Biomedical subjects

Yao Zhang

Publications and source records attributed to Yao Zhang.

12 recordsLinked to original sources

PubMed2026

The application of the CRISPR-Cas system in Pseudomonas aeruginosa infections.

Due to the extensive drug resistance of Pseudomonas aeruginosa (P. aeruginosa), it is still a great clinical challenge. The clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) system has become a promising strategy against this pathogen. This review critically evaluates the multifaceted applications of CRISPR-Cas technology in P. aeruginosa, including its role in antimicrobial resistance, diagnostics, genome editing, and emerging therapeutic and vaccine strategies. In addition to conducting a comprehensive analysis of various studies, we also compared the performance and limitations of various CRISPR platforms, and discussed the main technologies and transformation obstacles in this field. Finally, we look forward to the direction of applying these experimental tools to clinical research in the future.

Pseudomonas aeruginosa↗

PubMed2026

Integrative Proteomics and Ubiquitomics Reveal on-Targets and off-Targets of PROTAC dBET1.

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that induce selective degradation of target proteins by hijacking the ubiquitin-proteasome system (UPS). Despite their transformative potential in eliminating disease-associated proteins, comprehensively identifying off-target degradation events remains technically challenging. Here, we employed an integrated proteomic and ubiquitinomic strategy to systematically profile the degradation landscape of the PROTAC molecule dBET1 in Jurkat T cells. By capturing the upstream ubiquitination events─which serve as earlier and more sensitive indicators than total protein abundance─our approach enabled the identification of previously overlooked off-target candidates. While dBET1 efficiently degraded its canonical BET family targets, our data also revealed the mitochondrial outer membrane protein VDAC1 as a putative off-target, evidenced by its depletion and increased multisite ubiquitination. Notably, our analysis framework enabled site-specific resolution of degradation events within BRD3, revealing preferential ubiquitination at functionally essential bromodomains, suggesting that degron-enriched regions may underlie domain-selective degradation. Additionally, dBET1 treatment was associated with mitochondrial depolarization and calcium homeostasis disruption, defects that we hypothesize may be functionally linked to the observed VDAC1 depletion. Together, this study demonstrates that integrating ubiquitomics provides a superior sensitivity layer for PROTAC safety assessment, capable of uncovering mechanism-based liabilities that escape conventional global proteomic screening.

Humans↗

PubMed2026

Development of a rapid antiviral screening assay based on GFP reporter virus of bovine enterovirus.

In recent years, bovine enterovirus (BEV) has been increasingly associated with diarrhea in cattle in China, posing new challenges for disease control in the cattle industry. However, the mechanisms underlying BEV pathogenesis and virulence remain poorly understood. Infectious cDNA clones provide a powerful tool for dissecting viral replication and pathogenic mechanisms. In this study, we generated a full-length infectious cDNA clone of the BEV-F isolate HB19-1. Three overlapping fragments spanning the complete viral genome were amplified by RT-PCR and assembled downstream of a cytomegalovirus (CMV) promoter placed immediately upstream of the 5' untranslated region (5'UTR). To establish a reporter virus system, the green fluorescent protein (GFP) gene was inserted between the 5'UTR and the N terminus of VP4, followed by a 2A cleavage sequence (IKTAG) at the C terminus of GFP. The recombinant rHB19-GFP virus was successfully rescued. Growth curve analysis demonstrated that rHB19-GFP exhibited slower replication kinetics at early time points relative to the parental HB19-1 virus, with no significant difference in their peak viral titers. This GFP-expressing reporter virus enables convenient monitoring of BEV replication and provides a useful platform for antiviral screening. Using this system, we found that 5-(N-Ethyl-N-isopropyl)amiloride (EIPA) inhibited BEV replication, suggesting its potential as an antiviral candidate. Overall, the rHB19-GFP infectious clone developed here offers a practical tool for studying BEV biology and for identifying antiviral compounds against BEV.

Animals↗

PubMed2026

A Robust, Self-Digestion-Resistant LysN with Superior Activity and Cleavage Fidelity for Advanced Proteomic Workflows.

LysN is a valuable protease in proteomics because it cleaves peptide bonds N-terminal to lysine, generating peptides with physicochemical properties complementary to those produced by LysC and trypsin. However, the broader adoption of LysN in proteomic workflows has been limited by the lack of commercially available enzymes that combine high activity, low missed-cleavage rates, and sufficient stability under practical sample-processing conditions. Here, we report the recombinant production and proteomic characterization of a self-digestion-resistant and highly active LysN from Shewanella loihica (SL-LysN). Using terminomics, we mapped the mature N- and C-termini of the enzyme and established the primary structure of the active protease. We further developed a high-density fermentation, refolding, and purification workflow to obtain highly purified recombinant SL-LysN. Biochemical and proteomic benchmarking showed that SL-LysN displayed 3.3-fold higher specific activity than commercial LysN and reduced missed cleavages by approximately 80%. Notably, SL-LysN retained high activity in the presence of 8 M urea or 1% SDS and showed strong resistance to autolysis, indicating exceptional robustness for proteomic sample preparation. In complex mammalian proteome digests, SL-LysN achieved >95% cleavage specificity and a missed-cleavage rate of only 5.9%. These features address a long-standing bottleneck in N-terminal proteolysis and establish SL-LysN as a high-performance enzymatic tool for advanced proteomic workflows, including deep protein sequencing, quantitative proteomics, terminomics, de novo sequencing and analyses requiring efficient digestion under denaturing conditions.

Shewanella↗

PubMed2026

Auxin-induced ARF transcription factor degradation defines tissue boundaries.

How organs partition themselves into discrete domains with distinct functions is a fundamental question in biology. The gynoecium of flowering plants provides an excellent system to address this question. Here, we show that the boundary between the stigma and style at the gynoecium apex is established by the complementary distribution of the phytohormone auxin and the Auxin Response Factor (ARF), ETTIN (ETT). Mechanistically, auxin induces ETT protein destabilization via the ubiquitin-proteasome pathway. A short sequence motif within an intrinsically disordered region is required for this auxin-triggered degradation. Disruption of this motif leads to ectopic ETT accumulation at the gynoecium apex and consequently abolishes stigma-style boundary development. We further demonstrate that this previously unrecognized mode of auxin-induced ARF instability is evolutionarily conserved among ETT orthologs across angiosperms. In summary, this study reveals how graded auxin distribution affects ARF transcription factor activity, contributing to the establishment of the stigma-style boundary, ensuring correct gynoecium formation and reproductive success in flowering plants.

Indoleacetic Acids↗

PubMed2026

Dosimetric Parameters of the Heart and Its Substructures in Predicting Cardiac Events or Survival in Patients With Lung Cancer After Radiation Therapy: A Systematic Review and Meta-analysis.

The predictive value of radiation dose to the whole heart (WH) and cardiac substructures (CS) for cardiac events (CEs) and survival in patients with lung cancer remains uncertain. The goal of this study was to conduct a systematic review and meta-analysis to provide an evidence-based estimate of the relationship between these associations. A systematic meta-analysis was performed following PRISMA guidelines. Risk of bias was assessed using the JBI Critical Appraisal Checklist for Case Series. Outcomes were classified into major adverse cardiac events (MACE), arrhythmias, pericardial effusion, and survival. Depending on heterogeneity, random- or fixed-effects models were applied to calculate pooled hazard ratios (HRs) for univariable and multivariable analyses. A total of 80 studies, including 21,645 patients, were analyzed. Of these, 25 studies reported CEs, and 69 reported survival outcomes. Among 91 WH and 215 CS parameters evaluated, several showed significant associations. Key findings from our meta-analysis include: (1) left anterior descending (LAD) V15 was significantly associated with MACE. The mean heart dose (MHD), as well as ventricle and LAD doses, were significantly associated with ischemic events. (2) Multiple CS parameters were associated with different arrhythmia subtypes. (3) MHD, heart V5/V35/V55 and pericardial doses were significantly associated with pericardial effusion. (4) MHD was significantly associated with survival; CS parameters also showed predictive value, and especially, heart base dose being the most significant. (5) We also identified several thresholds with potential predictive values, such as LAD V15 <10% for MACE, left pulmonary vein (LPV) V55 <2%, and right pulmonary vein (RPV) V10 <54% for atrial fibrillation (AF), right atrium (RA) V60 <0.03 cc for non-AF supraventricular tachyarrhythmia, and left main artery (LMA) V10 ≥1 cc for bradyarrhythmia. This study identified 130 WH and CS dosimetric parameters associated with CEs and 131 with survival outcomes. These findings enhance our understanding of radiation-induced heart injury mechanisms and provide guidance for potential protective and intervention strategies.

Humans↗

PubMed2026

Ocean warming enhances iron use efficiencies of marine ammonia-oxidizing archaea.

Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean, playing a fundamental role in the marine nitrogen cycle. Although temperature and trace metal availability each individually influence the growth and activity of marine AOA, there is only a very limited understanding of the interactive effects of these two major factors on AOA in the rapidly changing ocean. Here, we show that the iron requirements of the model marine AOA species Nitrosopumilus maritimus SCM1 are highly sensitive to temperature changes. A 5 °C increase in growth temperature reduced SCM1 iron requirements by >80%, and was associated with a substantial increase in iron use efficiencies (IUE, mol C fixed/h/mol cellular Fe) under iron-limited and warming conditions. A thermally enhanced IUE enables SCM1 to more efficiently utilize scarce available iron supplies to support its growth. Whole-cell proteomic analysis revealed that iron limitation decreased expression of a ferredoxin and increased expression of a copper-dependent plastocyanin that became more pronounced with warming, suggesting coordinated electron transport response regulation under combined iron and temperature stress. The global impacts of these temperature-dependent changes to AOA iron demands were assessed using sensitivity experiments with a state-of-the-art biogeochemical model. Simulations showed that impacts on nitrification were concentrated at higher latitudes, but the alterations to ammonia concentrations were redistributed toward lower latitudes by mode and intermediate water transport. These findings reveal a previously unrecognized mechanism by which ocean warming may alleviate iron limitation of AOA, enhance their ecological competitiveness, and reshape ocean nitrogen cycling throughout marine ecosystems.

Iron↗

PubMed2026

Widespread marine and freshwater distributions of active sulfoquinovose-degrading bacteria.

Sulfoquinovose (SQ), a sulfonated sugar produced on a gigaton scale each year, contributes to global sulfur cycling, yet the microbes and pathways mediating its turnover in the environment have been inferred largely from genomic potential rather than direct activity. Here, we coupled incubations of environmental samples with 13C-labeled SQ to DNA-stable isotope probing to identify active SQ carbon assimilators across estuary, mangrove, and lake ecosystems. In estuarine communities, Vibrio and Cognatishimia incorporated SQ-derived 13C; Novosphingobium dominated in the mangrove, and Agrobacterium in the lake. Pure-culture experiments, coupled with comparative proteomics and gene knockout validation, demonstrated that Vibrio strains degrade SQ via modified sulfoglycolytic Embden-Meyerhof-Parnas and Entner-Doudoroff pathways to produce the environmentally significant organosulfur 2,3-dihydroxypropanesulfonate. Comparative genomic analyses suggested that closely related genome representatives of Novosphingobium, Cognatishimia, and Agrobacterium encode the sulfolytic SQ monooxygenase pathway. A global survey of aquatic microbial genomes indicated that over 9% harbor SQ degradation clusters, supporting a widespread distribution of bacterial SQ catabolic potential in aquatic environments.

Fresh Water↗

PubMed2025

Elevated triglyceride-glucose index and risk of thymoma-associated myasthenia gravis: a prospective analysis from the UK Biobank.

BACKGROUND: Thymoma-associated myasthenia gravis (MG) is a clinically significant but uncommon condition, affecting up to half of thymoma patients and associated with worse outcomes than either disease alone. Reliable biomarkers for early risk stratification remain scarce. The triglyceride-glucose (TyG) index and triglyceride-to-high-density lipoprotein cholesterol (TG/HDL-C) ratio are established biomarkers reflecting insulin resistance and dyslipidemia. However, their clinical associations with thymoma-associated MG remain incompletely characterized. METHODS: A total of 501,954 UK Biobank participants were included. After exclusions, 422,397 (313 cases) were analyzed for TyG index and 422,691 (314 cases) for TG/HDL-C ratio. Exposures were stratified into quartiles, and assessed continuously per unit increase. Cox proportional hazards models estimated hazard ratios (HRs), restricted cubic splines (RCS) assessed non-linear associations, and subgroup analyses were stratified by body mass index (BMI). Sensitivity analyses examined TyG index and MG alone. RESULTS: An elevated TyG index was associated with increased risk of thymoma-associated MG. Compared to Q1, Q4 had higher risk (HR = 1.66, 95% CI: 1.20-2.31, P = 0.003); the overall HR per unit increase was 1.42 (95% CI: 1.17-1.73, P = 0.0005). TG/HDL-C ratio showed similar patterns: Q4 vs Q1 HR = 1.54 (95% CI: 1.11-2.15, P = 0.01); overall HR per unit increase was 1.06 (95% CI: 1.02-1.10, P = 0.002). Non-linear relationships were observed, with suggested inflection points at TyG index 8.7 and TG/HDL-C ratio 2.8, rather than strict thresholds. Subgroup analyses revealed stronger associations in normal-weight and obese participants, although tests for interaction were not statistically significant. Sensitivity analyses confirmed consistent associations between TyG index and MG risk, including for isolated MG. CONCLUSION: Elevated TyG index and TG/HDL-C ratio were independently associated with higher thymoma-associated MG risk in this large prospective cohort, with evidence of non-linear relationships and BMI-related heterogeneity. These findings provide novel epidemiologic evidence linking metabolic markers of insulin resistance with thymoma-associated MG, but clinical translation requires further validation.

Humans↗

PubMed2025

Phosphoproteomics delineates hepatocellular carcinoma subtypes and pinpoints therapeutic targets.

BACKGROUND AND AIMS: Only a minority of patients could benefit from systemic therapy owing to the high heterogeneity of HCC. Therefore, a deeper understanding of the pathogenesis of HCC is essential for precision therapy. Genomic and proteomic studies of HCC have enhanced our understanding of HCC. However, the phosphoproteomic characterization of HCC remains poorly understood. APPROACH AND RESULTS: We conducted an in-depth analysis of a clinical cohort of HCC using high-coverage phosphoproteomic. Effective therapeutic targets were validated using liver cancer cell lines and HCC patient-derived xenograft mouse models that correspond to the phosphoproteomic subtypes of HCC. Phosphoproteomic analysis classified HCC into 3 subtypes, A, B, and C, with increasing malignancy and correlation with clinical features, including patient prognosis, tumor staging, serum alpha-fetoprotein levels, tumor thrombus, and tumor size. Phosphoproteomic subtyping deeply reflected the biological characteristics and clinical features of patients with HCC. The profiles of HCC-dysregulated kinase activities inferred from the different phosphoproteomic subtypes consistently identify increased kinase activity related to cell proliferation. Subtype-C HCC patients showed the most significant dysregulation, indicating a potential therapeutic target. The corresponding drug, bosutinib, demonstrated efficacy in inhibiting the growth of subtype C tumors in liver cancer cell lines and HCC patient-derived xenograft mouse models representative of the phosphoproteomic HCC subtypes. CONCLUSIONS: Our study provides a comprehensive exploration of the phosphoproteomic landscape of HCC, establishing new subtypes that match clinical features and identifying potential therapeutic targets for the most malignant C subtype.

Carcinoma, Hepatocellular↗

PubMed2024

Clinical features and ALDH5A1 gene findings in 13 Chinese cases with succinic semialdehyde dehydrogenase deficiency.

BACKGROUND AND AIMS: To investigate the clinical features, ALDH5A1 gene variations, treatment, and prognosis of patients with succinic semialdehyde dehydrogenase (SSADH) deficiency. MATERIALS AND METHODS: This retrospective study evaluated the findings in 13 Chinese patients with SSADH deficiency admitted to the Pediatric Department of Peking University First Hospital from September 2013 to September 2023. RESULTS: Thirteen patients (seven male and six female patients; two sibling sisters) had the symptoms aged from 1 month to 1 year. Their urine 4-hydroxybutyrate acid levels were elevated and were accompanied by mildly increased serum lactate levels. Brain magnetic resonance imaging (MRI) showed symmetric abnormal signals in both sides of the globus pallidus and other areas. All 13 patients had psychomotor retardation, with seven showing epileptic seizures. Among the 18 variants of the ALDH5A1 gene identified in these 13 patients, six were previously reported, while 12 were novel variants. Among the 12 novel variants, three (c.85_116del, c.206_222dup, c.762C > G) were pathogenic variants; five (c.427delA, c.515G > A, c.637C > T, c.755G > T, c.1274T > C) were likely pathogenic; and the remaining four (c.454G > C, c.479C > T, c.1480G > A, c.1501G > C) were variants of uncertain significance. The patients received drugs such as L-carnitine, vigabatrin, and taurine, along with symptomatic treatment. Their urine 4-hydroxybutyric acid levels showed variable degrees of reduction. CONCLUSIONS: A cohort of 13 cases with early-onset SSADH deficiency was analyzed. Onset of symptoms occurred from 1 month to 1 year of age. Twelve novel variants of the ALDH5A1 gene were identified.

Child, Preschool↗

PubMed2024

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

Archaea↗