most large-scale screens are conducted in two-dimensional (2D) culture systems that fail to recapitulate tumor organization and behavior. To uncover architecture-dependent vulnerabilities in breast cancer, we performed parallel CRISPR interference (CRISPRi) screens in 2D and three-dimensional (3D) cultures of MCF7 cells, an estrogen receptor-positive (ER+) breast cancer model representative of a high risk of relapse, luminal subtype. Knockdown of IFNAR2 and TYK2 conferred a growth advantage in 3D cultures, implicating type I interferon signaling as a tumor-intrinsic suppressor of proliferation in 3D spheroids. Transcriptomic and functional analyses demonstrated that type I IFN signaling is endogenously activated in 3D spheroids via RIG-I-mediated sensing of cytosolic double-stranded RNA, leading to TBK1 activation and induction of interferon-stimulated genes (ISGs). This tumor-intrinsic IFN response slowed proliferation in 3D culture, independent of exogenous stimuli or the presence of immune cells. Analysis of bulk, single-cell, and spatial transcriptomic datasets from breast cancer patients revealed that a subset of tumors exhibit elevated IFN signaling in cancer cells, including in immune-depleted tumor cores, consistent with a tumor-intrinsic IFN signature. Our findings uncover an IFN-mediated growth-suppressive program shaped by 3D tumor architecture, and contribute towards a better understanding of the role of tumor-intrinsic IFN activity.

cancer biology↗

bioRxiv2025

An evolutionary leap in plant reproduction: From archegonia and motile sperm to embryo sacs and pollen tubes

The transition of plants from water to land marks a pivotal step in their evolutionary history, with the change in reproductive mode being the most fundamental. This change freed plant reproduction from aquatic dependence, fostering terrestrial lifes prosperity. Key to the shift from archegonial to embryo sac reproduction are pollen tube emergence and female gametophyte changes, though their evolutionary trajectories and mechanisms remain unclear. Ginkgo, a basal gymnosperm, occupies a pivotal position in this transition, retaining motile sperm, simplified archegonia, and primitive pollen tubes, making it an ideal model. To study how the transition between these two reproductive modes occurred, we collected transcriptome data from the reproductive organs of Ginkgo and evolutionarily representative species. Our findings reveal the MYB98-CRP-ECS module- critical for angiosperm pollen tube guidance--in Ginkgos mature archegonia, with pollen tubes containing guidance components. While egg cells are transcriptionally and functionally conserved across land plants, changes in the cell fate of other female gametophyte component cells drove the shift from archegonia to embryo sacs. Pollen tubes may originate from fern male gametophyte internalization and modification. These findings clarify the evolutionary path and molecular basis of this major reproductive transition.

plant biology↗

bioRxiv2025

A Precision Ultrasound-Localized Sonoporation-Equipment (PULSE) Enabling Intratumoral Delivery for Cancer Immunotherapy

Cancer immunotherapy offers a promising long-term treatment for solid tumors by activating the immune system, but side effects and systemic toxicity limit its broad clinical translation. While intratumoral delivery addresses these limitations, elevated stiffness within solid tumors continues to hinder both intracellular and extracellular delivery. Here, a novel therapeutic platform, the Precision Ultrasound-Localized Sonoporation-Equipment (PULSE), is presented to enable spatiotemporally controlled, ultrasound-mediated gene and drug delivery for intratumoral immunotherapy. The PULSE incorporates forward and sideward-looking miniaturized ultrasound transducers, integrated into either a 7-French catheter (cPULSE) or a 16-gauge needle (nPULSE), to minimally invasively sonicate a centimeter-sized tumor. Following the design, prototyping, and characterization of PULSE, its dual capability for intracellular and extracellular delivery is demonstrated through comprehensive in vitro cell-based sonoporation tests and phantom-based drug penetration tests. Luciferase assays (activity: ~104 RLU/g level) in the cell studies confirm significantly enhanced gene transfection with cPULSE, while increased dye diffusion (width: ~1 cm level) in the phantom tests validates improved perfusion with nPULSE. The reported PULSE shows promise for spatiotemporally precise, controlled, and localized therapeutic delivery in early-stage tumors for intratumoral immunotherapy.

bioengineering↗

bioRxiv2025

Remodeling of the immune-metabolic landscape triggered by long-term high-altitude exposure

Growing evidence indicates that immunological and metabolic outcomes are key mediators of long-term high-altitude exposure (LTHAE) adaption, but the underlying mechanisms remain poorly understood. This study employs plasma metabolomics and peripheral blood single-cell transcriptomic sequencing to analyze the metabolic and immune dynamic regulation in 46 young male lowlanders following a 90-day adaptation period at high altitude. Single-cell analysis shows a pattern of "innate immune activation and adaptive immune suppression" under LTHAE, characterized by facilitated maturation of neutrophils, enhanced cytotoxicity of CD56dim NK cells, and increased immune responsiveness of cDC2 and pDC, while inhibited maturation of plasmablasts and suppressed immune responsiveness of CD8{square}TEM and CD4+ T cells. Plasma metabolic analysis reveals significant alterations, involving enhanced steroid hormone synthesis, unsaturated fatty acid and amino acid metabolism under LTHAE, which in turn are associated with immune remodeling. Moreover, transcriptomic-metabolic integration analysis indicates the molecular mechanisms of enhanced aerobic oxidation efficiency under LTHAE. Collectively, these findings provide integrated insights into immune-metabolic landscape remodeling and suggest potential mutual regulatory relationship between immune and metabolic state following LTHAE, offering a molecular foundation for high-altitude adaptation research.

genomics↗

bioRxiv2025

Comparison of the 2-CT method and the 2-ΔΔCT method for real-time qPCR data analysis

[purpose]The [Formula] method proposed by Livak and Schmittgen in 2001 is used for real-time quantitative polymerase chain reaction (RT-qPCR) data analysis. This methods fundamental logic involves normalizing all data against the control group to achieve relative quantification of gene expression. During our practical calculations, we identified an inherent bias in this method: the practice of directly taking arithmetic means of a set of C (or {Delta}C) values during [Formula] calculations fails to fully account for the exponential nature of CT values (where CT values serve as exponents in power-of-2 operations), leading to deviations in computational results. In this study, we elucidate this systematic bias and propose an innovative approach to circumvent it. [Methods]We propose the [Formula] method, which bases calculations on [Formula] values and computes the fold-change of target genes relative to control group target genes. The computational logic of the [Formula] method strictly adheres to the exponential characteristics of CT values, avoiding the use of arithmetic averaging at CT and {Delta}CT levels, thereby more accurately reflecting gene expression levels in datasets. In this paper, we detail the computational process of the [Formula] method and compare results from both methodologies. [Results]Calculations based on Livak and Schmittgens published data show differences between the two methods, though the discrepancies are relatively small. In calculations from our recent cadmium exposure experiments, the [Formula] method indicates that 8-hour cadmium exposure increases irg-6 gene expression in C. elegans from 1.314 to 7.125-fold, while the [Formula] method shows an increase from 1 to 4.124-fold. The two methods exhibit nearly 70% discrepancy in irg-6 gene fold-change quantification, with statistical p-values of 0.0002 and 0.0015 respectively. In all calculations presented in the paper, the [Formula] method fails to produce an exact unit value (mean fold-change = 1) for control groups, whereas the [Formula] method consistently yields control group results of exactly 1, demonstrating its capability for precise normalization. [Conclusions]In summary, the [Formula] method demonstrates superior computational rigor, and we recommend its adoption in RT-qPCR data analysis. This improvement proves particularly valuable for experimental datasets with substantial CT value variability among different samples, establishing a more reliable computational paradigm for RT-qPCR analysis.

molecular biology↗

bioRxiv2025

Functional Comparison to Ezh2 Reveals PRC2-Independent Functions of Jarid2 in Hematopoietic Stem Cell Lineage Commitment

Previous studies showed the Polycomb Repressive Complex 2 (PRC2) co-factor Jarid2 represses self-renewal transcriptional networks in mouse multipotent progenitor cells (MPPs). But only a fraction of de-repressed HSC-specific genes were associated with loss of H3K27me3, implying Jarid2 may have non-canonical (PRC2-indpendent) in hematopoiesis. Here we sought to delineate any PRC2-independnent functions by comparing stem and progenitor cells genetically deficient for either Jarid2 or Ezh2 (enzymatic component of PRC2). Loss of Ezh2 increased myeloid differentiation in transplantation assays. In contrast, loss of Jarid2 enhanced T-cell output. Single cell transcriptomics showed while loss of Jarid2 had minimal impact across progenitor populations, loss of Ezh2 led to accumulation of lymphoid-biased MPP4 cells and B-cell progenitors in the bone marrow. Functional assays confirmed a differentiation block at the pre-pro B-cell stage. The maturational arrest of Ezh2-deficient B-cell progenitors contrasts with increased T-cell output from loss of Jarid2, suggesting Jarid2 has non-canonical functions in hematopoiesis.

genetics↗

bioRxiv2025

Effect of Caenorhabditis elegans U6 Promoters on CRISPR/Cas9-Mediated Gene Editing Efficiency

ObjectiveThis study investigated the effects of endogenous C. elegans U6 promoters on dpy-10 gene editing efficiency. MethodsWe screened endogenous U6 snRNA genes from the WormBase database and constructed 14 editing plasmids targeting dpy-10 by replacing the U6r07e5.16 promoter in pSX524 (Peft-3::cas9::tbb-2 terminator::U6 r07e5.16::dpy-10 sgRNA) through molecular cloning. Following standardized microinjection protocols, we quantified gene editing efficiency and high-efficiency gene editing index based on dpy-10 mutant phenotypes in F1 progeny. ResultsFifteen U6 snRNA genes (r07e5.16, f35c11.9, t20d3.13, k09b11.15, k09b11.16, w05b2.8, c28a5.7, f54c8.9, k09b11.11, k09b11.12, k09b11.14, t20d3.12, f54c8.8, f54c8.10, k09b11.13) were identified from WormBase database. Comparative analysis revealed four U6 promoters (w05b2.8, c28a5.7, f54c8.9, and k09b11.11) significantly enhanced gene editing compared to other U6 promoters, including commonly used U6r07e5.16 and U6k09b11.12 promoters in C. elegans community. Notably, the gRNAF+E scaffold showed no improvement over the gRNA scaffold when paired with the optimal U6w05b2.8 promoter. ConclusionThis study identifies superior U6 promoters for C. elegans gene editing and demonstrates the critical role of promoter optimization in CRISPR systems, providing novel insights for technical refinement.

molecular biology↗

bioRxiv2025

Thioredoxin-1 inhibits granulosa cell ferroptosis to rescue ovarian aging through mitophagy-dependent activation of BNIP3L

Ovarian aging is closely associated with a decline in fertility and an increase in reproductive dysfunction. Ovarian granulosa cells (GCs) support oocyte homeostasis and development, yet insight into GC dysfunction during aging is limited. Here, we show that aged GCs of humans and mice have indications of elevated ferroptosis, including increased ferroptosis-related metabolites, lipid peroxidation, and iron accumulation. The ferroptosis inhibitor Ferrostatin-1 reversed ovarian impairment and fertility of aged mice in vivo. We show that the age-related reduction in the expression of TXN (thioredoxin) leads to ferroptosis in human and mouse GCs by blocking BNIP3L-dependent mitophagy. Exogenous activation of TXN could promote mitophagy, thereby clearing excessive ROS and inhibiting ferroptosis. These results suggest that anti-ferroptosis-related treatments may assist in treating aging-related reproductive disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/664497v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1b97e8forg.highwire.dtl.DTLVardef@123f8d0org.highwire.dtl.DTLVardef@a44c61org.highwire.dtl.DTLVardef@92b32e_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsO_LIFerroptosis signatures are upregulated in aged GCs from human and mouse ovaries C_LIO_LITXN is deregulated in aged GCs, leading to mitochondrial and ROS metabolic dysfunction C_LIO_LITXN binds to DNA to regulate autophagy and mitophagy genes, including BNIP3L C_LIO_LIInhibition of ferroptosis can ameliorate GC dysfunction C_LI

cell biology↗

bioRxiv2025

Structural basis of DNA N6-adenine methylation in eukaryotes

As a transcription-associated epigenetic mark abundantly present in many unicellular eukaryotes, DNA N6-adenine methylation (6mA) is maintained by the AMT1 complex. However, the structure-function relationship of the AMT1 complex remains to be fully elucidated. Here, we employ AlphaFold3 (AF3) for de novo structural modeling of the AMT1 complex, complemented by molecular dynamics simulations. Functional relevance of key structural features, especially those of the AMT1 ternary complex with the double-stranded DNA (dsDNA) substrate and the cofactor, are validated by extensive mutagenesis, both in vivo and in vitro. Our analysis reveals the structural basis for DNA substrate recognition, base flipping, and catalysis in this prototypical eukaryotic DNA 6mA-methyltransferase. It also allows us to delineate the reaction pathway for processive methylation involving translocation of the AMT1 complex along the dsDNA. As the active site is conserved across the MT-A70 family of eukaryotic N6-adenine methyltransferases, the structural insight will facilitate rational design of specific inhibitors.

molecular biology↗

bioRxiv2025

SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain

A role for the trafficking receptor SORLA in reducing A{beta} levels has been well-established, however, relatively little is known with respect to whether and how SORLA can potentially affect tau pathology in vivo. Here, we show that transgenic SORLA upregulation (SORLA TG) can reverse pathological effects in aged PS19 (P301S tau) mouse brain, including tau phosphorylation and seeding, ventricle dilation, synapse loss, LTP impairment and glial hyperactivation. Proteomic analysis indicates reversion of PS19 profiles in PS19/SORLA TG hippocampus, including pathological changes in synapse-related proteins as well as key drivers of synaptic dysfunction such as Apoe and C1q. snRNA-seq analysis reveals suppression of PS19- signatures with SORLA upregulation, including proinflammatory induction of Plxnb1/Plxnb2 in glia. Tau seeding and aggregation, neuroinflammation, as well as PlxnB1/B2 induction are exacerbated in PS19 hippocampus with SORLA deletion. These results implicate a global role for SORLA in neuroprotection from tau toxicity in PS19 mouse brain.

neuroscience↗

bioRxiv2025

Long Noncoding RNAs Enforce Pancreatic Cancer Identity and Block Reprogramming

The Yamanaka factors (OCT4, SOX2, KLF4, and MYC; OSKM) can rejuvenate aging phenotypes in somatic cell types by resetting the epigenetic landscape. Curiously, most solid tumor cells remain largely resistant to reprogramming despite their well-documented plasticity, and the underlying mechanisms are unclear. Here, we combined genomic profiling and in vivo assays to investigate OSKM-mediated reprogramming of pancreatic ductal adenocarcinoma (PDAC). In the initial stages, we found that cancer-specific genes were refractory while mesodermal/ECM programs, normally silenced by PRC2, were aberrantly upregulated. A CRISPR interference screen for OSKM reprogramming coupled with functional analyses revealed that suppression of cancer-associated long noncoding RNAs (lncRNAs) erased malignant epithelial programs, restored tumor suppressor activity, and impaired tumorigenicity in vivo. We further identified that ATXN7L3-AS1 lncRNA sustains the PDAC malignant identity through its association with active epithelial oncogenic programs and poised PRC2-targeted developmental genes, thereby supporting both plasticity and memory. Thus, by exploring why cancer cells are resistant to reprogramming, we identify lncRNAs as gatekeepers of malignant identity, suggesting that targeting lncRNAs could be a generalizable therapeutic strategy in treating solid tumors.

cancer biology↗

bioRxiv2025

Agropyron cristatum genome provides a new insight for wheat improvement with wild relatives

Exploring novel genetic variation for target traits is crucial for advancing wheat breeding and genetic improvement. Since 1990, we have been transferring genes from Agropyron cristatum, a promising wild relative genetic resource featuring robust spike morphology and stress tolerance, into common wheat by distant hybridization. To efficiently harness A. cristatum genes, we de novo assembled a 25.62-Gb high-quality genome of an autotetraploid accession Z559 with 28 chromosomes, and uncovered its specific genome features and an extensive repertoire of genes associated with yield and resistance to abiotic and biotic stresses. We systematically characterized A. cristatum genome introgressions by resequencing 431 wheat-A. cristatum derivatives and cloned the gene AcGNS1, which functions in the regulation of grain number per spike in wheat. Subsequently, we developed an optimized genome-selection model for wheat-A. cristatum breeding derivatives, enabling the rapid selection of new potential varieties. These findings demonstrate a genomic breeding strategy for leveraging novel genetic resources of wild relatives and advancing wheat improvement.

genomics↗

bioRxiv2025

Amazon biodiversity is at risk from metal contamination due to mining activity

The Amazon basin hosts the most biodiverse and intact ecosystems on Earth, yet human activities are an increasing threat. Metal contamination due to mining constitutes one of these major threats, but its impacts remain poorly quantified. We provide the first quantitative assessment of biodiversity exposure to mining-associated metals--mercury [Hg], arsenic [As], copper [Cu], Zinc [Zn], and lead [Pb]--across the Amazon. Around 66% of the Amazons 38,890 species of birds, plants, mammals, reptiles, amphibians, and fishes are exposed to metal contamination, including biodiversity hotspots and Indigenous territories. Safeguarding the Amazons role as a global reservoir of biodiversity, ecosystem function, and cultural heritage requires addressing metal contamination not only as a localized issue, but as a pervasive threat to global biodiversity.

ecology↗