Biomedical subjects

Xueli Zhang

Publications and source records attributed to Xueli Zhang.

9 recordsLinked to original sources

PubMed2026

Base editing for precision therapeutics.

Base editing (BE), the precise installation of single-nucleotide changes in DNA or RNA without inducing double-strand breaks, holds substantial therapeutic promise for correcting single-nucleotide variants, which constitute more than half of the known pathogenic genetic variants. Recent advances have improved base editor specificity, efficiency, and delivery, enabling clinically oriented procedures. Clinically, BE has shown early success or strong translational promise in sickle cell disease, β-thalassemia, leukemia (via CAR T and epitope engineering), hypercholesterolemia (PCSK9 and ANGPTL3), alpha-1-antitrypsin deficiency, and glycogen storage disease type Ia. Key remaining challenges include bystander editing within the activity window, residual off-target DNA and RNA editing, delivery constraints (payload size, tissue targeting, and redosing limits), immunogenicity, and the need for durable long-term safety evidence across relevant cell types and disease contexts. Continued technological refinements, careful preclinical validation, and rigorous clinical assessment will be essential to fully realize BE's transformative potential in precision medicine.

Humans↗

PubMed2025

Stage-dependent proteomic alterations in aqueous humor of diabetic retinopathy patients based on data-independent acquisition and parallel reaction monitoring.

BACKGROUND: Diabetic retinopathy (DR), a microvascular complication of diabetes mellitus (DM), represents the predominant cause of preventable vision loss in working-age populations globally. While the pathophysiological mechanisms underlying DR progression remain incompletely understood, our study employs comprehensive proteomic profiling of aqueous humor (AH) to identify stage-specific biomarkers and therapeutic targets in type 2 diabetes mellitus (T2DM) patients across DR progression. METHODS: Utilizing data-independent acquisition (DIA) mass spectrometry, we quantified AH proteomes in a discovery cohort comprising 24 subjects: 18 T2DM patients stratified by DR severity [6 non-DR, 6 non-proliferative DR (NPDR), 6 proliferative DR (PDR)] and 6 cataract controls without diabetes (non-DM). Validation cohort analysis (including 10 AH samples in each group) was performed using parallel reaction monitoring (PRM) strategy for verification of target proteins. Comprehensive bioinformatics analyses included gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, protein-protein interaction (PPI) network construction, receiver operating characteristic (ROC) curve analysis, and ConnectivityMap (Cmap)-based drug prediction. RESULTS: Proteomic profiling identified 739 quantifiable AH proteins (62% extracellular) with clear separation among the four clinical stages in the discovery cohort. GSEA uncovered altered expression of proteins mainly related to complement and coagulation cascades, folate metabolism, and the selenium micronutrient network in patients with DR. WGCNA-derived protein modules yielded 83 PRM-validated targets, including 5 hub proteins differentiating NPDR from non-DR and 33 hub proteins showed significant upregulation in PDR versus NPDR comparison. Clinical correlation analysis identified F2, FGG, FGB, RBP4, AMBP, VTN, C8A, CPB2, and C2 associated with clinical traits. C6, FAM3C, SPP1, and JCHAIN levels were altered post-anti-VEGF treatment. Pharmacological prediction identified potential therapeutic compounds, including perindopril, triciribine, and XAV-939 for NPDR, and topiramate, triciribine, and vecuronium for PDR. CONCLUSION: This study established a comprehensive AH proteomic signature of DR progression, offering insights into the pathogenesis of DR and highlighting potential biomarkers and novel therapeutic targets.

Humans↗

PubMed2005

Studies on the mechanism of Indigo Carmine removal by solvent sublation.

Indigo Carmine (C16H8N2Na2O8S2), an anionic dye, was removed from aqueous solution by solvent sublation of Indigo Carmine-cetyltrimethylammonium bromide (CTAB) complex (sublate) into 2-octanol. A stoichiometric amount of surfactant (surfactant:dye=2:1) was demonstrated to be able to remove over 93% IC from the aqueous solution in 5 min. The apparent activation energy of attachment of the sublate to bubbles was calculated as 1.3 kJ/mol. Parameters were considered. At the same time, on the base of the complete transport mechanism, a mathematical model for the dye-surfactant complexation was obtained. Furthermore, the simulation of the mathematical and experimental data was made with good results.

Journal Article↗

PubMed2005

The removal of humic acids from water by solvent sublation.

The application of solvent sublation in the removal of humic acids was investigated in the present study. The humic acids (HA) were removed from an aqueous solution by solvent sublation of humic acid-hexadecylpyridium chloride (HPC) complex (sublate) into isopentanol. Several parameters were examined towards the optimization of humic acid removal; the dosage of a surfactant was found to be the major one, controlling the overall efficiency of the progress. The removal rate was somewhat enhanced by higher airflow rate and almost independent of the volume of the organic solvent floating on the top of the aqueous column. The effects of electrolytes (e.g., NaCl), nonhydrophobic organics (e.g., ethanol), and pH of the solution upon the process were studied. Under the optimized condition, the treatment performance was found to be very efficient, reaching almost 100%, indicating that solvent sublation can serve as a possible alternative technology for the removal of humic acids. The solvent sublation process follows first-order kinetics. A characteristic parameter, apparent activation energy of attachment of the sublate to bubbles, was estimated at a value of 9.48 kJ/mol. Furthermore, the simulation of a mathematical model with the experiments on the solvent sublation of humic acid-HPC was described here.

Letter↗

PubMed2005

Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system.

Sequence retrieval from single bands of polymerase chain reaction (PCR)-denaturing gel electrophoresis (DGE) profiles is an important but often difficult step for molecular diversity analysis of complex microbial communities such as activated sludge systems. We analyzed the temperature gradient gel electrophoresis (TGGE) profiles of PCR-amplified 16S rDNA fragments from an activated sludge sample of a coking wastewater treatment plant. Single bands were excised, and a clone library was constructed for each. Sequence heterogeneity in each single band was found to be significantly overestimated due to single-stranded DNA (ssDNA) contamination formed during the PCR amplification, since only 10-60% of library clones of each single TGGE band had identical migration behavior compared with the parent band. Three methods, digestion with mung bean nuclease, optimization of PCR amplification, and purification via denatured polyacrylamide gel electrophoresis (d-PAGE), were compared for their ability to minimize ssDNA contamination, with the last one being the most efficient. After using d-PAGE to minimize ssDNA to a nearly nondetectable level, 70-100% of library clones for each single TGGE band had identical migration compared with the parent band. Several sequences were found in each of six single bands, and this co-migration could be predicted with the Poland software. The predominant bacteria of the activated sludge were assessed via a combination of sequence retrieval from each single TGGE band and band intensity analysis. Only beta and alpha subclasses of the Proteobacteria were detected, 93.8% and 6.2%, respectively. Our work suggests that prior to constructing a clone library to retrieve the actual sequence diversity of a single DGE band, it is advisable to minimize ssDNA contamination to a nondetectable level.

Alphaproteobacteria↗

PubMed2004

Microdiversity of phenol hydroxylase genes among phenol-degrading isolates of Alcaligenes sp. from an activated sludge system.

Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting classified 97 phenol-degrading isolates with identical amplified ribosomal DNA restriction analysis (ARDRA) patterns into six genotypic groups. The 16S rRNA gene of the representative isolate of each group had higher than 99.47% common identity with each other and higher than 98% identity with the type strain of Alcaligenes faecalis. PCR-TGGE (temperature gradient gel electrophoresis) analysis of the genes of the largest subunit of the multi-component phenol hydroxylase (LmPH) in each isolate followed with sequencing showed that isolates within each ERIC-PCR group had identical LmPH gene sequences. Among the six different ERIC-PCR groups, two were found to harbor two different LmPH genes encoding low- and high-Ks (affinity constants) phenol hydroxylases, and the low-Ks type LmPH was identical in sequence with one predominant LmPH of the parental activated sludge. Three ERIC-PCR groups had only the high-Ks type and one had no sequence similar to the known LmPHs. Our work suggests that there is no correlation between the phylogenetic groupings of phenol-degrading bacteria and their LmPH genotypes possibly due to extensive horizontal gene transfer of this functional gene.

Alcaligenes↗

PubMed2002

[Inhibition of proliferation of human vascular smooth muscle cells by overexpression of p21 gene].

OBJECTIVE: To observe the apoptosis of human vascular smooth muscle cells (HVSMCs) transfected with p21 gene and investigate its potential mechanism. METHODS: An adenoviral expression vector with full-length cDNA of p21 gene insert (Ad-p21) was constructed and transfected into HVSMC. A mock vector, pAdeno-X-lac Z constructed with the same method, was transfected into HVSMCs as control. Western blotting and DS-PAGE were used to detect the expression of p21 gene. Fluorescence staining was used to observe the changes in nuclei of apoptotic cells and calculate the cell survival rate. Expression of tissue transglutaminase (tTG) in HVSMC was examined by DIG-marked probe. RESULTS: Fluorescence staining showed marked fragmentation of nucleus and pyknosis of chromatin in pAdeno-X-p21 transfected cells. The expression of tTG was at a higher level in pAdeno-X-p21 transfected cells than in normal cells and pAdeno-X-lac transfected HVSMCs. CONCLUSION: Overexpression of p21 gene inhibits the proliferation of HVSMC through apoptosis induced by p21 which may relate with overexpression of tTG.

Apoptosis↗

PubMed2000

[Study on Methylation of p15(INK4B) Gene in Acute Myeloid Leukemia and Chronic Myeloid Leukemia]

In order to explore the role of p15(INK4B) gene with highly methylated CpG island in the pathogenesis of leukemia, the expression levels of p15(INK4B) gene was detected in patients with AML and CML. Methylation-specific PCR (MSP) assay was employed in the experiments. The methylation incidence was 83.9% (26/31) in AML and 0% (0/28) in CML. The results showed that methylation of p15(INK4B) gene was the one of the major ways for inactivation of the gene, and the methylation could be appeared in clinical development of the disease and patients condition worsened. Methylation of p15(INK4B) did not occur and its function probably is normal in CML.

Journal Article↗

PubMed2000

[Detection of High Methylation of p15(INK4B) and p16(INK4A) Genes in Multiple Myeloma]

To study the action, characteristics and expression of high methylation of p15(INK4B) and p16(INK4A) genes in multiple myeloma (MM), the sensitive methylation specific PCR method was employed to detect the hypermethylation of p15(INK4B) and p16(INK4A) in 24 patients with MM. Results showed that the methylation incidence of p15(INK4B) and p16(INK4A) genes were 70.8% (17/24) and 58.3% (14/24) in the MM patients, with the products of 148 bp and 150 bp fragments, respectively. The methylation of p15(INK4B) and p16(INK4A) genes were simultaneously happened in MM patients of plasmocytoma type with two cases at II phase and two cases at III phase. The simultaneous non-methylation of p15(INK4B) and p16(INK4A) genes were founded in five cases of MM patients, all of the tumor cells were of small plasmocyte type with mature differention. Conclusion suggested that there were high incidence of methylation of p15(INK4B) and p16(INK4A) genes in patients with MM. Hypermethylation can be detected in the early stage of disease, which was associated with its progress. It indicated a bad prognosis when methylation happended simultaneously in the two genes. Methylation of p15(INK4B) and p16(INK4A) genes may be related to the pathogeny of MM.

Journal Article↗