Biology subjects

Shao, D.

Publications and source records attributed to Shao, D..

14 recordsLinked to original sources

bioRxiv2026

A Selective Multivalent NET-Associated Chromatin Neutralizer Resolves Infection-Associated Inflammation in Severe Sepsis

Targeting the overwhelming inflammation driven by neutrophil extracellular traps (NETs) during infection provides an opportunity to manage severe sepsis. This potential needs to be realized by exploring selective NET-neutralization materials, which remains a challenge. Herein, we report a multivalent macromolecular strategy that targets NET-associated DNA-histone chromatin complexes while preserving antibacterial activity of aminoglycoside. We identify 8-arm PEG-conjugated netilmicin (8-arm Netil) as a lead NETs-neutralizer from a library of multivalent aminoglycoside-displayed materials. When compared with 2- and 4-arm counterparts, 8-arm Netil exhibits potent antibacterial activity and high-affinity binding to DNA-histone chromatin complexes through stable multivalent noncovalent interactions, thereby suppressing NET-induced TLR4/TLR9 activation and macrophage inflammatory responses. In severe septic mice, intravenously administered 8-arm Netil preferentially accumulates in inflamed tissues, leading to improved survival protection, owing to the reduction of bacterial dissemination, NET accumulation, systemic cytokine production, and multiple-organ injury. These findings establish NET-associated DNA-histone chromatin complexes as actionable extracellular targets and demonstrate multivalent chromatin targeting as a rational material design strategy for selective NET neutralization and inflammation control in severe sepsis.

bioengineering↗

bioRxiv2026

Monoclonal nephritic factors reveal insights into C3 convertase dynamics and dysregulation

C3- and C5-nephritic factors are potent but poorly understood autoantibodies that dysregulate complement convertases. To date, their underlying mechanisms of action, epitopes, and sequences remain unknown. To address this knowledge gap, we immune profiled B cells from a nephritic factor-positive C3 glomerulopathy patient and identified the first monoclonal C3- and C5-nephritic factors. We present the structure of a C3-nephritic factor bound to a C3 convertase with the convertase protease domain unexpectedly rotated and inhibited. This rotation advances our understanding of complement convertase progression and decay, explains disease-associated convertase variants, and reveals the molecular mechanism by which nephritic factors can either activate or inhibit convertase activity. We also detail heterogeneity within and between C3- and C5-nephritic factors in terms of convertase binding, stabilizing capacity, regulator inhibition, fluid-phase activation, and disease contribution. These findings improve stratification of patients with C3 glomerulopathy, redefine basic C3 convertase dynamics, and provide insights into antibody-mediated modulation of the complement system.

immunology↗

bioRxiv2026

Cell-Cell-Seq resolves contact-associated NK cell activation in defined tumor cell dyads

Cell-cell interactions shape immune recognition, but most single-cell transcriptomic methods measure cells after their interaction history has been lost or inferred. Here we apply Cell-Cell-Seq, a Nanovial-based workflow for sequencing defined cell pairs, to resolve contact-associated activation of natural killer cells paired with leukemia targets. Nanovials enabled controlled dyad formation, incubation, flow enrichment and droplet-based sequencing while reducing uncontrolled partner exchange and aggregation seen in suspension co-culture. Cell-Cell-Seq recovered a reproducible activation program marked by chemokine, cytokine, cytotoxic and immediate-early response genes. Compared with randomly mixed suspension co-culture, defined dyads emphasized contact-proximal activation, whereas suspension co-culture showed stronger features of early overstimulation. Dyad-resolved measurements also benchmarked computational models of cell-cell communication, identifying inferred signalling axes that were recovered and contact-induced programs missed by current approaches. These results establish Cell-Cell-Seq as a scalable strategy for mapping how defined immune-tumour encounters reshape cell state.

bioengineering↗

bioRxiv2026

Therapeutic targeting inflammation linking periodontitis and atherosclerotic comorbidities using cell-free DNA-capturing nanomaterials

Periodontitis-associated systemic inflammation makes it a great challenge to explore therapeutic options applicable to periodontitis and atherosclerotic comorbidities. Here, we identify the crucial role of cell-free DNA (cfDNA) that underlies these comorbidities. Hypothesizing cfDNA as a therapeutic target, we engineer polyamidoamine dendrimer-functionalized nanomaterials to modulate such local-systemic inflammatory crosstalk. Periodontium-originated DNA can be systemically captured by cationic nanomaterials, and capturing cfDNA, whether locally or systemically, alleviates both periodontitis and atherosclerosis prior to severe atherosclerotic development in vivo. The transcriptomic and single-cell RNA sequencing analyses together reveal that cfDNA-capturing nanomaterials regulate inflammatory foam cell transformation in macrophages by modulating the expression of lipid-related foamy markers Spp1 and Fabp4. This study provides a proof of concept for cfDNA-driven periodontitis-atherosclerosis crosstalk, and offers a cfDNA-capturing nanoplatform for therapeutic intervention targeting periodontitis and atherosclerotic comorbidities in a holistic fashion.

immunology↗

bioRxiv2025

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692823v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@123b221org.highwire.dtl.DTLVardef@83ba0aorg.highwire.dtl.DTLVardef@2b0ab0org.highwire.dtl.DTLVardef@1cae35e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

CRISPRi-based functional genomic screening identifies genes essential for CH4-dependent growth in the methanotroph Methylococcus capsulatus Bath.

Aerobic methanotrophic bacteria are the primary organisms that consume atmospheric methane (CH4) and have potential to mitigate the climate-active gas. However, a limited understanding of the genetic determinants of methanotrophy hinders the development of biotechnologies leveraging these unique microbes. Here, we developed and optimized a CRISPR interference (CRISPRi) system to enable functional genomic screening in methanotrophic bacteria. We built a genome-wide single guide RNA (sgRNA) library in the industrial methanotroph, Methylococcus capsulatus, consisting of [~]45,000 unique sgRNAs mediating inducible, CRISPRi-dependent transcriptional repression. A selective screen during growth on CH4 identified 233 genes whose transcription repression resulted in a fitness defect and repression of 13 genes associated with a fitness advantage. Enrichment analysis of the 233 putative essential genes linked many of the encoded proteins with critical cellular processes like ribosome biosynthesis, translation, transcription, and other central biosynthetic metabolism, highlighting the utility of CRISPRi for functional genetic screening in methanotrophs. The CRISPRi screen uncovered that 50 ppb Co2+ in methanotroph Nitrate Mineral Salts medium is growth inhibitory and decreasing Co2+ to < 10 ppb improved biomass productivity from CH4. Collectively, our results show that the CRISPRi system and sgRNA library developed here can be used for facile gene-function analyses and genomic screening to identify novel genetic determinants of methanotrophy and isolation of improved methanotroph biocatalysts.

microbiology↗

bioRxiv2024

Machine learning engineered PoLixNano nanoparticles overcome delivery barriers for nebulized mRNA therapeutics

There continues to be a dearth of competent inhalable mRNA delivery although it holds great potential for addressing a wide variety of refractory diseases. The huge advances seen with parenteral-administered lipid nanoparticle (LNP) have not been translated into nebulized mRNA delivery due to the aggressive nebulization process and insurmountable barriers inherent to respiratory mucosa. Here, we show amphiphilic block copolymers revealed by machine learning (ML) can spontaneously form stabilized nanoparticles (PoLixNano) with the lipids components of LNP and simultaneously impart the PoLixNano with "shield" (shear force-resistant) and "spear" (pulmonary barriers-penetrating abilities) capabilities. We present a ML approach that leverages physicochemical properties and inhaled mRNA transfection profiles of a chemically diverse library of polymeric components to validate the integration of "shield" and "spear" properties as highly predictive indicators of transfection efficiency. This quantitative structure-mRNA transfection prediction (QSMTP) model identifies top-performing amphiphilic-copolymers from more than 10000 candidates and suggests their mucus-penetrating ability outweights the shear force-resistant property in contributing to efficient mRNA transfection. The optimized PoLixNano substantially outperforms the LNP counterpart and mediates up to 1114-times higher levels of mRNA transfection in animal models with negligible toxicities. The PoLixNano promotes overwhelming SARS-CoV-2 antigen-specific sIgA antibody secretion and expansion of TRM cells which collectively confers 100% protection in mice against lethal SARS-CoV-2 challenges and blocks the transmission of Omicron variant between hamsters. PoLixNano also displays versatile therapeutic potential in lung carcinoma and cystic fibrosis models. Our study provides new insights for designing delivery platforms of aerosol-inhaled mRNA therapeutics with clinical translation potential.

synthetic biology↗

bioRxiv2023

Trade-off between light deprivation and desiccation in intertidal seagrasses due to periodic tidal inundation and exposure: insights from a data-calibrated model

Many seagrass species thrive in shallow intertidal zones globally, adapting to periodic tidal inundation and exposure with distinctive physiological traits and offering crucial ecosystem services. However, predicting the responses of intertidal seagrasses to external stressors is hampered by the complexity of the dynamic and harsh environments they occupy. Consequently, intertidal seagrass growth models, especially those incorporating dynamic physiological responses, are scarce in the literature. Our study comprehensively collated relevant data from the literature to parameterize the relationship between air exposure, seagrass leaf water content and photosynthetic efficiency to inform new growth rate functions for generalisable intertidal seagrass growth models. We tested the applicability of these model formulations for scenarios with varying physiological process assumptions, seagrass species, tidal conditions, meadow elevations and water turbidity. We found that neglecting air-exposed physiological responses (i.e., leaf water content loss and reduced photosynthetic efficiency) can substantially overestimate seagrass growth rates. We also observed a trade-off between light deprivation and desiccation on intertidal seagrass growth under specific tidal ranges and turbidity conditions. This can yield an "optimal" elevation where combined stressors of desiccation (increasing with meadow elevation) and light deprivation (decreasing with meadow elevation) are minimized. The predicted optimal elevation, i.e., the most suitable habitat for intertidal seagrass, moves upward as water turbidity increases. Our study provides both conceptual and quantitative guidance for ecological modellers to include air exposure responses of intertidal seagrasses in coastal ecosystem models. The model also helps to evaluate the viability of intertidal seagrass habitats and inform site selection for seagrass restoration.

ecology↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗

bioRxiv2022

Hinokitiol alters Gene Expression in Aspergillus fumigatus, protects against fungal keratitis by Reducing Fungal Load, LOX-1, Proinflammatory cytokines and Neutrophil Infiltration

Hinokitiol (HK), a tropolone-related compound found in cupressaceous plants, has antifungal and anti-inflammatory properties. But its roles in Aspergillus fumigatus ( A.F. ) keratitis remains unknown. This study examined the antifungal activity of HK against A.F. and investigated its possible mechanisms at the ultrastructural and transcriptional levels. We tested the minimum inhibitory concentration (MIC) of HK against A.F.. Our data showed that the MIC50 was 2 g/ml and MIC90 was 8 g/ml, and HK could significantly inhibit the spore germination and mycelial growth of A.F.. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations showed that HK induced significant changes in hyphal morphology and microstructure, including cell membrane rupture and intracellular structural disorder. Adhesion assay and biofilm assay experiments showed that HK reduced the adhesion of spores to human corneal epithelial cells (HCECs) and inhibited the formation of biofilms. The genetic changes of A.F. after HK treatment were analyzed by RNA sequencing, and a total of 2487 differentially expressed genes (DEGs) were identified, including the down-regulated DEGs related to carbohydrate and various amino acid metabolism, ribosome biogenesis, asexual reproduction, and up-regulated DEGs related to steroid biosynthesis through GO and KEGG enrichment analysis. RNA-seq results suggested that HK may play an antifungal effect by destroying the structural integrity of its wall and membrane, inhibiting protein biosynthesis and the growth and reproduction of A.F..10 g/ml HK, which had no effect on proliferation and migration of HCECs, was used in the treatment of murine fungal keratitis (FK). We found that HK eyedrop treatment could reduce the severity of FK by reducing corneal fungal burden, neutrophil infiltration, and the expression of LOX-1 and pro-inflammatory factors. HK is expected to be a safe and effective new drug for FK treatment. Author summaryFK is a serious common blind-causing eye disease. The current clinical antifungal drugs have the disadvantages of low bioavailability and high corneal toxicity, which greatly limit the clinical effectiveness. Therefore, there is an urgent need for a new, safe and effective treatment for FK. HK had shown great antifungal capacity against A.F., amazingly well anti-inflammatory effect and real improvement in murine FK in our research. These findings provide a theoretical basis for the application of HK as an antifungal drug and reveal the potential of HK to be applied in the clinical treatment of FK.

microbiology↗

bioRxiv2021

PEGR: a flexible management platform for reproducible epigenomic and genomic research

Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this challenge as high-throughput sequencing data is generated at an unprecedented pace. Here we report on our development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with the Galaxy platform.

bioinformatics↗

bioRxiv2020

Mosquito defensins enhance Japanese encephalitis virus infection by facilitating virus adsorption and entry within mosquito

Japanese encephalitis virus (JEV) is a viral zoonosis which can cause viral encephalitis, death and disability. Culex is the main vector of JEV, but little is known about JEV transmission by this kind of mosquito. Here, we found that mosquito defensin facilitated the adsorption of JEV on target cells via both direct and indirect pathways. Mosquito defensin bound the ED III domain of viral E protein and directly mediated efficient virus adsorption on the target cell surface, Lipoprotein receptor-related protein 2 expressed on the cell surface is the receptor affecting defensin dependent adsorption. Mosquito defensin also indirectly down-regulated the expression of an antiviral protein, HSC70B. As a result, mosquitos defensin enhances JEV infection in salivary gland while increasing the possibility of viral transmission by mosquito. These findings demonstrate that the novel effects of mosquito defensin in JEV infection and the mechanisms through which the virus exploits mosquito defensin for infection and transmission.

microbiology↗

bioRxiv2019

Frequency of mutations in 21 hereditary breast and ovarian cancer susceptibility genes among high-risk Chinese individuals

PurposeTo determine the prevalence and clinical prediction factors associated with deleterious mutations among 882 high-risk Chinese individuals who underwent multigene panel testing for hereditary breast and ovarian cancer (HBOC) risk assessment.\n\nExperimental DesignSubjects were selected from individuals referred for genetic testing using a 21-gene panel (Oseq-BRCA) between January 2015 and March 2018. The distribution and prevalence of deleterious mutations were analyzed for the full cohort as well as subtypes.\n\nResultsOverall, 176 deleterious mutations were observed in 19.50% (n = 172) individuals. Of these, 26 mutations are not reported in public databases and literatures. In the ovarian cancer only subgroup, 115 deleterious mutations were identified in 429 patients (48.6%). Patients with ovarian cancer with mutations were enriched for a family history of breast or ovarian cancers (p < 0.05). In the breast cancer only subgroup, 31 deleterious mutations were identified in 261 patients. Most mutations occurred in BRCA1 (8; 25.8%) and BRCA2 (11; 35.5%). An additional 12 deleterious mutations (38.7%) were found in 7 other susceptibility genes. An increased frequency of mutation rate (57.9%) was observed in the subgroup of subjects with histories of both breast and ovarian cancer.\n\nConclusions19.50% of individuals carried a deleterious mutation in HBOC susceptibility genes in our cohort. Subgroup of subjects with histories of both breast and ovarian cancer had the highest prevalence of mutations. Our results highlighted the genetic heterogeneity of HBOC and the efficiency of multigene panel in performing risk assessment.

cancer biology↗

bioRxiv2018

Composition and consistence of the bacterial microbiome in upper, middle and lower esophagus before and after Lugol’s iodine staining

Esophageal bacteria, as the integral composition of human ecosystem, have been reported to be associated with esophageal lesions. However, few studies focus on microbial compositions in different esophageal segments, especially after Lugols iodine staining (LIS) in the endoscopic examination for the screening of esophageal cancer. To investigate the composition of the bacterial microbiome in upper, middle and lower esophagus and if LIS would affect the detection of bacteria, 141 fasting samples including the upper, middle and lower esophagus from 27 participants were collected by brushing the mucosal surface of the esophagus before (Eso) and after (Lug) LIS. Bacterial V3-V4 region of 16S rRNA gene was amplified and sequenced by Illuminas sequencing platform and analyzed using LEfSe system to identify specific microbiota. The top six abundant bacterial phyla taxa among three locations from both Eso and Lug groups were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and TM7. In terms of genera, the bacterium in three locations from two groups was all characterized by a highest relative abundance of Streptococcus. Bacteria diversity and the relative abundance between Eso and Lug were comparable (P > 0.05). Bacteria diversity was consistent in different esophageal locations for an individual, but it was significantly distinguishing in different subjects (P < 0.05). In Conclusion, the bacterial microbiome in healthy esophagus are highly diverse and consistent even among three physiological stenosis at all clades. Lugols iodine staining would not change local microenvironment in term of microbial composition. These finding provide an essential baseline for future studies investigating local and systemic bacterial microbiome and esophageal diseases.

epidemiology↗