Biomedical subjects

Linlin Wang

Publications and source records attributed to Linlin Wang.

9 recordsLinked to original sources

PubMed2026

Integrated single-cell transcriptomics, Mendelian randomization, and machine learning identify CEBPZ as an immune-related biomarker in oral lichen planus.

BACKGROUND: Oral lichen planus (OLP) is a chronic, immune-mediated oral mucosal disease with complex pathophysiology and potential for malignant transformation. Understanding its molecular basis is critical for the development of precise diagnostic and therapeutic strategies. OBJECTIVES: We aimed to identify key immune-related biomarkers and characterize cellular dynamics in OLP, with a particular focus on the role of CEBPZ in disease pathogenesis. MATERIAL AND METHODS: We analyzed single-cell RNA sequencing (scRNA-seq) data from OLP lamina propria samples (GSE211630) to identify disease-specific T-cell subpopulations using high-dimensional weighted gene co-expression network analysis (hdWGCNA) for oxidative stress-related gene modules.-data-based Mendelian randomization (SMR) integrated FinnGen genome-wide association study (GWAS; 342,499 Europeans) data with Genotype-Tissue Expression (GTEx) expression quantitative trait loci (eQTL) data to identify causal genes. Machine learning (ML) models (least absolute shrinkage and selection operator (LASSO) and convolutional neural network (CNN)) were developed using bulk RNA-seq datasets (GSE52130 and GSE38616) for diagnostic purposes. RESULTS: We identified OLP-specific T-cell populations (clusters 0, 3, 5, 7, 13, and 15) with enhanced migration inhibition factor (MIF) pathway signaling toward B cells and monocytes. Two oxidative stress-associated modules contained hub genes, including CEBPZ. Summary-data-based Mendelian randomization analysis identified 231 OLP-associated genes, with CEBPZ uniquely intersecting LASSO-selected markers (odds ratio (OR) = 1.057, 95% confidence interval (95% CI) = 1.013-1.102, p = 0.010). Machine learning models achieved area under the curve (AUC) values ranging from 0.653 to 0.745, with the CNN model reaching a validation accuracy of 0.735. CEBPZ showed elevated expression in OLP T cells and correlated with enhanced MIF-(CD74+CXCR4) signaling. CONCLUSIONS: This integrative approach identifies CEBPZ as a pivotal biomarker linking genetic susceptibility, oxidative stress, and immune dysregulation in OLP. Our diagnostic models offer promising tools for OLP management.

CEBPZ↗

PubMed2026

Genomic instability, postoperative recurrence and therapeutic vulnerabilities in resectable non‑small cell lung cancer (Review).

Resectable non‑small cell lung cancer (NSCLC) is managed largely according to anatomical stage, pathological risk and actionable driver alterations, yet these factors do not fully explain postoperative recurrence. Genomic instability may contribute to recurrence by promoting clonal diversification, intratumoral heterogeneity, occult dissemination, persistence of residual tumor cells, and immune escape. In the present review, chromosomal instability (CIN), copy‑number complexity, whole‑genome doubling, DNA repair defects, replication stress, and extrachromosomal DNA (ecDNA) were critically evaluated using a three‑axis translational framework encompassing biological consequences, potential clinical roles, and strength of evidence. Current evidence suggests that clonal diversity and copy‑number complexity have the clearest near‑term prognostic rationale. By contrast, CIN and whole‑genome doubling are supported more strongly by evolutionary and mechanistic rather than prospective clinical evidence. Defects in DNA repair, replication stress, and ecDNA represent potential therapeutic vulnerabilities, but their clinical relevance remains to be established. To date, no treatment‑predictive biomarkers based on genomic instability have been identified for resectable NSCLC. Direct clinical evidence linking any specific genomic instability feature to the presence or longitudinal dynamics of postoperative molecular residual disease (MRD) remains limited. Postoperative circulating tumor DNA‑defined MRD provides prognostic information more directly related to residual disease but remains assay‑dependent and should not be considered a genomic‑instability phenotype. Therefore, features of genomic instability should remain investigational and should not replace established clinical, pathological, or molecular decision‑making. Their near‑term value lies in refining biological risk models and generating testable hypotheses for biomarker‑defined perioperative trials.

Humans↗

PubMed2026

Epigenetic safety of in vitro maturation in PCOS: genome-wide DNA methylation profiling of cord blood from a randomized controlled trial.

BACKGROUND: In vitro maturation (IVM) provides a safer alternative to conventional in vitro fertilization (IVF) for women with polycystic ovary syndrome (PCOS) by mitigating the risk of ovarian hyperstimulation. However, concerns persist regarding whether IVM perturbs epigenetic reprogramming in the offspring. Current evidence is constrained by candidate-gene approaches or a lack of parental controls. This study aimed to evaluate the genome-wide DNA methylation safety of IVM compared with conventional IVF using a rigorous trio-based design. METHODS: This secondary epigenetic analysis was nested within a randomized controlled trial (RCT) (ClinicalTrials.gov: NCT03463772). We included 10 nuclear families (trios), comprising five IVM-conceived and five IVF-conceived singleton offspring alongside their biological parents. Both groups utilized a uniform freeze-only single-blastocyst transfer strategy to minimize hormonal confounding. Genomic DNA from umbilical cord blood (UCB) and parental peripheral blood was analyzed using reduced representation bisulfite sequencing (RRBS). Genome-wide methylation patterns and differentially methylated regions (DMRs) were subsequently compared between the groups. RESULTS: Clinical characteristics were comparable between the IVM and IVF groups. Genome-wide analyses demonstrated high concordance in UCB methylation patterns, revealing no significant differences in global CpG methylation levels or distributions across key genomic features (promoters, CpG islands, and gene bodies). Only three rare DMRs were identified in UCB (representing ~ 0.0001% of the genome), none of which mapped to imprinted or developmentally critical loci. Furthermore, methylation variability remained consistent between the groups. CONCLUSIONS: Our findings provide robust mechanistic evidence supporting the epigenetic safety of IVM. The remarkable stability of the neonatal methylome confirms that specific IVM conditions do not compromise early developmental programming, thereby endorsing IVM as a safe and viable alternative for women with PCOS. TRIAL REGISTRATION: ClinicalTrials.gov registry, NCT03463772. Registered on March 13, 2018.

Humans↗

PubMed2006

Growth factor receptors as regulators of hematopoiesis.

Nearly 15 years have elapsed since the US Food and Drug Administration last approved a major new hematopoietic cytokine. Promiscuous binding to multiple receptors, or to receptors expressed by multiple tissues, reduces growth factor specificity and promotes side effects. Here we show that hematopoiesis can be differentially regulated using receptors rather than ligands. Conditional derivatives of both fibroblast growth factor receptor-1 (F36VFGFR1) and the thrombopoietin receptor (F36VMpl) induced a sustained expansion of mouse marrow cells ex vivo, and erythroid cells in vivo. Only F36VFGFR1 could support the ex vivo expansion of short-term repopulating hematopoietic stem cells (HSCs), the ex vivo survival of long-term repopulating HSCs, and the prolonged in vivo expansion of granulocytes, monocytes, and platelets. Only F36VMpl induced a response sufficiently rapid to accelerate recovery from radiation-induced anemia. These results establish receptors as a new class of hematopoietic regulators possessing activities unobtainable with growth factors.

Amino Acid Substitution↗

PubMed2006

Definitive-like erythroid cells derived from human embryonic stem cells coexpress high levels of embryonic and fetal globins with little or no adult globin.

Human embryonic stem cells are a promising tool to study events associated with the earliest ontogenetic stages of hematopoiesis. We describe the generation of erythroid cells from hES (H1) by subsequent processing of cells present at early and late stages of embryoid body (EB) differentiation. Kinetics of hematopoietic marker emergence suggest that CD45+ hematopoiesis peaks at late D14EB differentiation stages, although low-level CD45- erythroid differentiation can be seen before that stage. By morphologic criteria, hES-derived erythroid cells were of definitive type, but these cells both at mRNA and protein levels coexpressed high levels of embryonic (epsilon) and fetal (gamma) globins, with little or no adult globin (beta). This globin expression pattern was not altered by the presence or absence of fetal bovine serum, vascular endothelial growth factor, Flt3-L, or coculture with OP-9 during erythroid differentiation and was not culture time dependent. The coexpression of both embryonic and fetal globins by definitive-type erythroid cells does not faithfully mimic either yolk sac embryonic or their fetal liver counterparts. Nevertheless, the high frequency of erythroid cells coexpressing embryonic and fetal globin generated from embryonic stem cells can serve as an invaluable tool to further explore molecular mechanisms.

Cell Differentiation↗

PubMed2005

Anatomical compartments modify the response of human hematopoietic cells to a mitogenic signal.

Methods for specifically regulating transplanted cells have many applications in gene and cell therapy. We examined the response of human cord blood CD34+ cells to a specific mitotic signal in vivo. Using a conditional signaling molecule (F36VMpl) that is specifically activated by an artificial ligand called a chemical inducer of dimerization (CID), human hematopoietic cells transplanted into immune deficient mice were induced to proliferate. Only differentiating erythroid precursors and multipotential and erythroid progenitors (colony-forming unit [CFU]-mix and burst forming unitserythroid [BFUe]) responded; however, the nature of the response differed markedly between bone marrow and spleen. In the marrow, F36VMpl induced a 12- to 17-fold expansion of differentiated erythroid precursors and a loss of CFU-mix and BFUe. In the spleen, F36VMpl induced a marked rise in BFUe and CFU-mix and, relative to marrow, a much less prominent rise in more mature red cells. Clonal analysis was most consistent with the interpretation that the spleen and bone marrow differentially regulate the response of human progenitors to a mitotic signal, possibly influencing progenitor expansion versus differentiation. These findings establish CIDs as in vivo growth factors for human hematopoietic cells.

Animals↗

PubMed2005

Air quality modeling of interpollutant trading for ozone precursors in an urban area.

Emission trading is a market-based approach designed to improve the efficiency and economic viability of emission control programs; emission trading has typically been confined to trades among single pollutants. Interpollutant trading (IPT), as described in this work, allows for trades among emissions of different compounds that affect the same air quality end point, in this work, ambient ozone (O3) concentrations. Because emissions of different compounds impact air quality end points differently, weighting factors or trading ratios (tons of emissions of nitrogen oxides (NO(x)) equivalent to a ton of emissions of volatile organic compounds [VOCs]) must be developed to allow for IPT. In this work, IPT indices based on reductions in O3 concentrations and based on reductions in population exposures to O3 were developed and evaluated using a three-dimensional gridded photochemical model for Austin, TX, a city currently on the cusp of nonattainment with the National Ambient Air Quality Standards for O3 concentrations averaged over 8 hr. Emissions of VOC and NO(x) from area and mobile sources in Austin are larger than emissions from point sources. The analysis indicated that mobile and area sources exhibited similar impacts. Trading ratios based on maximum O3 concentration or population exposure were similar. In contrast, the trading ratios did exhibit significant (more than a factor of two) day-to-day variability. Analysis of the air quality modeling indicated that the daily variability in trading ratios could be attributed to daily variations in both emissions and meteorology.

Air Pollutants↗

PubMed2004

An oligonucleotide decoy for nuclear factor-kappa B inhibits tumor necrosis factor-alpha-induced human umbilical cord vein endothelial cell tissue factor expression in vitro.

Abnormal tissue factor (TF) expression on vascular endothelial cells may account for thrombotic events associated with cardiovascular disease. The transcription factor nuclear factor-kappa B (NF-kappa B) activation plays a key role in endothelial cell injury and TF expression. Disruption of NF-kappa B activation in endothelial cells may inhibit TF expression and be protective in thrombosis. The purpose of the study was to determine whether NF-kappa B transcription factor decoy (TFD) could block TF expression. NF-kappa B TFD was transferred into cultured human umbilical cord vein endothelial cells (HUVEC) by liposomes, and the transfection efficiency was detected by flow cytometry. The effect of NF-kappa B TFD on TF mRNA levels was determined by reverse transcription-polymerase chain reaction. The expression of surface TF antigen was analyzed by flow cytometry. TF activity was studied by measuring enzymatic activation of factor X by the TF-activated factor VII complex. The results suggested that NF-kappa B decoy could be successfully transferred into HUVEC by liposome. The NF-kappa B TFD competed with the endogenous kappa B site sequence in the TF promoter for binding to transcription factor NF-kappa B in tumor necrosis factor-alpha-stimulated HUVEC, which could block the tumor necrosis factor-alpha-induced increase in TF mRNA levels, the upregulation of surface TF antigen and TF activity. This study demonstrated that NF-kappa B decoy could block HUVEC TF gene expression. Targeted genetic disruption of endothelial TF expression by NF-kappa B decoy may provide a possible therapeutic method for cardiovascular and thrombosis disease.

Binding Sites↗

PubMed2004

Flow cytometric detection of nonneoplastic antigenic polymorphisms of donor origin after allogeneic marrow transplant: a report of two cases.

Multidimensional flow cytometry found an abnormal lack of CD16 expression detected on neutrophils after hematopoietic stem cell transplantation (HSCT) in bone marrow specimens from 2 patients. Chimerism studies were used to determine that the CD16- myeloid cells were donor in origin, consistent with a normal polymorphic variant, most likely a previously described Fc gamma receptor IIIB gene deletion. Identical phenotypes were recognized in peripheral blood samples obtained subsequently from the respective donors. These donor-specific phenotypic abnormalities were transferred to patients who underwent successful HSCT. The distinction of these phenotypic abnormalities from neoplastic changes such as secondary myelodysplasias or relapse of original disease is important in posttransplantation monitoring of hematopoietic diseases.

Antigens↗