Biomedical subjects

Zhiwei Liu

Publications and source records attributed to Zhiwei Liu.

10 recordsLinked to original sources

PubMed2026

Heterozygous germline deletion in Hif3a exacerbates esophageal squamous cell carcinoma development.

Germline variations contribute to esophageal squamous cell carcinoma (ESCC) susceptibility. We identified a germline deletion (exons 7-8) in HIF3A in an ESCC family and investigated its functional impact using CRISPR/Cas9-engineered cells and Hif3a-eKO1 mice (heterozygous for exons 7-8 deletion). Multi-omics analysis of Hif3a-eKO1 and WT mice revealed dysregulated pathways in normal esophagus and during 4NQO-induced carcinogenesis, with key biomarkers validated by immunohistochemistry. Hif3a deficiency enhanced ESCC cell proliferation and invasion in vitro and accelerated 4NQO-induced tumorigenesis in vivo, with Hif3a-eKO1 mice developing more and larger neoplastic lesions. Multi-omics analysis revealed downregulation of cytokeratin-related genes (notably Krt17) and γδ T cells in normal esophagus of Hif3a-eKO1 compared with WT. Consistently reduced Krt17 expression in Hif3a-eKO1 was confirmed by both esophageal immunohistochemistry and cellular Western blot analyses. During 4NQO-induced carcinogenesis, Hif3a deficiency upregulated DNA damage response markers, including Krüppel-like factor 4 (Klf4) and ATR serine/threonine kinase (Atr). Notably, epithelial cells with abundant γH2AX foci lacked Krt17 expression, while Krt17-positive cells showed minimal γH2AX foci. Heterozygous germline Hif3a deletion (exons 7-8) may promote ESCC by disrupting esophageal barrier function-impairing Krt17-mediated epithelial integrity and reducing γδ T cells-while exacerbating genomic instability. These findings reveal ESCC predisposition mechanisms and therapeutic targets. © 2026 The Pathological Society of Great Britain and Ireland.

HIF3A↗

PubMed2026

AI proteomics: from protein identification to virtual cells.

Artificial intelligence (AI) is transforming scientific research, including proteomics. In this Perspective, we highlight key mass spectrometry (MS)-based proteomics areas where AI is driving innovation, ranging from protein identification to building AI virtual cells. These include improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and, ultimately, enabling AI virtual cells. Finally, we call for global collaboration among data producers, data consumers and other stakeholders to establish an AI-friendly ecosystem for MS-based proteomics, laying the foundation for transformative advancements in proteomics driven by AI.

Proteomics↗

PubMed2006

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study.

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.

Acetanilides↗

PubMed2006

Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

The metadynamics or hills method is a relatively new molecular dynamics technique aimed to enhance the sampling of separated regions in phase space and map out the underlying free energy landscape as a function of a small number of order parameters or collective variables. The high efficiency allows for the application of metadynamics in combination with first principles dynamics methods, in particular with Car-Parrinello molecular dynamics, to study processes in which changes in the electronic structure play a dominant role, such as chemical reactions. The option to choose several independent collective variables is important to tackle complex and concerted transformations that lack an obvious a priori choice for a single reaction coordinate. In this Account, we discuss the role of metadynamics in the search of transition states, local minima, reaction paths, free energy profiles, and reaction coordinates among a growing list of alternative methods.

Journal Article↗

PubMed2004

Effects of protein deprivation on growth and small intestine morphology are not improved by glutamine or glutamate in gastrostomy-fed rat pups.

OBJECTIVES: Critically ill neonates often have their enteral intake severely limited shortly after birth. Whether glutamine (Gln) or glutamate (Glu) can preserve intestinal structure and function in the neonate undergoing limited enteral feeding is not clear. We hypothesize that Gln and Glu can similarly preserve intestinal structure in the developing small intestine of infant rats fed a low protein diet. METHODS: Using a gastrostomy-fed "pup-in-a-cup" rat model, the effects of Gln and Glu on the developing rat small intestine were examined. Four groups of 6- to 7-day-old pups were fed rat milk substitute (RMS) via gastrostomy tube. One group was provided 100% and three were provided 25% of the protein normally received from their mothers. Two of the groups fed 25% protein received additional Gln or Glu for 6 days. RESULTS: Pups receiving the 100% protein RMS were larger than pups receiving the 25% protein RMS with or without Gln/Glu supplementation (P < 0.001). Average villus height (P < 0.01) and area (P < 0.01) were greater in pups receiving 100% protein RMS than in pups given 25% protein RMS formula. There was no significant difference among the groups in mucosal maltase or alkaline phosphatase activities. Tight junction protein claudin-1 was significantly higher in the group fed 100% protein RMS diet, while occludin did not differ among the 4 groups. Neither Gln nor Glu increased claudin-1 or occludin in rats fed 25% protein. CONCLUSIONS: These results suggest that neither Gln nor Glu supplementation can substitute effectively for whole protein in the developing rat small intestine for the outcomes that were evaluated.

Alkaline Phosphatase↗

PubMed2004

Copper treatment alters the barrier functions of human intestinal Caco-2 cells: involving tight junctions and P-glycoprotein.

This study investigated the effects of copper on paracellular permeability and P-glycoprotein (P-gp) in Caco-2 cells. Apical treatment with 100-300 microM CuSO4 in Hanks' balanced salt solution (HBSS, up to 3 hours) induced a time- and concentration-dependent increase in permeability of Caco-2 cell monolayers monitored by transepithelial electrical resistance (TEER). Copper treatment also induced a concentration-dependent reduction of F-actin stain, but not of tight junctional protein ZO-1. In addition, without any adverse effects on TEER, apical treatment with 300 microM CuSO4 in complete medium (for 24 hours) could reduce basolateral-to-apical transport, and increase apical-to-basolateral transport of rhodamine-123 (Rho-123) and accumulation of Rho-123 in Caco-2 cells. Treatment with 10-100 microM CuSO4 in HBSS (up to 3 hours) also induced a time- and concentration-dependent increase in accumulation of Rho-123 in Caco-2 cells. The results indicated that copper treatment increased the paracellular permeability probably by perturbing F-actin skeleton, and inhibited P-gp, thus altering the barrier functions of Caco-2 cells.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2004

[Toxicological effects of copper on human intestinal Caco-2 cells].

OBJECTIVE: To study the toxicological effects of copper on human intestinal Caco-2 cells. METHODS: The effects of copper on human intestinal Caco-2 cells were evaluated by MTT conversion, intra-cellular production of reactive oxygen species (ROS), cloning efficiency and changes of P-glycoprotein (P-gp) activities in Caco-2 cells. In addition, Caco-2 cells and Salmonella enteritidis served as the models to examine the effect of copper on the host-parasite interaction. RESULTS: Copper induced a dose-dependent decrease of cell viability measured by MTT assay; by using the fluorescent probe 2, 7-dichlorofluorescin diacetate, a significant increase of ROS production in Cu-treated cells was detected; the significant time- and dose-dependent decrease of P-gp activities in Cu-treated cells was demonstrated by increased accumulation of rhodamine 123 in cells. Copper treatment also increased the efficiency of the bacterial invasion, but decreased the number of bacteria surviving in the intracellular environment. CONCLUSION: Copper induced a variety of toxicological endpoints which might be caused by oxidative damage, but the effect of copper on cell-bacteria interaction needs to be further investigated.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2004

[Caco-2 cell monolayers and it's application in toxicological research].

Caco-2 cells derived from a human colon adenocarcinoma, spontaneously differentiate after reaching confluence in culture, exhibiting several morphological and functional characteristics of mature enterocytes. Caco-2 cell monolayers represents a well-established model for the study of intestinal transport of nutrients and xenobiotics, and is wildly used in pharmacology and toxicology. In this review the cell culture conditions, characteristics and functional parameters of model were introduced. The application of Caco-2 cell monolayers in studying mechanism, uptake, transport and gastrointestinal toxicity of xenobiotics were also explained.

Biological Transport↗

PubMed2003

[A new toxicological concept-acute reference dose].

Acute reference dose (ARfD) is a new concept in toxicology and risk assessment, and mainly used for assessing health effect from short-time exposure to environmental chemicals. The ARfD of a chemical was defined as "an estimate of a substance in food or drinking water, expressed on a body weight basis, that can be ingested over a short period of time, usually during one meal or one day, without appreciable health risk to the consumer on the basis of all the known facts at the time of the evaluation. It is usually expressed in milligrams per kilogram of body weight." ARfD is different from ADI and reference dose. In this review the principles and methods in establishing ARfD were explained.

Dose-Response Relationship, Drug↗

PubMed2003

The regulatory effect of memantine on expression and synthesis of heat shock protein 70 gene in neonatal rat models with cerebral hypoxic ischemia.

OBJECTIVE: To evaluate the neuroprotective effect of memantine, a non-competitive antagonist at the N-methyl-D-aspartate receptor, against hypoxic ischemia (HI) by exploring its regulation on the expression and synthesis of heat shock protein 70 (HSP70) gene in neonatal rat models with cerebral HI. METHODS: Memantine was intraperitoneally injected at a dose of 20 mg/kg in neonatal rat models either before (PRE group) or after (POST group) induction of HI. The expression and synthesis of the HSP70 gene and its corresponding product were determined by rapid competitive PCR and immunohistochemistry, respectively. RESULTS: There was an increase in the expression of HSP70 mRNA two hours after induction of HI, which reached its peak at 48 hours, then decreased gradually. The same expression occurred at relatively low levels in the control group. Also, HSP70 synthesis was detected as early as 2h after HI, reached its peak between 48 and 72 hours, then declined over time. After memantine administration, the expression of the gene and its synthesis of the corresponding product decreased significantly during the time intervals 24 - 72 h for the gene and 48 - 72 h for the product compared to the HI group. CONCLUSION: It was shown that HI is very sensitive to the expression of the HSP70 gene and synthesis of its corresponding product, which could be regulated by memantine. The latter may have the ability to reduce brain damage; thus decreased HSP70 mRNA expression could be a marker for HI. It is suggested that memantine can be a promising agent for neuroprotection against HI, although an overall and objective assessment of memantine is required to see if it can be used on neonates clinically later on.

Animals↗