Biomedical subjects

Xiaoyan Zhu

Publications and source records attributed to Xiaoyan Zhu.

At least 19 recordsLinked to original sources

PubMed2026

PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.

MOTIVATION: Accurate detection of copy number variations (CNVs) from targeted panel sequencing remains challenging due to limited genomic coverage and pronounced sample-specific biases. Existing normalization strategies, including baseline-cohort, matched-control, and single-sample approaches, often struggle to balance noise suppression with adaptability, leading to inconsistent performance across heterogeneous samples. RESULTS: We present PScnv, a personalized self-normalizing framework for robust CNV detection from panel sequencing data. PScnv integrates a pre-built panel-of-normals (PoN) with sample-intrinsic stable chromosomes through ridge-regression normalization to generate individualized log2 ratio profiles with reduced systematic variation. CNVs are then identified using a hierarchical multi-phase segmentation pipeline incorporating z-score pre-partitioning, kernel-based correction, and circular binary segmentation. In 139 clinical tumor samples with orthogonal FISH validation at MET, ERBB2, and MTAP, PScnv showed improved accuracy and robustness over existing methods that do not require patient-matched normal samples, provided that a pre-built PoN cohort is available. AVAILABILITY: Source code is available for academic use at https://github.com/lvws/PScnv.

DNA Copy Number Variations↗

PubMed2025

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection.

Molecular residual disease (MRD) detection, initially developed for hematologic malignancies, has become a critical biomarker for monitoring solid tumors. MRD detection primarily relies on circulating tumor DNA (ctDNA) analysis using next-generation sequencing, offering high sensitivity and broad genomic coverage. However, challenges remain in designing cost-effective panels that maximize mutation detection while maintaining biological relevance. Fixed panels often lack sufficient patient-specific mutation coverage, while WES-based personalized MRD assays, despite their high sensitivity, are costly and less accessible. We developed a tumor comprehensive genomic profiling (CGP)-informed personalized MRD assay to detect tumor-derived mutations, which allowed us to design patient-specific personalized panels and meanwhile, provide a cost-effective alternative to whole exome sequencing (WES). To address these limitations, we developed MRDtarget, a heuristic multivariate Gaussian model-based targeted capture region selection method. By expanding beyond traditional hotspot regions, MRDtarget optimizes variant tracking for MRD detection, significantly improving sensitivity. Using a Bayesian inference-based heuristic approach, MRDtarget integrates multi-feature informativeness rates to identify optimal genomic regions for capture. Experimental results demonstrate that MRDtarget enables the detection of more variants per patient. This study underscores the importance of rational panel design to improve MRD sensitivity and provides a novel approach to enhance precision diagnostics and treatment for solid tumor patients.

Humans↗

PubMed2025

MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples.

MOTIVATION: Minimal residual disease (MRD) as critical biomarker for cancer prognosis and management plays a crucial role in improving patient outcomes. However, detecting MRD via next-generation sequencing-based circulating tumor DNA variant calling remains unstable due to the extremely low variant allele frequency and significant inter- and intra-sample heterogeneity. Although parameter optimization can theoretically enhance the detection performance of variants, achieving stable MRD detection remains challenging due to three key factors: (i) the necessity for individualized parameter tuning across numerous heterogeneous genomic intervals within each sample, (ii) the tightly interdependent parameter requirements across different stages of variant detection workflows, and (iii) the limitations of current automated parameter optimization methods. RESULTS: In this study, we propose MRDagent, a novel variant detection tool designed specifically for MRD detection. MRDagent incorporates an iterative and self-adaptive optimization framework capable of handling unknown objectives, varying constraints, and highly coupled parameters across stages. A key innovation of MRDagent is the integration of a convolutional neural network-based meta-model, trained on historical data to enable rapid parameter prediction. This significantly enhances computational efficiency and generalization performance. Extensive evaluations on simulated and real-world datasets demonstrate MRDagent's superior and stable performance, providing an efficient, reliable solution for MRD detection in clinical and high-throughput research applications. AVAILABILITY AND IMPLEMENTATION: MRDagent is freely available at https://github.com/aAT0047/MRDagent.git. The corresponding dataset and software archive are available at Zenodo: https://doi.org/10.5281/zenodo.15458496.

Circulating Tumor DNA↗

PubMed2025

THE CAUSAL ASSOCIATION OF CARDIOMETABOLIC DISEASES AND SEPSIS-RELATED OUTCOMES: A MENDELIAN RANDOMIZATION AND POPULATION STUDY.

Objective: The causality between cardiometabolic disease (CMD) and sepsis has remained largely unknown. To elucidate this, we conducted a Mendelian randomization (MR) and population study. Methods: First, we used univariable and multivariable MR analyses to investigate causal associations between CMD and sepsis-related outcomes. We obtained genome-wide association study summary from both the MRC Integrative Epidemiology Unit and the FinnGen consortium. Subsequently, a two-step mediation MR analysis was performed to explore mediators. Afterward, we conducted an observational study using the Medical Information Mart for Intensive Care IV database, in which multivariable logistic regression models were utilized to examine the relationship between CMD and sepsis-related outcomes. Results: In the MR study, type 2 diabetes mellitus (OR = 1.058, 95% CI = 1.017-1.100, P = 0.005), obesity (OR = 1.113, 95% CI = 1.057-1.172, P < 0.001), and heart failure (HF) (OR = 1.178, 95% CI = 1.063-1.305, P = 0.002) were independently causally related to sepsis. Obesity (OR = 1.215, 95% CI = 1.027-1.437, P = 0.023) and HF (OR = 1.494, 95% CI = 1.080-2.065, P = 0.015) also showed independent causal associations with sepsis critical care admission. Mediation MR analysis identified 23 blood metabolites potentially causally linked to sepsis ( P < 0.05), yet none mediated the relationship between CMD and sepsis. In the observational study, we found associations between sepsis and several conditions including type 2 diabetes mellitus, obesity, hypertension, stroke, HF, and hyperlipidemia after adjusting for confounding factors. Moreover, hypertension, stroke, HF, coronary artery disease, and hyperlipidemia were linked to sepsis critical care admission. Conclusion: This study has, for the first time, revealed indicative evidence of a causal relationship between CMD and sepsis through observational and genetic evidence. Taken together, clinical attention to sepsis may be warranted among patients with CMD.

Humans↗

PubMed2006

Sustained Notch signaling in progenitors is required for sequential emergence of distinct cell lineages during organogenesis.

Mammalian organogenesis results from the concerted actions of signaling pathways in progenitor cells that induce a hierarchy of regulated transcription factors critical for organ and cell type determination. Here we demonstrate that sustained Notch activity is required for the temporal maintenance of specific cohorts of proliferating progenitors, which underlies the ability to specify late-arising cell lineages during pituitary organogenesis. Conditional deletion of Rbp-J, which encodes the major mediator of the Notch pathway, leads to premature differentiation of progenitor cells, a phenotype recapitulated by loss of the basic helix-loop-helix (bHLH) factor Hes1, as well as a conversion of the late (Pit1) lineage into the early (corticotrope) lineage. Notch signaling is required for maintaining expression of the tissue-specific paired-like homeodomain transcription factor, Prop1, which is required for generation of the Pit1 lineage. Attenuation of Notch signaling is necessary for terminal differentiation in post-mitotic Pit1+ cells, and the Notch-repressed Pit1 target gene, Math3, is specifically required for maturation and proliferation of the GH-producing somatotrope. Thus, sustained Notch signaling in progenitor cells is required to prevent conversion of the late-arising cell lineages to early-born cell lineages, permitting specification of diverse cell types, a strategy likely to be widely used in mammalian organogenesis.

Animals↗

PubMed2006

Liquid chromatographic/mass spectrometry assay of triptolide in dog plasma and its application to pharmacokinetic study.

A rapid and sensitive method for the determination of triptolide in dog plasma was developed and validated, using high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (LC/APCI/MS). Sample preparation consisted of liquid-liquid extraction with ethyl acetate from dog plasma. The analytes and internal standard prednisolone were well separated on a Zorbax Extend-C18 analytical column. Detection was performed on a triple quadrupole mass spectrometer using selected-ion monitoring (SIM) mode on the deprotonated ions [M-H]- at m/z 359. Calibration curves were linear over the concentration range of 0.5-200 ng/mL of triptolide with the intra- and inter-day precision (the relative standard deviation values) were being less than 7%. Triptolide was stable under different conditions. The intra-day and inter-day accuracy were 99.3-105.2% and 101.3-107.0%, respectively. The lower limit of quantification was 0.5 ng/mL. The method was successfully applied to a pharmacokinetic study after an intragastric administration (i.g.) of triptolide to dogs with a dose of 0.05 mg/kg. The results confirm that the assay is suitable for the pharmacokinetic study of triptolide.

Animals↗

PubMed2006

Critical roles of the p160 transcriptional coactivators p/CIP and SRC-1 in energy balance.

Several transcriptional coactivators have been implicated in modulating the transcriptional activities of nuclear hormone receptors in vitro. Potential roles of these cofactors in important physiological processes such as energy homeostasis remain unknown. We report here that a developmental arrest in interscapular brown fat and defective adaptive thermogenesis occur in mice lacking both the p160 family transcriptional coactivators SRC-1 and p/CIP due to a failure in induction of selective PPARgamma target genes involved in adipogenesis and mitochondrial uncoupling. In the absence of p/CIP and SRC-1, mice eat more food on both regular chow and a high-fat diet because of decreased blood leptin levels. However, the p/CIP(-/-)/SRC-1(-/-) mice are lean and resistant to high-fat-diet-induced obesity. They exhibit increased basal metabolic rates and heightened levels of physical activity. Therefore, p/CIP and SRC-1 play critical roles in energy balance by controlling both energy intake and energy expenditure.

Adipogenesis↗

PubMed2006

Surgical excision combined with autologous whole tumor cell vaccination is an effective therapy for murine neuroblastoma.

BACKGROUND: Although a whole tumor cell vaccine strategy based on the synergistic action of granulocyte macrophage-colony-stimulating factor (GM-CSF) transduced tumor cells and CpG oligodeoxynucleotides induces potent tumor-specific immunity, such therapy is not curative in the face of large established tumors. PURPOSE: The primary goal of this study was to determine if combining surgical resection of the tumor with whole tumor cell vaccination is an effective therapeutic strategy for established neuroblastoma. We also wished to determine if the phenotype of the immune response generated by this vaccine strategy was altered by the presence of bulky established tumor. METHODS: The murine neuroblastoma model was used in which syngeneic Neuro-2a was grown subcutaneously in A/J mouse. The whole tumor cell vaccine consisted of irradiated Neuro-2a as the vehicle for tumor antigens admixed with GM-CSF and CpG oligonucleotides (100 microg). RESULTS: In the presence of large tumors, dendritic cells were effectively activated by the vaccine, but secretion of intereferon-gamma from vaccinated splenocytes in response to antigen stimulation was suppressed. The tumor's inhibitory effect on interferon-gamma production from vaccinated splenocytes was reversed after resection of the primary tumor. The use of prepared GM-CSF-secreting bystander cells simplified production of an autologous whole tumor cell vaccine that was remarkably effective in curing large tumors when combined with tumor excision. CONCLUSIONS: These findings suggest that at least part of the immunosuppressive effects of the cancer can be reversed after surgical excision of the primary tumor. Thus, in the context of minimal residual disease, this dendritic cell-targeted immunotherapeutic approach may prove effective for the treatment of neuroblastoma.

Animals↗

PubMed2006

Survivin mRNA levels are associated with biology of disease and patient survival in neuroblastoma: a report from the children's oncology group.

Alterations in apoptotic mechanisms favoring cell survival may be vital for modifying tumor behavior. Survivin, an inhibitor of apoptosis, and caspase 8, a proapoptotic enzyme, are key players in cellular apoptotic mechanisms. We investigated whether the levels of survivin and caspase 8 and the ratio between these 2 apoptotic factors correlate with tumor biology and predicts outcome in patients with neuroblastoma. Survivin and caspase 8 levels were quantified in 38 primary tumor specimens and analyzed individually and in relation to each other. High survivin expression and high survivin:caspase 8 ratios were associated with MYCN amplification, unfavorable histology, and high-risk group of disease (P<0.0008). High survivin mRNA levels were associated with worse overall survival (P=0.02) although the median follow up was only 22.6 months with a range of 1 day to 3.3 years. Low caspase 8 expression was associated with stage 4 disease, high-risk group, MYCN amplification, and unfavorable histology. Although the survivin:caspase 8 ratio was associated with these risk factors, the ratio did not improve the predictive value of survivin alone in this small series. Quantifying multiple apoptotic genes in neuroblastoma may supplement current risk stratification. Moreover, categorizing aberrant apoptotic gene expression in neuroblastoma may translate into novel therapeutic targets.

Caspase 8↗

PubMed2005

A hybrid method for relation extraction from biomedical literature.

PURPOSE: Over recent years, there has been a growing interest in extracting entities and relations from biomedical literature. There are a vast number of systems and approaches being proposed to extract biological relations, but none of them achieves satisfactory results. These methodologies are either parsing-based or pattern-based, which are not competent to handle the grammatical complexities of biomedical texts, or too complicated to be adapted. It is well known that appositive, coordinative propositions and such grammatical structures are extremely common in biomedical texts, particularly in full texts. However, these problems are still untouched for most of researchers. METHODS: In this paper, we have proposed a new approach, which is hybrid with both shallow parsing and pattern matching, to extract relations between proteins from scientific papers of biomedical themes. In the method, appositive and coordinative structures are interpreted based on the shallow parsing analysis, with both syntactic and semantic constraints. Then long sentences are splitted into sub-ones, from which relations are extracted by a greedy pattern matching algorithm, along with automatically generated patterns. RESULTS: Our approach is experimented to extract protein-protein interactions from full biomedical texts, and has achieved an average F-score of 80% on individual verbs, and 66% on all verbs. With the help of shallow parsing analysis, pattern matching is improved remarkably. Compared with the traditional pattern matching algorithm, our approach achieves about 7% improvement of both precision and F-score. In contrast to other systems, our approach achieves performance comparable to the best. A demo system has been available at http://spies.cs.tsinghua.edu.cn.

Abstracting and Indexing↗

PubMed2005

Discovering patterns to extract protein-protein interactions from the literature: Part II.

MOTIVATION: An enormous number of protein-protein interaction relationships are buried in millions of research articles published over the years, and the number is growing. Rediscovering them automatically is a challenging bioinformatics task. Solutions to this problem also reach far beyond bioinformatics. RESULTS: We study a new approach that involves automatically discovering English expression patterns, optimizing them and using them to extract protein-protein interactions. In a sister paper, we described how to generate English expression patterns related to protein-protein interactions, and this approach alone has already achieved precision and recall rates significantly higher than those of other automatic systems. This paper continues to present our theory, focusing on how to improve the patterns. A minimum description length (MDL)-based pattern-optimization algorithm is designed to reduce and merge patterns. This has significantly increased generalization power, and hence the recall and precision rates, as confirmed by our experiments. AVAILABILITY: http://spies.cs.tsinghua.edu.cn.

Abstracting and Indexing↗

PubMed2005

Genetic control of pituitary development and hypopituitarism.

The pituitary gland functions as a relay between the hypothalamus and peripheral target organs that regulate basic physiological functions, including growth, the stress response, reproduction, metabolism and lactation. The development of the pituitary gland has been studied extensively in mice, and has begun to be explored in zebrafish, an animal model system amenable to forward genetics. Multiple signaling molecules and transcription factors, expressed in overlapping but distinct spatial and temporal patterns, are required at various stages of pituitary development. Defects in this precisely regulated genetic program lead to diverse pituitary dysfunction. The animal models have greatly enhanced our understanding of molecular mechanisms underlying pituitary development in addition to congenital pituitary disorders in humans.

Animals↗

PubMed2004

Ginsenosides may reverse the dexamethasone-induced down-regulation of glucocorticoid receptor.

The effects of glucocorticoid (GC) hormones are mediated via an intracellular receptor, the glucocorticoid receptor (GR). It has been established that glucocorticoid down-regulate GR. Ginsenosides (GSS) from extract of Panax ginseng have demonstrated glucocorticoid-like activities in homeostasis and regulation of immunity, etc. We hypothesize that ginsenosides might mediate some of their actions by binding to the GR. The present study is aimed to determine whether GSS can act like a GC analog in the activation of glucocorticoid response element-luciferase activity in HL7702 cells. We found that GSS alone had no effect on the expression of reporter gene, but it enhanced dexamethasone (Dex)-induced transcription of reporter gene. To further explore the effects of GSS, we examined the influence of GSS on the gene and protein expression as well as hormone binding activity of GR by semi-quantitative RT-PCR, Western blot, and radioligand-binding assay, respectively. GSS partially reversed the Dex-induced decrease in GR expression and hormone binding activity with an optimal dose of 25 microg/ml, implicating a positive regulatory effect of GSS on GR expression and binding activity. Therefore, our result suggests that GSS may reverse partially the dexamethasone-induced down-regulation of glucocorticoid receptor.

Blotting, Western↗

PubMed2004

Pten loss causes hypertrophy and increased proliferation of astrocytes in vivo.

Somatic mutations of PTEN are found in many types of cancers including glioblastoma, the most malignant astrocytic tumor. PTEN mutation occurs in 25 to 40% of glioblastomas but is rarely observed in low-grade glial neoplasms. To determine the role of Pten in astrocytes and glial tumor formation, we inactivated Pten by a Cre-loxP approach with a GFAP-cre transgenic mouse that induced Cre-mediated recombination in astrocytes. Pten conditional knockout mice showed a striking progressive enlargement of the entire brain. Increased nuclear and soma size was observed in both astrocytes and neurons, which contributed in part to the increase in brain size. Pten-deficient astrocytes showed accelerated proliferation in vitro and aberrant ongoing proliferation in adult brains in vivo. In contrast, neurons lacking Pten did not show alterations in proliferation. This study shows cell-type dependent effects of Pten loss in the adult brain, including increased astrocyte proliferation that may render astroglial cells susceptible to neoplastic transformation or malignant progression.

Animals↗

PubMed2004

Discovering patterns to extract protein-protein interactions from full texts.

MOTIVATION: Although there are several databases storing protein-protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein-protein interactions from biomedical texts. RESULTS: We present a novel and robust approach for extracting protein-protein interactions from literature. Our method uses a dynamic programming algorithm to compute distinguishing patterns by aligning relevant sentences and key verbs that describe protein interactions. A matching algorithm is designed to extract the interactions between proteins. Equipped only with a dictionary of protein names, our system achieves a recall rate of 80.0% and precision rate of 80.5%. AVAILABILITY: The program is available on request from the authors.

Algorithms↗

PubMed2004

Chronic ethanol ingestion by mice increases expression of CD80 and CD86 by activated macrophages.

Results from previous studies from our laboratory have shown that T cells obtained from the spleens of C57BL/6 mice that consumed ethanol chronically have increased expression of activation markers and increased second signal-independent production of interferon-gamma (IFN-gamma). We now report that in vitro-activated CD11b(+) splenocytes obtained from C57BL/6 and BALB/c mice that consumed ethanol chronically express increased levels of the T cell co-stimulatory molecules CD80 and CD86. CD11b(+) splenocytes encompass at least two populations: the CD11b(+)Gr.1(-) population, which is primarily monocytes-macrophages, and a smaller CD11b(+)Gr.1(+) population, which is in the myelocytic-monocytic cell series and contains precursors of both macrophages and neutrophils. Evaluation of cultures of purified CD11b(+) cells, obtained from mice that consumed ethanol chronically, incubated overnight, showed increased up-regulation of CD80 and CD86 expression on Gr.1(-) mouse splenic macrophages. Results of functional studies of purified CD11b(+) cells have demonstrated that CD11b(+) cells obtained from C57BL/6 mice that were exposed to ethanol chronically secrete higher levels, in comparison with the levels secreted by CD11b(+) cells obtained from control animals, of nitric oxide and several proinflammatory cytokines after stimulation by the oligodeoxynucleotide (ODN) CpG 1826. These findings indicate that CD11b(+) splenocytes are in some way sensitized to activating stimuli by chronic ethanol exposure in vivo. Such cells may contribute to systemic immunodysregulation, including T-cell activation, by providing abnormal second signals to T cells, or through excessive release of cytokines, such as interleukin (IL)-6 or IL-12.

Alcohol Drinking↗

PubMed2004

T-cell activation after chronic ethanol ingestion in mice.

Chronic excessive consumption of ethanol causes immunodeficiency in human beings and in mice. Immunologic changes have been described in both species, including T-cell and innate immune system cell activation, among others. The features of chronic ethanol-induced activation have similarities in the two species, including an increased effector subset in both CD4+ and CD8+ T cells. There are also features of activation observed in the splenic macrophages of mice consuming ethanol chronically, including increased up-regulation of CD80 and CD86. Because these molecules are involved in T-cell-antigen-presenting cell interactions in vivo, it is of interest to ask whether these and other pathways of interaction are important in the T-cell activation and cytokine skewing described in chronic ethanol abuse. Preliminary findings from comparisons of wild-type, CD40 ligand knock-out, and CD28 knock-out C57BL/6 mice strongly support the suggestion of a critical role for T-cell-antigen-presenting cell interactions in the immune alterations observed in chronic ethanol abuse.

Alcoholism↗

PubMed2004

Transcriptional control of precursor proliferation in the early phases of pituitary development.

The anterior pituitary is derived from Rathke's pouch arising from the oral ectoderm. The initial apparently uniform precursor cells proliferate and differentiate into six different cell types that are present in mature gland by integrative interactions between different signaling molecules and transcription factors. This system provides an opportunity to understand gene regulation in the cellular processes of precursor cell proliferation, determination, and differentiation events during organogenesis. Recent studies have made significant advances in our appreciation of the molecular mechanisms by which transcription factors regulate these cellular processes.

Animals↗