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Biomedical subjects

Yue Wang

Publications and source records attributed to Yue Wang.

At least 37 records · Page 2Linked to original sources
PubMed2026

Oncogenic Mutations and Tumor Microenvironment Alterations in Diffuse Large B-Cell Lymphoma With Bulky Disease.

BACKGROUND: Bulky disease represents a clinically aggressive subset of diffuse large B-cell lymphoma (DLBCL) associated with adverse clinical outcomes. The aim of this study was to investigate the influence of oncogenic mutations and tumor microenvironment alterations on bulky disease in DLBCL. METHODS: We analyzed a cohort of 939 patients with newly diagnosed DLBCL. Using DNA (n = 934) and RNA (n = 524) sequencing, we compared oncogenic mutations and tumor microenvironment (TME) alterations based on tumor diameter, with cutoff values at 5.0 cm and 10.0 cm. Further stratification by mutations in key genes (CD58, STAT6, EBF1) correlated with tumor diameter revealed distinct transcriptomic and immunologic profiles. Subsequent single-cell RNA sequencing, guided by these mutational signatures, resolved the cellular heterogeneity within the TME. RESULTS: Integrative analysis revealed that tumor diameter correlated with increased incidence of mutations in CD58, STAT6, and EBF1; adverse genetic subtypes such as EZB-like MYC+ and TP53Mut; activation of oncogenic pathways (JAK/STAT, BCR, PI3K, and MYC); and an immunosuppressive tumor microenvironment. Notably, immune checkpoint molecules varied across the bulky stages, with CTLA-4, TIGIT, ICOS, and CD28 expression inversely correlated with tumor diameter, while CD70 and 4-1BBL expression positively correlated. Single-cell RNA sequencing further revealed mutation-specific tumor microenvironment insights. CD58-mutated tumor exhibited a profoundly immune-deserted microenvironment dominated by malignant B cells with minimal immune infiltration, whereas STAT6-mutated tumor was associated with increased fibroblasts and CD4 + T cells, particularly regulatory T cells (Treg) and Th1-like cells; EBF1-mutated tumor was characterized by increased proportions of malignant B cells. CONCLUSIONS: Collectively, our findings highlight the biological complexity of bulky disease, identifying candidate molecular targets and providing a biological framework for future therapeutic hypothesis generation in this clinically aggressive subset of DLBCL.

Humans↗
PubMed2025

Direct estimation and inference of higher-level correlations from lower-level measurements with applications in gene-pathway and proteomics studies.

This paper tackles the challenge of estimating correlations between higher-level biological variables (e.g. proteins and gene pathways) when only lower-level measurements are directly observed (e.g. peptides and individual genes). Existing methods typically aggregate lower-level data into higher-level variables and then estimate correlations based on the aggregated data. However, different data aggregation methods can yield varying correlation estimates as they target different higher-level quantities. Our solution is a latent factor model that directly estimates these higher-level correlations from lower-level data without the need for data aggregation. We further introduce a shrinkage estimator to ensure the positive definiteness and improve the accuracy of the estimated correlation matrix. Furthermore, we establish the asymptotic normality of our estimator, enabling efficient computation of P-values for the identification of significant correlations. The effectiveness of our approach is demonstrated through comprehensive simulations and the analysis of proteomics and gene expression datasets. We develop the R package highcor for implementing our method.

Proteomics↗
PubMed2025

Efficient genome editing in Pseudomonas syringae pv. actinidiae using the CRISPR/FnCas12a system.

CRISPR-based gene editing has rarely been studied in plant pathogens. In this report, the CRISPR/FnCas12a system was successfully established for gene editing in Pseudomonas syringae pv. actinidiae (Psa), which causes bacterial canker (BC) of kiwifruit. The system was constructed in a Psa-suitable vector pBBR1-MCS2 to edit hopH1 or/and hopZ5, which encode effectors only present in Psa biovar 3 (Psa3) responsible for BC pandemic in kiwifruit worldwide. Two different CRISPR RNAs (crRNA) were designed to edit either hopH1 or/and hopZ5, and two different sets of PCR primers were used to screen deletions of the target genes and the presence of the vector in Psa. The deletion in Psa was impacted by the position of the DNAs targeted by the crRNAs. The vector-eliminated mutant could receive the editing system iteratively. Interestingly, the double mutant ΔhopZ5ΔhopH1 showed significantly stronger virulence than the wild-type Psa on Actinidia eriantha cv. White (resistant to BC), but weak virulence on A. chinensis cv. Hongyang (highly susceptible to BC), respectively, suggesting that hopH1 or/and hopZ5 potentially matches an unknown resistance gene in White. In summary, we have established the CRISPR/FnCas12a genome-editing system to probe gene function in the pathogen and to explore effector-target interactions in kiwifruit-Psa-pathosyetem.

Bacterial canker↗
PubMed2024

Integrative Omics Reveals the Metabolic Patterns During Oocyte Growth.

Well-controlled metabolism is associated with high-quality oocytes and optimal development of a healthy embryo. However, the metabolic framework that controls mammalian oocyte growth remains unknown. In the present study, we comprehensively depict the temporal metabolic dynamics of mouse oocytes during in vivo growth through the integrated analysis of metabolomics and proteomics. Many novel metabolic features are discovered during this process. Of note, glycolysis is enhanced, and oxidative phosphorylation capacity is reduced in the growing oocytes, presenting a Warburg-like metabolic program. For nucleotide biosynthesis, the salvage pathway is markedly activated during oocyte growth, whereas the de novo pathway is evidently suppressed. Fatty acid synthesis and channeling into phosphoinositides are specifically elevated in oocytes accompanying primordial follicle activation; nevertheless, fatty acid oxidation is reduced in these oocytes simultaneously. Our data establish the metabolic landscape during in vivo oocyte growth and serve as a broad resource for probing mammalian oocyte metabolism.

Animals↗
PubMed2007

Obesity hypoventilation syndrome: prevalence and predictors in patients with obstructive sleep apnea.

Patients with obesity hypoventilation syndrome (OHS) have a lower quality of life, more healthcare expenses, a greater risk of pulmonary hypertension, and a higher mortality compared to eucapnic patients with obstructive sleep apnea (OSA). Despite significant morbidity and mortality associated with OHS, it is often unrecognized and treatment is frequently delayed. The objective of this observational study was to determine the prevalence of OHS in patients with OSA seen at the sleep disorders clinic of a large public urban hospital serving predominantly minority population and to identify clinical--not mechanistic--predictors that should prompt clinicians to measure arterial blood gases. In the first stage, we randomly selected 180 patients referred to our sleep disorders clinic between 2000 and 2004 for suspicion of OSA. From this retrospective random sample we calculated the prevalence of OHS in patients with OSA and identified independent clinical predictors using logistic regression. In the second stage, we prospectively validated these predictors in a sample of 410 consecutive patients referred to the sleep disorders clinic for suspicion of OSA between 2005 and 2006. The prevalence of OHS in patients with OSA was 30% in the retrospective random sample and 20% in the prospective sample. Three variables independently predicted OHS in both samples: serum bicarbonate level (p < 0.001), apnea-hypopnea index (p = 0.006), and lowest oxygen saturation during sleep (p < 0.001). Due to the serious morbidity associated with OHS, we selected a highly sensitive threshold of serum bicarbonate level. A threshold of 27 mEq/l had a sensitivity of 92% and a specificity of 50%. Only 3% of patients with a serum bicarbonate level <27 mEq/l had hypercapnia compared to 50% with a serum bicarbonate > or =27 mEq/l. In conclusion, OHS is common in severe OSA. A normal serum bicarbonate level excludes hypercapnia and an elevated serum bicarbonate level should prompt clinicians to measure arterial blood gases.

Adult↗
PubMed2006

Critical role of DNA checkpoints in mediating genotoxic-stress-induced filamentous growth in Candida albicans.

The polymorphic fungus Candida albicans switches from yeast to filamentous growth in response to a range of genotoxic insults, including inhibition of DNA synthesis by hydroxyurea (HU) or aphidicolin (AC), depletion of the ribonucleotide-reductase subunit Rnr2p, and DNA damage induced by methylmethane sulfonate (MMS) or UV light (UV). Deleting RAD53, which encodes a downstream effector kinase for both the DNA-replication and DNA-damage checkpoint pathways, completely abolished the filamentous growth caused by all the genotoxins tested. Deleting RAD9, which encodes a signal transducer of the DNA-damage checkpoint, specifically blocked the filamentous growth induced by MMS or UV but not that induced by HU or AC. Deleting MRC1, the counterpart of RAD9 in the DNA-replication checkpoint, impaired DNA synthesis and caused cell elongation even in the absence of external genotoxic insults. Together, the results indicate that the DNA-replication/damage checkpoints are critically required for the induction of filamentous growth by genotoxic stress. In addition, either of two mutations in the FHA1 domain of Rad53p, G65A, and N104A, nearly completely blocked the filamentous-growth response but had no significant deleterious effect on cell-cycle arrest. These results suggest that the FHA domain, known for its ability to bind phosphopeptides, has an important role in mediating genotoxic-stress-induced filamentous growth and that such growth is a specific, Rad53p-regulated cellular response in C. albicans.

Alleles↗
PubMed2006

Distinguishing lung tumours from normal lung based on a small set of genes.

Identifying specific molecular markers and developing sensitive detection methods are two of the fundamental requirements for detection and differential diagnosis of cancer. Toward this goal, we first performed cDNA array analysis using 65 non-small cell lung cancer and non-involved normal lung tissues. We then used several complementary statistical and analytical methods to examine gene expression profiles generated by us and others from four independent sets of normal and neoplastic lung tissues. We report here that several sets of roughly 20 genes were sufficient to provide a robust distinction between normal and neoplastic tissues of the lung. Next we assessed the predictive ability of these gene sets by using Flow-Thru Chips (FTC) (MetriGenix, Baltimore, MD) containing 20 genes to screen 48 primary lung tumours and normal lung tissues. Gene expression changes detected by FTC distinguished lung cancers from the normal lung tissues using an RNA amount equivalent to that present in as few as 300 cells. We also used an independent set of 24 genes and showed that their expression profile was equally effective when measured by quantitative polymerase chain reaction (Q-PCR). Our results demonstrate that lung cancers can be identified based on the expression patterns of just 20 genes and that this approach is applicable for cancer diagnosis, prognosis, and monitoring using small amount of tumour or biopsy samples.

Biomarkers, Tumor↗
PubMed2006

Digital logic circuit based on a single molecular system of salicylidene Schiff base.

The salicylidene Schiff base N-3,5-dichloro-salicylidene-(S)-alpha-phenylethylamine (SPEA) has been synthesized and characterized. Stimulated by one optical input (UV light) and two chemical inputs (OH(-) and Zn(2+)), SPEA undergoes reactions of photochemistry, deprotonation, and complexation. Tailing these reactions by means of the UV-vis absorption spectra and fluorescence spectra, two obvious optical outputs, an absorption band at 323 nm and a fluorescent emission peak at 460 nm, have been obtained. On the basis of encoding binary digits in these inputs and outputs applying positive logic conventions, one monomolecular circuit, which integrates one OR, two NOT, and four AND gates, has been achieved.

Journal Article↗
PubMed2006

Assessing the effectiveness of antiretroviral adherence interventions. Using marginal structural models to replicate the findings of randomized controlled trials.

Randomized controlled trials of interventions to improve adherence to antiretroviral medications are not always feasible. Marginal structural models (MSM) are a statistical methodology that aims to replicate the findings of randomized controlled trials using observational data. Under the assumption of no unmeasured confounders, 3 MSM estimators are available to estimate the causal effect of an intervention. Two of these estimators, G-computation and inverse probability of treatment weighted (IPTW), can be implemented using standard software. G-computation relies on fitting a multivariable regression of adherence on the intervention and confounders. Thus, it is related to the standard multivariable regression approach to estimating causal effects. In contrast, IPTW relies on fitting a multivariable logistic regression of the intervention on confounders. This article reviews the implementation of these methods, the assumptions underlying them, and interpretation of results. Findings are illustrated with a theoretic data example in which MSM are used to estimate the effect of a behavioral intervention on adherence to antiretroviral therapy.

Anti-HIV Agents↗
PubMed2006

Multistate/multifunctional switches based on photochromic Schiff base.

The salicylidene Schiff base derivative, namely, N-salicylidene-(S)-alpha-naphthylethylamine (SNEA) has been synthesized to study the characterization of multistate/multifunctional switches. Upon the stimulations of optical inputs (UV light and visible light) and chemical inputs (pH and Zn(2+)), SNEA undergoes reversible photochromism, deprotonation and complexation reactions. In this case, four chemical species are involved. These interconversions of SNEA between four states have been systematically investigated by the absorption and the emission spectra. Spectroscopic studies indicate that the photochromic switch, pH switch and fluorescent switch can be realized using the single molecular entity of SNEA.

Cations, Divalent↗
PubMed2006

Nucleotide change of codon 38 in the X gene of hepatitis B virus genotype C is associated with an increased risk of hepatocellular carcinoma.

BACKGROUND/AIMS: The hepatitis B virus (HBV) genotype C is associated with the development of hepatocellular carcinoma (HCC). In addition, the HBV X gene, which encodes the pleiotropic transactivator HBx, has also been associated with the development of HCC. In this study, we investigated whether nucleotide changes in the X gene of genotype C are associated with the development of HCC. METHODS/RESULTS: We sequenced the X gene in age- and sex-matched 39 HBV-infected patients with HCC and 36 HBV-infected patients without HCC. A novel nucleotide change that resulted in a proline to serine substitution at codon 38 in HBx (codon-38 change) was preferentially found in patients with HCC. Then, sera were collected from a new group of age- and sex-matched 52 patients with HCC and 51 patients without HCC. In this cohort also, the codon-38 change was associated with HCC. Multiple logistic regression analysis showed the prevalence of the codon-38 change was significantly associated with HCC in all patients (P=0.001, odds ratio: 4.89). CONCLUSION: The codon-38 change in genotype C is an independent risk factor for the development of HCC and may serve as a useful molecular marker for predicting the clinical outcomes in patients infected with HBV.

Biopsy↗
PubMed2006

The pi-pi stacked geometries and association thermodynamics of quinacridone derivatives studied by 1H NMR.

The pi-pi stacked associations of three N,N'-di(n-butyl) quinacridone derivatives, widely used dopants in organic light-emitting diodes, with different sizes of substituents were investigated in solution at various temperatures by (1)H NMR spectroscopy. The pi-pi stacked geometries were estimated by both the magnitudes of peak shifts with concentration and the directions of peak shifts induced by polar solvents. Two patterns of geometries with different pi-pi interaction strengths were found to coexist in solution for all the three samples. In both of the patterns, the preferential orientation of the stacking is the approach of the carbonyl groups on one molecule to the nitrogen atoms on the stacked partner, which makes the pi-deficient aromatic atoms interact with both pi-rich and pi-deficient aromatic atoms of the stacked partner to maximize the electrostatic complementarity. Differently, whereas the molecules in one pattern are face-to-face stacked in a parallel fashion and slip two rings relative to one another along with the long axis of the conjugated ring systems, the molecules in the other are either face-to-face stacked in an antiparallel fashion with slight slipping between layers or stacked in a turning fashion. Both association constants obtained by fitting the dilution curves and thermodynamic parameters obtained from van't Hoff analyses revealed unexpectedly three thermodynamic processes of aggregations for all the three samples in the temperature region of 298-213 K. The size of substituents on the outer aromatic rings significantly influences the pi-pi stacked structures and association thermodynamics.

Journal Article↗
PubMed2006

Comparative proteomics analysis to annexin B1 DNA and protein vaccination in mice.

DNA vaccines have been widely reported to elicit both effective humoral and cellular immune responses, but the mechanisms of antigen processing and presentation in DNA immunization is still ambiguous. Aiming to molecular mechanisms involved in DNA immunization, comparative serum proteomics was introduced to discover differentially expressed proteins after different immunizations. Using two-dimensional electrophoresis and matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry, 23 three-fold or greater up-regulated proteins were separated and identified, including 14 from ANXB1 DNA immunized mice and 9 from annexin B1 protein immunized mice. The histocompatibility class I molecule H2-Q10 (HA10_MOUSE) and proteasome activator PA28 alpha-subunit (PSME1_MOUSE) were found up-regulated in ANXB1 DNA immunized mice, which may contribute to the augmented activation of T lymphocytes. These proteins may serve as potential surrogate markers of successful vaccination and provide research targets for molecular mechanisms of vaccinology.

Animals↗
PubMed2006

Grazing angle mirror-backed reflection (GMBR) for infrared analysis of monolayers on silicon.

An easy handling infrared measurement, grazing angle mirror-backed reflection (GMBR), has been established to analyze the silicon-based organic monolayer. Theoretical prediction gave the optimal configuration with p-polarized irradiation near a grazing angle 78.1 degrees of incidence. Experimental measurement of hydrogen-terminated, undecylenic acid (UA) and N-hydroxysuccinimide (NHS) functionalized silicon (111) surfaces showed good signal peaks and reproducibility.

Letter↗
PubMed2006

Differential DNA methylation profiles in gynecological cancers and correlation with clinico-pathological data.

BACKGROUND: Epigenetic gene silencing is one of the major causes of carcinogenesis. Its widespread occurrence in cancer genome could inactivate many cellular pathways including DNA repair, cell cycle control, apoptosis, cell adherence, and detoxification. The abnormal promoter methylation might be a potential molecular marker for cancer management. METHODS: For rapid identification of potential targets for aberrant methylation in gynecological cancers, methylation status of the CpG islands of 34 genes was determined using pooled DNA approach and methylation-specific PCR. Pooled DNA mixture from each cancer type (50 cervical cancers, 50 endometrial cancers and 50 ovarian cancers) was made to form three test samples. The corresponding normal DNA from the patients of each cancer type was also pooled to form the other three control samples. Methylated alleles detected in tumors, but not in normal controls, were indicative of aberrant methylation in tumors. Having identified potential markers, frequencies of methylation were further analyzed in individual samples. Markers identified are used to correlate with clinico-pathological data of tumors using chi2 or Fisher's exact test. RESULTS: APC and p16 were hypermethylated across the three cancers. MINT31 and PTEN were hypermethylated in cervical and ovarian cancers. Specific methylation was found in cervical cancer (including CDH1, DAPK, MGMT and MINT2), endometrial cancer (CASP8, CDH13, hMLH1 and p73), and ovarian cancer (BRCA1, p14, p15, RIZ1 and TMS1). The frequencies of occurrence of hypermethylation in 4 candidate genes in individual samples of each cancer type (DAPK, MGMT, p16 and PTEN in 127 cervical cancers; APC, CDH13, hMLH1 and p16 in 60 endometrial cancers; and BRCA1, p14, p16 and PTEN in 49 ovarian cancers) were examined for further confirmation. Incidence varied among different genes and in different cancer types ranging from the lowest 8.2% (PTEN in ovarian cancer) to the highest 56.7% (DAPK in cervical cancer). Aberrant methylation for some genes (BRCA1, DAPK, hMLH1, MGMT, p14, p16, and PTEN) was also associated with clinico-pathological data. CONCLUSION: Thus, differential methylation profiles occur in the three types of gynecologic cancer. Detection of methylation for critical loci is potentially useful as epigenetic markers in tumor classification. More studies using a much larger sample size are needed to define the potential role of DNA methylation as marker for cancer management.

Adult↗
PubMed2006

Auditing as part of the terminology design life cycle.

OBJECTIVE: To develop and test an auditing methodology for detecting errors in medical terminologies satisfying systematic inheritance. This methodology is based on various abstraction taxonomies that provide high-level views of a terminology and highlight potentially erroneous concepts. DESIGN: Our auditing methodology is based on dividing concepts of a terminology into smaller, more manageable units. First, we divide the terminology's concepts into areas according to their relationships/roles. Then each multi-rooted area is further divided into partial-areas (p-areas) that are singly-rooted. Each p-area contains a set of structurally and semantically uniform concepts. Two kinds of abstraction networks, called the area taxonomy and p-area taxonomy, are derived. These taxonomies form the basis for the auditing approach. Taxonomies tend to highlight potentially erroneous concepts in areas and p-areas. Human reviewers can focus their auditing efforts on the limited number of problematic concepts following two hypotheses on the probable concentration of errors. RESULTS: A sample of the area taxonomy and p-area taxonomy for the Biological Process (BP) hierarchy of the National Cancer Institute Thesaurus (NCIT) was derived from the application of our methodology to its concepts. These views led to the detection of a number of different kinds of errors that are reported, and to confirmation of the hypotheses on error concentration in this hierarchy. CONCLUSION: Our auditing methodology based on area and p-area taxonomies is an efficient tool for detecting errors in terminologies satisfying systematic inheritance of roles, and thus facilitates their maintenance. This methodology concentrates a domain expert's manual review on portions of the concepts with a high likelihood of errors.

Biology↗
PubMed2006

Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus.

Two full-length genomes of recently emerged virulent isolates of porcine reproductive and respiratory syndrome virus (PRRSV) were sequenced and compared to other PRRSV strains. The results revealed that these two isolates (named MN184), of North American lineage, represented the shortest PRRSV genomes sequenced to date with a nucleotide length of 15019 bases. Genetic analysis demonstrated that the two isolates were not identical and shared approximately 87 and 59% nucleotide identity with prototype North American strain VR-2332 and European strain Lelystad, respectively. Three quite variable regions were identified, corresponding to putative nsp1beta, putative nsp2 and ORF5. Nsp2, the most variable region, shared only 66-70% amino acid similarity to other sequenced North American-like PRRSV nsp2 proteins. Further study revealed that the nsp2 protein of the MN184 isolates contained three discontinuous deletions when compared to strain VR-2332 nsp2 protein, with the sizes of 111, 1, and 19 amino acids corresponding to strain VR-2332 positions 324-434, 486 and 505-523, respectively. The results suggest that targeted manipulation of PRRSV through nsp2 modification by reverse genetics may yield promising vectors for vaccine development, as has been recently demonstrated [Han, J., Faaberg, K.S., Wang, Y., Liu, H., 2005. Non-structural protein 2 mutants of PRRSV strain VR-2332 infectious clone based on deletions seen in RFLP184 isolates are viable. In: PRRS International Symposium Proceedings, vol. 8, Saint Louis, MO].

Amino Acid Sequence↗