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Biomedical subjects

Qi Wang

Publications and source records attributed to Qi Wang.

17 recordsLinked to original sources

Epithelial tumor suppressor deletion promotes neuroendocrine differentiation in bladder cancer and reveals homoharringtonine as a candidate vulnerability.

Neuroendocrine bladder carcinoma (NEBC) is a highly aggressive malignancy with unresolved lineage determinants and limited preclinical models, hindering mechanistic investigation and therapeutic development. Here, we sought to assess whether bladder epithelial-derived models are competent to acquire neuroendocrine lineage programs under defined tumor suppressor alterations and to identify candidate therapeutic vulnerabilities in these systems. We integrated genomic and transcriptomic analyses of human NEBC with genetically engineered mouse models, epithelial-derived bladder organoids, and patient-derived NEBC models. Human NEBC exhibited dominant RB1 and TP53 alterations and an epithelial transcriptional continuum consistent with lineage plasticity. In vivo, intravesical Adeno-Cre-mediated tumor suppressor deletion predominantly generated sarcoma-like tumors, whereas epithelial-restricted organoid models recapitulated the molecular and neuroendocrine features of human NEBC, supporting epithelial lineage competence for neuroendocrine differentiation. Patient-derived models and human NEBC specimens further supported epithelial identity in NEBC. Using these complementary platforms, drug screening identified homoharringtonine (HHT) as a candidate therapeutic vulnerability in the tested NEBC systems. HHT suppressed neuroendocrine marker expression, induced apoptosis, and attenuated IL6-JAK-STAT3 signaling. Together, these findings describe complementary epithelial-derived NEBC models and support further investigation of HHT as a candidate therapeutic vulnerability.

Journal Article

Natural variation in GmSOP5 regulates seed oil and protein content during soybean domestication.

Seed oil content, protein content, and yield are agronomically important, correlated traits that determine the economic value of soybean (Glycine max). However, improving seed quality and yield simultaneously is challenging because gains in one breeding target often compromise the other, and the genetic basis of this trade-off is poorly understood. Here, we performed a genome-wide association study of 429 diverse soybean accessions and identified Seed Oil and Protein 5 (SOP5), which encodes a kinesin protein, as a key locus associated with seed oil and protein content. Knockout and overexpression experiments demonstrated that GmSOP5 positively affects seed oil content and 100-seed weight and negatively influences seed protein content. GmSOP5 is located in a selective sweep region, and the domestication-related GmSOP5H1 allele is nearly fixed in cultivated soybean, contributing to increased seed size, weight, and oil content and reduced protein content. Field trials demonstrated that neither loss-of-function GmSOP5-edited mutants, which have increased seed protein content, nor GmSOP5-overexpression lines, which have increased seed oil content, differed significantly in yield from wild-type plants, because changes in plant architecture were offset by changes in seed weight. Our results shed light on soybean domestication and suggest how pleiotropy can be harnessed in breeding to enhance seed quality without compromising yield.

GWAS

13C Stable Isotope Tracing-Based MFA Reveals the Contribution of Glucose to Glycolytic and TCA Fluxes and Its Application in Depression Research.

Metabolomics is widely applied to dissect metabolic pathways and their correlations with biological phenotypes. Unlike genomics and proteomics, metabolites exhibit substantial heterogeneity in chemical structure, physicochemical properties, and biological origin. Accordingly, pathway enrichment and annotation relying merely on alterations in metabolite abundance are prone to incomplete coverage, ionization bias, and ambiguous annotation, which inevitably impair the accuracy of pathway interpretation. Metabolic flux analysis (MFA) coupled with stable isotope-resolved metabolomics (SIRM) offers a powerful quantitative framework for tracing in vivo carbon flow and estimating reaction fluxes across key metabolic nodes. Glucose metabolism lies at the core of systemic energy homeostasis; however, most current investigations are confined to cell lines or in vitro systems, and a simple, easy-to-implement computational pipeline for in vivo glucose flux analysis in animal models is still lacking. Herein, we established an in vivo 13C-labeling-based MFA workflow to trace and resolve the systemic metabolic fate of glucose in rats. The pipeline covers tracer administration, sample preparation, LC-MS detection, isotopologue data acquisition and correction, construction of a glucose-metabolism-related metabolite database, MFA model establishment, and metabolic flux quantification. By infusing rats with [U-13C6]-glucose and [U-13C3]-sodium L-lactate, we precisely characterized the in vivo metabolic fates of circulating glucose and lactate and quantified their respective contributions to glycolytic flux and tricarboxylic acid (TCA) cycle flux. We further applied this workflow to profile energy metabolic reprogramming in depression. The results revealed a systemic shift toward aerobic glycolysis in rats exposed to chronic unpredictable mild stress (CUMS). Overall, the expanded application of this MFA strategy can provide mechanistic and quantitative insights into the regulation of metabolic pathways.

Animals

Induced pluripotent stem cell reprogramming: methodological evolution and challenges in clinical translation.

Cell reprogramming can transform somatic cells into induced pluripotent stem cells providing a platform for patient-specific disease modeling, drug screening and regenerative medicine research. Since the advent of OKSM-mediated reprogramming, the system of technical approaches has evolved continuously - from integrated viral vectors to non-integrated episomal systems and, more recently, chemical reprogramming and CRISPR approaches. The simultaneous advances in single-cell multi-omics, biomaterials engineering, and artificial intelligence have further refined the controllability and precision of the reprogramming process. Despite these innovations, problems persist that hinder clinical translation: incomplete epigenetic resetting, ongoing clonal heterogeneity, genomic instability in long-term culture, and the lack of standardized Good Manufacturing Practice protocols for large-scale manufacturing. This review summarizes the trajectory of iPSC reprogramming technologies, with special emphasis on the translational applicability of each modality. We evaluated viral and nonviral delivery systems, chemical reprogramming, strategies that aid gene editing, and emerging engineering platforms, including microfluidics, smart biomaterials, and artificial-intelligence-driven process optimization. We further identify the core "translational triltrilas", namely, the inherent tradeoffs between security, homogeneity, and scalability, and propose a comprehensive strategy to overcome these bottlenecks. By linking basic mechanistic understandings with industrial and regulatory considerations, this review aims to provide a route for transitioning iPSC technology from a laboratory tool to a clinically viable manufacturing platform.

clinical translation

A Case Report of Infantile Dopa-Responsive Dystonia Onset With Sleep Disorder Complicated With Autism Spectrum Disorder.

AIMS/BACKGROUND: Dopa-responsive dystonia (DRD) is a rare genetic disorder with complex and diverse clinical manifestations, resulting in a high rate of misdiagnosis. This case report describes an infantile case of DRD complicated by autism spectrum disorder (ASD), initially presenting with a sleep disorder. We aim to summarize its clinical manifestations, diagnostic process, treatment, and follow-up outcomes in order to improve clinical understanding of this disease. CASE PRESENTATION: A retrospective analysis was performed on a male infant who was treated at Jinhua Maternal and Child Health Care Hospital in 2020. The patient presented at one month of age with sleep disturbances, delayed motor development, and intermittent upward deviation of the eyes. Genetic testing identified two heterozygous pathogenic variants in the tyrosine hydroxylase (TH) gene. Among them, the c.738-2A>G variant was not recorded in the Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD), or 1000 Genomes Asian population databases. During follow-up, the patient was also found to have comorbid ASD. RESULTS: Genetic testing confirmed biallelic TH mutations, establishing the diagnosis of infantile DRD. The patient exhibited marked clinical response to levodopa/benserazide, though dose titration was required with growth. CONCLUSION: For infants with unexplained sleep disorder accompanied by delayed motor development, genetic testing should be performed as early as possible to facilitate the identification of the root cause and implement timely treatment. In addition, close follow-up should be conducted to detect comorbid neurodevelopmental disorders.

Humans

Genomic and One Health insights into Vibrio parahaemolyticus from environmental, seafood and clinical sources.

Vibrio parahaemolyticus is a leading cause of seafood-borne gastroenteritis worldwide, with climate warming facilitating its spread to high-latitude areas. In this study, we analyzed 212 genomes of environmental and seafood-associated isolates collected from seven cities in Zhejiang Province, China (2019-2024), alongside 228 clinical genomes from public databases. The 212 isolates were assigned to 172 sequence types (STs), with ST490 being the most frequent (5/212, 2.36%). Forty-four serotypes were identified, dominated by OL3:KUT (12.68%). High ST and serotype diversity were observed across different sample types and sources, with median pairwise single nucleotide polymorphisms (SNPs) ranging from 57,431 to 58,378, indicating comparable genetic diversity across groups. All isolates carried tlh and T3SS1 but lacked tdh and T3SS2. Resistance rates against ampicillin and cefazolin were 54.72% (116/212) and 44.34% (94/212), respectively, with multidrug resistance (MDR) detected in nine isolates, predominantly from seafood (7/9). A total of 63 distinct antimicrobial resistance genes (ARGs) spanning seven classes were identified. Isolates from aquaculture farms and wet markets exhibited greater resistance category diversity and higher ARG carriage than those from coastal or riverine sites. In contrast, the 228 clinical isolates harbored only 25 ARGs across two classes, with a significantly lower proportion of isolates carrying multiple ARG classes (0.44% vs. 6.13%, P&#xa0;<&#xa0;0.001). Human isolates formed tighter phylogenetic clusters, although a minority were closely related to environmental/foodborne strains. Overall, our findings demonstrate the genetic diversity and resistance potential of V. parahaemolyticus across environmental, seafood, and clinical sources, highlighting the importance of the One Health approach to comprehensive public health risk assessment.

Vibrio parahaemolyticus

Column switching liquid chromatography dual mass spectrometry system for simultaneous untargeted metabolomics and targeted exposomics.

Exposome-wide association studies (ExWAS) require the detection of metabolites and exposures with diverse chemical properties across wide concentration ranges, a task that typically demands multiple analytical methods. To address this challenge, we develop an integrated column-switching two-dimensional liquid chromatography-dual mass spectrometry (2DLC-dual-MS) system. This system employs a 2DLC setup to sequentially separate polar and non-polar compounds with log P ranging from -8 to 15. The separated fractions are directed via a three-way valve to a high-resolution MS (HRMS) and a triple quadrupole MS (TQMS), enabling simultaneous untargeted metabolome analysis and targeted quantification of 601 exposures. The method is particularly suited for the concurrent analysis of metabolome and exposome in human blood, where their concentrations typically differ by 2-3 orders of magnitude. In a demonstration application on lung adenocarcinoma ExWAS, the system exhibits good stability over more than 300 consecutive injections for both metabolome and exposome analysis, confirming its robustness for ExWAS applications.

Metabolomics

Metabolic engineering of Candida yeasts for biotechnological applications.

Candida yeasts represent a versatile yet underexploited platform for industrial biotechnology. These yeasts utilize a remarkably broad range of carbon sources, particularly for hydrophobic carbon sources, coupled with robust growth and diverse biosynthetic capacities, making them promising hosts for sustainable production of chemicals, fuels, and proteins. Despite these advantages, industrial deployment of Candida species has been hindered by concerns regarding opportunistic pathogenicity and the historical lack of efficient genetic manipulation tools, leading to a substantial gap between metabolic potential and practical utilization. Recent advances in functional genomics, genome editing, and systems metabolic engineering are rapidly overcoming these barriers, enabling more precise and efficient strain development. In this review, we systematically summarize recent progress in the metabolic engineering of Candida species as microbial cell factories, with particular emphasis on expanding genetic toolkits, utilizting renewable and non-conventional carbon sources, and biosynthesizing high-value compounds. In addition, we propose a biosafety-oriented classification framework to support their safe industrial deployment. Finally, we discuss current challenges and emerging opportunities, emphasizing that the synergy of synthetic biology and artificial intelligence-driven design holds the key to unlocking the biotechnological potential of Candida yeasts.

Candida

Emergence of cefiderocol resistance in carbapenem-resistant Escherichia coli ST167 prior to clinical use: A multifactored resistance landscape.

OBJECTIVES: Cefiderocol is a novel siderophore cephalosporin with potent activity against multidrug-resistant Gram-negative bacteria. Here, we reported the prevalence and mechanisms of cefiderocol resistance in carbapenem-resistant Escherichia coli (CREC) in China before its clinical use. METHODS: A total of 443 non-duplicate CREC isolates collected from 67 hospitals in China (2013-2021) underwent antimicrobial susceptibility testing according to CLSI guidelines. Whole-genome sequencing, transcriptomic analysis, siderophore quantification, and targeted genetic manipulation were performed to investigate the underlying resistance mechanisms. RESULTS: Among the 443 CREC isolates, 102 (23.0%) were resistant to cefiderocol, and 34 (7.6%) showed intermediate susceptibility. Multivariable logistic regression identified ST167 lineage (OR, 3.05; 95% CI, 1.12-8.29; P = 0.028), blaNDM-5 carriage (OR, 9.04; 95% CI, 2.96-27.57; P < 0.001), and cirA truncation (OR, 49.56; 95% CI, 20.33-120.79; P < 0.001) as independent factors associated with cefiderocol resistance. Among ST167 isolates, cefiderocol-resistant isolates showed increased yersiniabactin carriage and siderophore production but comparable TonB-dependent transporter expression profiles. Phylogenetic analysis revealed that cefiderocol-resistant ST167 isolates clustered into a distinct subclade enriched with resistance-associated determinants, including a recurrent FhuA P50S substitution detected in 59/64 (92.2%) resistant isolates. Functional assays showed that the P50S substitution increased cefiderocol minimum inhibitory concentration (0.032-0.125 &#xb5;g/mL), particularly in an NDM-5-producing background (0.032-0.5 &#xb5;g/mL). CONCLUSIONS: Cefiderocol resistance is highly prevalent among high-risk ST167 CREC isolates before the clinical introduction of cefiderocol in China, highlighting the need for continued surveillance of this epidemic lineage. Cefiderocol resistance is mediated by multiple resistance determinants, and we identify the recurrent FhuA P50S substitution as a novel contributor to reduced cefiderocol susceptibility.

Antimicrobial resistance

Integrated transcriptomic and metabolomic analyses reveal key regulators associated with lipid metabolic differences between subcutaneous and visceral adipose tissues in sheep.

The location of fat deposition has a significant impact on meat quality and body health, and different adipose tissues exhibit significant differences in lipid metabolism and immune regulation. This study aimed to systematically compare the phenotypic characteristics, transcriptome, and metabolome of subcutaneous adipose tissue (SAT) and two types of visceral adipose tissue (VAT) in sheep, in order to reveal the metabolic differences between SAT and VAT and their potential regulatory mechanisms. The results showed that compared with VAT, SAT had stronger triglyceride deposition ability and obvious cellular hypertrophy. Through integrative analysis, 15 key lipid metabolism genes and 12 differential metabolites were identified. Among them, ACACA, FASN, ELOVL6, SCD, as well as metabolites palmitic acid and glycerol-3-phosphate, may play a central role in SAT lipid synthesis and storage; whereas IGFBP2, ADRB3, LTA4H, and metabolites arachidonic acid and leukotriene B4 may be involved in the lipolysis regulation and inflammatory response of VAT. These findings may provide deeper insights into the regulatory mechanisms of fat deposition in sheep.

Animals

Machine learning-based drug susceptibility prediction from Candida genomic data.

OBJECTIVES: Invasive Candida infection is an increasing clinical concern, with antifungal resistance rising across multiple species. However, rapid and accurate antifungal susceptibility testing (AFST) remains limited in routine practice. The study evaluated species distribution and antifungal susceptibility of invasive Candida isolates in China and assessed the feasibility of combining whole-genome sequencing (WGS) with machine learning to predict minimum inhibitory concentrations (MICs). METHODS: Consecutive non-repetitive isolates were collected from 20 hospitals in 13 provinces during 2022-2023. MICs of nine antifungal agents were determined by broth microdilution, and WGS was performed for species accounting for >5% of the total isolates. Genomic 11-mer features were extracted and used to train random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGBoost) models, followed by optimization of the best-performing algorithm. RESULTS: A total of 337 isolates were obtained from blood (n = 232) and sterile body fluids (n = 105), comprising C. albicans (n = 103), C. tropicalis (n = 71), C. parapsilosis (n = 67), and C. glabrata (n = 63). Non-albicans Candida showed higher azole and echinocandin resistance, with C. tropicalis notably resistant to azoles and C. glabrata to echinocandins. Among the three models, RF demonstrated the best performance on 304 sequenced isolates. The optimized RF model was evaluated by the receiver operating characteristic (ROC) curve analysis and achieved an average area under the ROC curve (AUC) of 0.979 (95% CI: 0.974-0.984), essential agreement over 90.1%, and categorical agreement over 93.2% across species. CONCLUSIONS: These findings underscore the clinical challenge posed by non-albicans Candida resistance, and indicate that WGS-based MIC prediction may offer a highly accurate reference for earlier antifungal therapy.

Antifungal Agents

Exploring potential targets and molecular mechanisms of traumatic brain injury exacerbated by Benzo(a)pyrene via network toxicology and&#xa0;molecular&#xa0;dynamics simulation.

Benzo(a)pyrene (BaP) is a common environmental pollutant from combustion sources that promotes oxidative stress, neuroinflammation and disruption of blood-brain barrier (BBB). However, its contribution to worsening traumatic brain injury (TBI) remains unclear. In this study, we aimed to assess the contribution of BaP to secondary injury in TBI. By integrating data from e.g., the Comparative Toxicogenomics Database, GeneCards, and Online Mendelian Inheritance in Man, 121 overlapping core targets were identified between BaP and TBI. Enrichment analyses via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, combined with protein-protein interaction networks and topological algorithms (degree, closeness centrality, betweenness centrality, average shortest path length, topological coefficient and partner of multi-edged node pairs), highlighted five hub genes (TP53, EGFR, AKT1, ACTB, and TNF) implicated in mitogen-activated protein kinase signaling, oxidative stress, and neuroinflammation. Molecular docking showed strong binding affinities of BaP to these hub proteins, with energies from -9.3 to -12.1&#xa0;kcal/mol, tighter than co-crystal ligands and existing protein-binding drugs. Molecular dynamics simulations confirmed interaction stability through low root-mean-square deviation (<&#x2009;0.5&#xa0;nm), fluctuation, and radius of gyration values. Calculation of binding free energies using MM-PBSA validated the strong binding affinity between BaP and binding pockets of each hub genes. Toxicity prediction analysis revealed an oral LD50 of 316&#xa0;mg/kg for BaP, with high probabilities for neurotoxicity, BBB permeability, carcinogenicity, and mutagenicity, associated with aryl hydrocarbon receptor activation. These findings reveal a "neurovascular homeostasis disruption" network underlying BaP-exacerbated TBI pathology and highlight potential targets to reduce pollution-related risks in TBI management.

Benzo(a)pyrene

Decoding Arginine Dimethylation Isomers via pH-Tuned Reactivity with Methylglyoxal: A Chemical Approach for Functional Proteomics.

Arginine dimethylation, encompassing asymmetric and symmetric configurations, represents a fundamental post-translational modification. Despite sharing identical chemical formulas, the two arginine dimethylation isomers exhibit different or even opposite biological effects. Therefore, it is necessary to determine their specific structure before conducting a further biological investigation. However, current methods for arginine dimethylation analysis face great challenges in efficient isomer differentiation, preventing the functional investigation of arginine dimethylation. To overcome this obstacle, herein, we introduce a novel chemical strategy leveraging pH-tuned reactivity with methylglyoxal (MGO) to decode these dimethylation isomers. By utilizing molecular dynamics simulation analysis, we revealed the different chemical reactivities of asymmetrically and symmetrically dimethylated arginine when reacted with MGO at different pH conditions. This property enabled the development of a pH-tuned chemical strategy by combining the MGO reaction with boronate affinity enrichment to simultaneously enrich and differentiate the dimethylation isomers. This strategy can effectively distinguish dimethylated arginine isomers in complex cell samples, and the good feasibility of this strategy was verified by orthogonal validation with the neutral loss. Of the obtained data set, this strategy identified sDMA at R112 of SNRPN, which is confirmed to be modified by PRMT5. Further functional analysis reveals its crucial role in maintaining protein stability and in regulating spliceosome assembly. Overall, by transforming the inherent pH sensitivity of MGO reactions into a powerful analytical tool, our work establishes the first chemical platform for functional proteomic dissection of arginine dimethylation isomers, which paves the way for further regulating mechanism investigations of protein methylation.

Pyruvaldehyde

Genome-scale CRISPR screen identifies TMEM198 driving double membrane vesicle formation in swine alphacoronavirus and murine betacoronavirus infected cells.

COVID-19 pandemic caused by the SARS-CoV-2 which is well-publicized cross-species transmissibility. SARS-CoV-2 belongs to genus Betacoronavirus, several pathogenic alphacoronaviruses have shown similar patterns of emergence. Much less attention paid to host factors required for alphacoronavirus replication compared to those of betacoronaviruses. Here, we utilized a genome-wide CRISPR-Cas9-based screen to identify TMEM198 as a critical host protein for double-membrane vesicle (DMVs) formation during the replication of swine alphacoronavirus. Gene deletion of TMEM198 led to a reduction in the levels of viral infection in cells, whereas the ectopic expression of TMEM198 correspondingly resulted in an increase in infection levels. At the mechanistic level, TMEM198 directly binds to the C-terminal of nonstructural protein 3 (nsp3c) and nonstructural protein 4 (nsp4) to participate in the formation of DMVs. The first 35 amino acids at the N-terminal of TMEM198 are critical for the formation of DMVs and viral replication. Moreover, mice with a gene deletion of TMEM198 exhibit reduced susceptibility to the Betacoronavirus MHV. These results identify the function of TMEM198 in the formation of DMVs during the replication of swine alphacoronavirus and murine betacoronavirus.

Animals

High temperature-responsive DEAR4 condensation confers thermotolerance through recruiting TOPLESS in Arabidopsis nucleus.

Global warming is harmful to plants and threatens crop yields in the world. In contrast to other abiotic stresses, the molecular mechanisms for plant high temperature perception and signaling are still not fully understood. Here, we report that transcription factor DREB AND EAR MOTIF PROTEIN 4 (DEAR4) positively regulates heat tolerance in Arabidopsis thaliana. We further reveal that DEAR4 proteins undergo liquid-liquid phase separation (LLPS) and high temperature could induce DEAR4 condensate formation in the nucleus. Moreover, DEAR4 recruits the transcriptional co-repressor TOPLESS (TPL) into the nuclear speckles under high temperature. The high temperature triggered DEAR4-TPL co-condensates enhance their transcriptional repression activity through modulating histone deacetylation levels of GASA5, which is a reported negative regulator of HEAT SHOCK PROTEINs (HSPs). A genome-wide transcriptional landscape study confirms that DEAR4 induces the expression of multiple HSPs. Taken together, we illustrate a transcriptional repression mechanism mediated by DEAR4 through LLPS to confer plants thermotolerance and open a new avenue for translating this knowledge into crops for improving their heat resistance.

Arabidopsis

MCT4-dependent lactate secretion suppresses antitumor immunity in LKB1-deficient lung adenocarcinoma.

Inactivating STK11/LKB1 mutations are genomic drivers of primary resistance to immunotherapy in KRAS-mutated lung adenocarcinoma (LUAD), although the underlying mechanisms remain unelucidated. We find that LKB1 loss results in enhanced lactate production and secretion via the MCT4 transporter. Single-cell RNA profiling of murine models indicates that LKB1-deficient tumors have increased M2 macrophage polarization and hypofunctional T&#xa0;cells, effects that could be recapitulated by the addition of exogenous lactate and abrogated by MCT4 knockdown or therapeutic blockade of the lactate receptor GPR81 expressed on immune cells. Furthermore, MCT4 knockout reverses the resistance to PD-1 blockade induced by LKB1 loss in syngeneic murine models. Finally, tumors from STK11/LKB1 mutant LUAD patients demonstrate a similar phenotype of enhanced M2-macrophages polarization and hypofunctional T&#xa0;cells. These data provide evidence that lactate suppresses antitumor immunity and therapeutic targeting of this pathway is a promising strategy to reversing immunotherapy resistance in STK11/LKB1 mutant LUAD.

Animals