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Chao Zhang

Publications and source records attributed to Chao Zhang.

7 recordsLinked to original sources
PubMed2026

Integrated transcriptomic and metabolomic analysis reveals candidate regulatory networks associated with starch accumulation in tetraploid potato.

Potato (Solanum tuberosum L.) tuber starch is a major determinant of crop quality and industrial value, yet the regulatory mechanisms underlying starch accumulation in autotetraploid cultivars remain poorly resolved. Here, we performed integrated transcriptomic and metabolomic analyses using a segregating tetraploid population derived from parents with contrasting starch content. Extreme phenotypes were selected to systematically dissect the molecular basis of starch accumulation. Transcriptome profiling revealed extensive transcriptional reprogramming between high- and low-starch genotypes, with differentially expressed genes significantly enriched in carbohydrate metabolism, particularly the starch and sucrose metabolism pathway. Notably, multiple transcription factor families, including AP2/ERF, MYB, and bHLH, were prominently represented, suggesting coordinated regulatory control. Metabolomic analysis identified substantial metabolic divergence, with differentially accumulated metabolites predominantly enriched in starch and sucrose metabolism as well as secondary metabolic pathways. Most metabolites exhibited negative associations with starch content, indicating competitive carbon allocation between primary and secondary metabolism. Integrative multi-omics analysis further resolved a core regulatory module comprising key structural genes and transcription factors tightly associated with starch-related metabolites. In particular, genes involved in sucrose cleavage and ADP-glucose metabolism, together with trehalose-6-phosphate synthase (TPS) and UDP-glucose-associated pathways, emerged as critical nodes linking carbon flux to starch biosynthesis. Correlation network analysis suggested that AP2/ERF-, MYB-, and bHLH-type transcription factors modulate these pathways by coordinating structural gene expression and metabolic flux distribution. Collectively, our study establishes a transcriptional-metabolic framework for starch accumulation in tetraploid potato, highlighting the central role of carbon allocation and signaling intermediates in shaping starch content, and providing candidate targets for molecular breeding and genome editing.

Solanum tuberosum↗
PubMed2026

Integrated Pan-Cancer, Single-Cell, and Spatial Transcriptomic Analyses Identify ZDHHC12 as a Biomarker Associated with Macrophage Infiltration and the Immune Landscape in Glioma.

BACKGROUND: The tumor immune microenvironment (TME) critically influences cancer progression and therapeutic response. However, the pan-cancer expression landscape, prognostic relevance, and spatial distribution of ZDHHC12 remain incompletely characterized. This study investigated the prognostic value of ZDHHC12 and its associations with immune microenvironmental features and drug sensitivity. METHODS: Data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) datasets were used to evaluate ZDHHC12 expression and prognosis across cancer types. Immune infiltration analyses, single-cell RNA sequencing, and spatial transcriptomics were integrated to characterize the associations of ZDHHC12 with the cancer immunity cycle and the spatial architecture of glioma. Drug sensitivity and immunotherapy-related metrics were assessed using pharmacogenomic databases and computational prediction models. RESULTS: ZDHHC12 was aberrantly expressed across multiple tumors and was associated with patient prognosis. Its expression was broadly correlated with immune cell recruitment- and activation-related signatures. In glioma, single-cell and spatial transcriptomic analyses showed enrichment of ZDHHC12 in monocyte/macrophage populations and spatial co-localization with BAK1, CD68, and CD163. ZDHHC12 expression was also associated with predicted drug sensitivity and immunotherapy-related metrics. CONCLUSION: ZDHHC12 may serve as a candidate pan-cancer prognostic biomarker. In glioma, its expression is associated with macrophage-enriched and immunosuppressive microenvironmental features. Functional studies are required to establish causality and determine its therapeutic relevance.

GBM↗
PubMed2026

Interface Excitons in van der Waals Sandwich Heterostructures.

Exciton engineering in van der Waals heterostructures (vdWHs) is essential for next-generation optoelectronics, yet they normally require near-perfect stacking and are highly sensitive to moiré potentials. Here, we demonstrate a polarity-engineering strategy using a γ-InSe/transition metal dichalcogenide/γ-InSe sandwich heterostructure. The out-of-plane spontaneous polarization of γ-InSe intrinsically breaks interfacial inversion symmetry, giving rise to interface excitons (IFXs) that exhibit a linear Stark effect with an ultrasmall dipole moment of 0.15 e·nm. First-principles calculations and Kelvin probe force microscopy reveal asymmetric interfacial charge transfer governed by γ-InSe's polarity. Transient spectroscopy shows nonmonotonic relaxation dynamics, including a characteristic signal reversal that indicates pre-existing interfacial charge states. Our results establish that exciton dipole moments, interlayer coupling, and relaxation dynamics can be precisely tuned through material polarity and thickness. Polarity engineering thus provides a versatile and robust route to control excitonic properties in vdWHs, offering expanded design strategies for advanced excitonic and optoelectronic devices.

Stark effect↗
PubMed2026

Metagenomic next-generation sequencing of cerebrospinal fluid reveals pathogen spectrum and mortality predictors among patients with advanced HIV-1 disease at a tertiary hospital in China.

BACKGROUND: Central nervous system (CNS) infections remain the major causes of morbidity and mortality among people living with HIV-1 (PLWH), particularly in resource-limited settings. However, the clinical characteristics and prognostic indicators of PLWH with suspected CNS infections are not well defined. In this study, we aim to characterize the spectrum of CNS pathogens, clinical characteristics, in-hospital mortality, and factors associated with death among people with advanced HIV-1 disease (AHD) in Guangxi, China. METHODS: Metagenomic next-generation sequencing (mNGS) was performed to analyze types of infection in cerebrospinal fluid (CSF) from 61 treatment-naive PLWH with suspected CNS infections. Clinical data, routine laboratory tests, and biochemical tests were collected and analyzed. RESULTS: Among the 61 CSF samples, primarily with AHD, a total of 206 pathogens were identified. Viral pathogens predominated, with Epstein-Barr virus being the most frequently identified, followed by cytomegalovirus. Compared with patients with single-pathogen infection, those with multiple infections (viral, bacterial, and fungal) exhibited significantly lower CD4 T cell counts, higher C-reactive protein levels, and markedly reduced lipid metabolism parameters. However, infection types were not significantly associated with in-hospital death. Multivariate logistic regression analysis identified plasma low density lipoprotein (LDL) and CSF lactate dehydrogenase (LDH) as independent predictors of in-hospital death. CONCLUSION: In PLWH with AHD and suspected CNS infections, multiple pathogens frequently coexist in the CSF. Plasma LDL and CSF LDH levels were independent predictors of death, indicating their potential value as early risk stratification in AHD.

Humans↗
PubMed2025

Serum N-glycomics for non-invasive detection of significant liver pathology across clinical phases of treatment-naïve chronic hepatitis B.

BACKGROUND: Early identification of significant liver pathology is crucial for timely antiviral intervention in individuals with chronic hepatitis B (CHB) infection. Current non-invasive methods show limited accuracy in detecting occult liver damage, particularly in those with normal ALT. This study evaluated serum N-glycan profiles for diagnosing significant liver pathology in treatment-na&#xef;ve CHB patients across clinical phases. METHODS: This cross-sectional study analyzed 626 treatment-na&#xef;ve CHB patients confirmed by liver biopsy, classified according to 2025 EASL guidelines. Serum N-glycan profiles were determined using DNA sequencer-assisted fluorophore-assisted carbohydrate electrophoresis. Significant liver pathology was defined as inflammation grade&#x2009;&#x2265;&#x2009;G2 and/or fibrosis stage&#x2009;&#x2265;&#x2009;S2 (per Scheuer scoring system). Multivariate logistic regression models were developed and compared with traditional non-invasive markers. RESULTS: Among 626 CHB patients, 66.0% had significant inflammation and 58.9% had significant fibrosis. Patients with significant pathology showed characteristic alterations, with elevated P1, P3, P6, P7, P11 peaks and decreased P0, P5, P8, P10 peaks (all p&#x2009;<&#x2009;0.0001). Compared to respective infection phases, hepatitis phases showed P1 increases of 19.6% and 36% in HBeAg(+) and HBeAg(-) patients, with P11 increases of 82.4% and 73.4%, while P0 decreased by 20.3% and 27.6%, and P10 by 21.6% and 20.3%. Relative to mild pathology (G and S&#x2009;<&#x2009;2), P1 increased by 27% in significant pathology (G and/or S&#x2009;&#x2265;&#x2009;2), reaching 58.7%/48.7% in G4/S4 stages (vs. G0/S0). In ALT-normal HBeAg(+) infection phase, P1 increased by 80.2%/65.8% in G4/S4 stages (vs. G0/S0), with P2 also increasing by 54.1%/45.2%. Multivariate analysis identified P11 as strongest risk factor (OR&#x2009;=&#x2009;3.84, 95%CI: 1.74-8.45, p&#x2009;=&#x2009;0.0008), followed by P1 (OR&#x2009;=&#x2009;2.04, 95%CI: 1.57-2.64, p&#x2009;<&#x2009;0.0001) and P7 (OR&#x2009;=&#x2009;1.75, 95%CI: 1.31-2.34, p&#x2009;=&#x2009;0.0002), while P2 (OR&#x2009;=&#x2009;0.07, 95%CI: 0.02-0.26, p&#x2009;<&#x2009;0.0001) and P0 (OR&#x2009;=&#x2009;0.30, 95%CI: 0.12-0.79, p&#x2009;=&#x2009;0.0140) served as protective factors. The glycomics combined model (AUC&#x2009;=&#x2009;0.876 (0.844-0.908)) achieved superior performance and outperformed the clinical model (AUC&#x2009;=&#x2009;0.818 (0.779-0.857)), LSM (AUC&#x2009;=&#x2009;0.817 (0.775-0.858)), APRI (AUC&#x2009;=&#x2009;0.830 (0.792-0.867)), and FIB-4 (AUC&#x2009;=&#x2009;0.672 (0.621-0.723)) (all p&#x2009;<&#x2009;0.001), with 78.7% sensitivity and 83.2% specificity. The optimized model reached AUC&#x2009;=&#x2009;0.917 (0.891-0.942) with accuracy 84.2%, with 78.7% sensitivity and 94.6% specificity. Both glycomics-based models maintained diagnostic capability in ALT-normal patients particularly in HBeAg(+) infection. CONCLUSIONS: Serum N-glycomics demonstrates promising potential for non-invasive identification of significant liver pathology in treatment-na&#xef;ve CHB patients, providing an alternative approach for early treatment decisions, especially in ALT-normal patients with occult liver damage.

Humans↗
PubMed2025

Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.

Increasing evidence indicates that the loss of soil microbial &#x3b1;-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial &#x3b1;-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal &#x3b1;- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal &#x3b1;-diversity declined under high environmental stress across three soil layers (0-20&#x2009;cm, 20-40&#x2009;cm and 40-60&#x2009;cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.

Soil Microbiology↗
PubMed2024

Association between Branched-Chain amino acids and Epilepsy: A Mendelian randomized study.

BACKGROUND: Branched-chain amino acids (BCAAs) have been affected epilepsy, yet conclusions remain inconclusive, lacking causal evidence regarding whether BCAAs affect epilepsy. Systematic exploration of the causal relationship between BCAAs and epilepsy could hand out new ideas for the treatment of epilepsy. METHODS: Utilizing bidirectional Mendelian randomization (MR) study, we investigated the causal relationship between BCAA levels and epilepsy. BCAA levels from genome-wide association studies (GWAS), including total BCAAs, leucine levels, isoleucine levels, and valine levels, were employed. Causal relationships were explored applying the method of inverse variance-weighted (IVW) and MR-Egger, followed by sensitivity analyses of the results to evaluate heterogeneity and pleiotropy. RESULTS: Through strict genetic variant selection, we find some related SNPs, total BCAA levels (9), leucine levels (11), isoleucine levels (7), and valine levels (6) as instrumental variables for our MR analysis. Following IVW and sensitivity analysis, total BCAAs levels (OR&#xa0;=&#xa0;1.14, 95&#xa0;% CI&#xa0;=&#xa0;1.019&#xa0;&#x223c;&#xa0;1.285, P&#xa0;=&#xa0;0.022) and leucine levels (OR&#xa0;=&#xa0;1.15, 95&#xa0;% CI&#xa0;=&#xa0;1.018&#xa0;&#x223c;&#xa0;1.304, P&#xa0;=&#xa0;0.025) had significant correlation with epilepsy. CONCLUSIONS: There exists a causal relationship between the levels of total BCAAs and leucine with epilepsy, offering the new ideas into epilepsy potential mechanisms, holding significant implications for its prevention and treatment.

Humans↗