Biomedical subjects

Hua Tang

Publications and source records attributed to Hua Tang.

At least 19 recordsLinked to original sources

PubMed2026

Uncovering heterogeneous effects via localized feature selection.

Identifying features that interact to trigger disease, while accounting for heterogeneity across diverse populations, is essential for the development of precision and targeted medicine. Despite the availability of vast and complex health-related datasets, most existing works focus on identifying disease-associated features at the population level or within a few subpopulations, often overlooking individual-level heterogeneity within these groups. To address this limitation, we propose a framework that utilizes localized test statistics to identify disease-associated features tailored to individual profiles. Our method leverages the recently developed knockoffs methodology to control the noise level of the selection set so that the results are replicable. Moreover, it allows for the discovery of hidden heterogeneous effects within the data, as demonstrated in an application to single-cell RNA sequencing data for Alzheimer's disease. By aggregating localized feature selection results, our framework also enables powerful population-level feature selection. Our framework provides a powerful tool for exploratory studies of precision medicine, offering the potential to generate novel hypotheses for confirmatory biological experiments.

Alzheimer Disease↗

PubMed2025

Colorectal Liver Metastasis Pathomics Model: Integrating Single-Cell and Spatial Transcriptome Analysis With Pathomics for Predicting Liver Metastasis in Colorectal Cancer.

The liver is the primary target organ for hematologic metastasis of colorectal cancer (CRC), and CRC liver metastasis (CRLM) often precludes radical resection, making it the leading cause of death in patients with CRC. To improve the identification and prediction of liver metastasis risk, we identified a cell type of liver metastasis--triggering malignant cells (LMTMCs) through integrating single-cell RNA sequencing and spatial transcriptome analysis. Multiomics cell communication analysis indicated that the interaction between fibroblasts and LMTMCs through the COL1A1-CD44/SDC4 and LAMA4-CD44 signaling axes could promote CRLM. By applying the one-class logistic regression algorithm, we developed a CRLM scoring system in the bulk RNA-sequencing data according to the abundance of LMTMCs in each individual. Using the grouping labels derived from the CRLM scoring system in the bulk data and the corresponding whole-slide images without any manual annotations at the region or pixel level, processed via slide-level weakly supervised learning, a deep-learning model based on the ResNet18 architecture, called Colorectal Liver Metastasis Pathomics Model, was developed to predict the risk of liver metastasis in patients with CRC. The Colorectal Liver Metastasis Pathomics Model achieved an area under the curve of 0.84 at the internal test set of The Cancer Genome Atlas-CRC histology images. In the external independent validation sets, namely the Affiliated Hospital of Southwest Medical University and the Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University cohorts, the areas under the curve were 0.89 and 0.72, respectively, indicating effective classification performances. This study provided new insights and tools for the early identification of CRLM and demonstrated the potential of combining multiomics with deep learning-based pathomics in cancer research.

Humans↗

PubMed2024

Integrated Multi-Omics Analyses Reveal Lipid Metabolic Signature in Osteoarthritis.

Osteoarthritis (OA) is the most common degenerative joint disease and the second leading cause of disability worldwide. Single-omics analyses are far from elucidating the complex mechanisms of lipid metabolic dysfunction in OA. This study identified a shared lipid metabolic signature of OA by integrating metabolomics, single-cell and bulk RNA-seq, as well as metagenomics. Compared to the normal counterparts, cartilagesin OA patients exhibited significant depletion of homeostatic chondrocytes (HomCs) (P = 0.03) and showed lipid metabolic disorders in linoleic acid metabolism and glycerophospholipid metabolism which was consistent with our findings obtained from plasma metabolomics. Through high-dimensional weighted gene co-expression network analysis (hdWGCNA), weidentified PLA2G2A as a hub gene associated with lipid metabolic disorders in HomCs. And an OA-associated subtype of HomCs, namely HomC1 (marked by PLA2G2A, MT-CO1, MT-CO2, and MT-CO3) was identified, which also exhibited abnormal activation of lipid metabolic pathways. This suggests the involvement of HomC1 in OA progression through the shared lipid metabolism aberrancies, which were further validated via bulk RNA-Seq analysis. Metagenomic profiling identified specific gut microbial species significantly associated with the key lipid metabolism disorders, including Bacteroides uniformis (P < 0.001, R = -0.52), Klebsiella pneumonia (P = 0.003, R = 0.42), Intestinibacter_bartlettii (P = 0.009, R = 0.38), and Streptococcus anginosus (P = 0.009, R = 0.38). By integrating the multi-omics features, a random forest diagnostic model with outstanding performance was developed (AUC = 0.97). In summary, this study deciphered the crucial role of a integrated lipid metabolic signature in OA pathogenesis, and established a regulatory axis of gut microbiota-metabolites-cell-gene, providing new insights into the gut-joint axis and precision therapy for OA.

Humans↗

PubMed2006

Regulation of urokinase receptor expression by protein tyrosine phosphatases.

Urokinase-type plasminogen activator (uPA) and its receptor (uPAR) play a major role in several physiological processes such as cell migration, proliferation, morphogenesis, and regulation of gene expression. Many of the biological activities of uPA depend on its association with uPAR. uPAR expression and its induction by uPA are regulated at the posttranscriptional level. Inhibition of protein tyrosine phosphatase-mediated dephosphorylation by sodium orthovanadate induces uPAR expression and, with uPA, additively induces cell surface uPAR expression. Sodium orthovanadate induces uPAR by increasing uPAR mRNA in a time- and concentration-dependent manner. Both sodium orthovanadate and uPA induce uPAR mRNA stability, indicating that dephosphorylation could contribute to uPA-induced posttranscriptional regulation of uPAR expression. Induction of the tyrosine phosphatase SHP2 in Beas2B and H157 cells inhibits basal cell surface uPAR expression and uPA-induced uPAR expression. Sodium orthovanadate also increases uPAR expression by decreasing the interaction of a uPAR mRNA coding region sequence with phosphoglycerate kinase (PGK) as well as by enhancing the interaction between a uPAR mRNA 3' untranslated sequence with heterogeneous nuclear ribonucleoprotein C (hnRNPC). On the contrary, overexpression of SHP2 in Beas2B cells increased interaction of PGK with the uPAR mRNA coding region and inhibited hnRNPC binding to the 3' untranslated sequence. These findings confirm a novel mechanism by which uPAR expression of lung airway epithelial cells is regulated at the level of mRNA stability by inhibition of protein tyrosine phosphatase-mediated dephosphorylation of uPAR mRNA binding proteins and demonstrate that the process involves SHP2.

Cells, Cultured↗

PubMed2006

Ancestry-environment interactions and asthma risk among Puerto Ricans.

BACKGROUND: Puerto Ricans, an admixed population of African, European, and Native American ancestries, have the highest asthma prevalence, morbidity, and mortality rates of any United States' population. Although socioeconomic status (SES) is negatively correlated with asthma incidence in most populations, no such relationship has been identified among Puerto Ricans. We hypothesized that, in this admixed population, the association between SES and asthma may interact with genetic ancestry. METHODS: We analyzed 135 Puerto Rican subjects with asthma and 156 control subjects recruited from six different recruitment centers in Puerto Rico. Individual ancestry for each subject was estimated using 44 ancestry informative markers. SES was assigned using the census tracts' median family income. Analyses of SES were based on the SES of the clinic site from which the subjects were recruited and on a subset of individuals on whom home address-based SES was available. RESULTS: In the two (independent) analyses, we found a significant interaction between SES, ancestry, and asthma disease status. At lower SES, European ancestry was associated with increased risk of asthma, whereas African ancestry was associated with decreased risk. The opposite was true for their higher SES counterparts. CONCLUSIONS: The observed interaction may help to explain the unique pattern of risk for asthma in Puerto Ricans and the lack of association with SES observed in previous studies when not accounting for varying proportions of ancestry.

Adolescent↗

PubMed2006

An ultraefficient affinity-based high-throughout screening process: application to bacterial cell wall biosynthesis enzyme MurF.

The authors describe the discovery of a new class of inhibitors to an essential Streptococcus pneumoniae cell wall biosyn-thesis enzyme, MurF, by a novel affinity screening method. The strategy involved screening very large mixtures of diverse small organic molecules against the protein target on the basis of equilibrium binding, followed by iterative ultrafiltration steps and ligand identification by mass spectrometry. Hits from any affinity-based screening method often can be relatively nonselective ligands, sometimes referred to as "nuisance" or "promiscuous" compounds. Ligands selective in their binding affinity for the MurF target were readily identified through electronic subtraction of an empirically determined subset of promiscuous compounds in the library without subsequent selectivity panels. The complete strategy for discovery and identification of novel specific ligands can be applied to all soluble protein targets and a wide variety of ligand libraries.

Anti-Bacterial Agents↗

PubMed2006

Kinase drug discovery by affinity selection/mass spectrometry (ASMS): application to DNA damage checkpoint kinase Chk1.

Kinase enzymes are involved in a vast array of biological processes associated with human disease; therefore, selective kinase inhibition by small molecules and therapeutic antibodies is an area of intense study. The authors show that drug candidates with immediate value for biological preclinical evaluation can be identified directly through ultra-efficient affinity screening of kinase enzymes and random compound mixtures. The screening process comprises sampling and trapping equilibrium binding between candidate ligands and protein in solution, followed by removal of unbound ligands via 3 rounds of ultrafiltration and direct identification of bound ligands by mass spectrometry. Evaluation of significant peaks is facilitated by automated integration and collation of the mass spectral data and import into custom software for analysis. One Chk1-selective ligand found by using this process is presented in detail. The compound is potent in both enzymatic and Chk1-dependent cellular assays, and specific contacts in the Chk1 active site are shown by X-ray crystallography.

Amino Acid Sequence↗

PubMed2006

A classical likelihood based approach for admixture mapping using EM algorithm.

Several disease-mapping methods have been proposed recently, which use the information generated by recent admixture of populations from historically distinct geographic origins. These methods include both classic likelihood and Bayesian approaches. In this study we directly maximize the likelihood function from the hidden Markov Model for admixture mapping using the EM algorithm, allowing for uncertainty in model parameters, such as the allele frequencies in the parental populations. We determined the robustness of the proposed method by examining the ancestral allele frequency estimate and individual marker-location specific ancestry when the data were generated by different population admixture models and no learning sample was used. The proposed method outperforms a widely used Bayesian MCMC strategy for data generated from various population admixture models. The multipoint information content for ancestry was derived based on the map provided by Smith et al. (2004) and the associated statistical power was calculated. We examined the distribution of admixture LD across the genome for both real and simulated data and established a threshold for genome wide significance applicable to admixture mapping studies. The software ADMIXPROGRAM for performing admixture mapping is available from authors.

Algorithms↗

PubMed2006

A statistical method for chromatographic alignment of LC-MS data.

Integrated liquid-chromatography mass-spectrometry (LC-MS) is becoming a widely used approach for quantifying the protein composition of complex samples. The output of the LC-MS system measures the intensity of a peptide with a specific mass-charge ratio and retention time. In the last few years, this technology has been used to compare complex biological samples across multiple conditions. One challenge for comparative proteomic profiling with LC-MS is to match corresponding peptide features from different experiments. In this paper, we propose a new method--Peptide Element Alignment (PETAL) that uses raw spectrum data and detected peak to simultaneously align features from multiple LC-MS experiments. PETAL creates spectrum elements, each of which represents the mass spectrum of a single peptide in a single scan. Peptides detected in different LC-MS data are aligned if they can be represented by the same elements. By considering each peptide separately, PETAL enjoys greater flexibility than time warping methods. While most existing methods process multiple data sets by sequentially aligning each data set to an arbitrarily chosen template data set, PETAL treats all experiments symmetrically and can analyze all experiments simultaneously. We illustrate the performance of PETAL on example data sets.

Animals↗

PubMed2006

Genomewide evolutionary rates in laboratory and wild yeast.

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

Evolution, Molecular↗

PubMed2006

Reconstructing genetic ancestry blocks in admixed individuals.

A chromosome in an individual of recently admixed ancestry resembles a mosaic of chromosomal segments, or ancestry blocks, each derived from a particular ancestral population. We consider the problem of inferring ancestry along the chromosomes in an admixed individual and thereby delineating the ancestry blocks. Using a simple population model, we infer gene-flow history in each individual. Compared with existing methods, which are based on a hidden Markov model, the Markov-hidden Markov model (MHMM) we propose has the advantage of accounting for the background linkage disequilibrium (LD) that exists in ancestral populations. When there are more than two ancestral groups, we allow each ancestral population to admix at a different time in history. We use simulations to illustrate the accuracy of the inferred ancestry as well as the importance of modeling the background LD; not accounting for background LD between markers may mislead us to false inferences about mixed ancestry in an indigenous population. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application of our method is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Genetics, Medical↗

PubMed2006

Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans.

Admixed populations such as African Americans and Hispanic Americans present both challenges and opportunities in genetic epidemiologic research. Because of variation in admixture levels among individuals, case-control association studies may be subject to stratification bias. On the other hand, admixed populations also present special opportunities both for examining the role of genetic and environmental factors for observed racial/ethnic differences, and for possibly mapping alleles that contribute to such differences. Here we examined the distribution and relationship of individual admixture (IA) estimates with BMI and three measures of blood pressure in two admixed populations in the NHLBI Family Blood Pressure Program (FBPP): African Americans and Mexican Americans. For the African Americans, we observed modest but significant differences in average African IA among four recruitment sites. We observed a slight excess of African IA among hypertensives compared to normotensives, and a positive (non-significant) regression of African IA on blood pressure in untreated participants. Within Mexican Americans, we found no difference in average IA between hypertensives and normotensives, but a positive (marginally significant) regression of African IA on diastolic blood pressure. We also observed a significant positive regression of Caucasian IA (and negative regression of Native American IA) on BMI. Our results are suggestive of genetic differences between Africans and non-Africans that influence blood pressure, but such effects are likely to be modest compared to environmental ones. Excess obesity among Native Americans compared to whites is not consistent with a simple genetic explanation.

Adult↗

PubMed2006

Selective regulation of hydrogen peroxide signaling by receptor tyrosine phosphatase-alpha.

Reactive oxygen species (ROS) are constantly produced in the human body and are involved in the pathogenesis of aging, cardiovascular diseases, and cancer. Emerging evidence indicates that oxidation and inhibition of protein tyrosine phosphatases (PTPs) are critical for ROS signal transduction. However, the role of individual PTPs in ROS signaling remains unclear. Here, we demonstrated that the receptor-like PTP alpha (RPTP alpha) was an effector of H2O2, the most stable form of ROS. H2O2 at nontoxic concentration rapidly induced the association of RPTP alpha with Src family kinases, platelet-derived growth factor receptor-beta, and protein kinase D in various cultured cells, although it markedly suppressed RPTP alpha phosphorylation on Tyr-789. We further identified that RPTP alpha selectively regulated the signal transduction pathways induced by H2O2. Particularly, RPTP alpha was required for the activation of protein kinase D and for the modulation of p130Cas tyrosine phosphorylation in response to H2O2. In contrast, the H2O2-induced inactivation of Src family kinases and suppression of paxillin phosphorylation on Tyr-118 were both largely independent of RPTP alpha. Our findings indicate that H2O2 signaling pathways are selectively regulated by RPTP alpha in cells, which may provide new insights into the functional regulation of ROS signal transduction by PTPs.

Cells, Cultured↗

PubMed2006

Endothelial stroma programs hematopoietic stem cells to differentiate into regulatory dendritic cells through IL-10.

Regulatory dendritic cells (DCs) have been reported recently, but their origin is poorly understood. Our previous study demonstrated that splenic stroma can drive mature DCs to proliferate and differentiate into regulatory DCs, and their natural counterpart with similar regulatory function in normal spleens has been identified. Considering that the spleen microenvironment supports hematopoiesis and that hematopoietic stem cells (HSCs) are found in spleens of adult mice, we wondered whether splenic microenvironment could differentiate HSCs into regulatory DCs. In this report, we demonstrate that endothelial splenic stroma induce HSCs to differentiate into a distinct regulatory DC subset with high expression of CD11b but low expression of Ia. CD11b(hi)Ia(lo) DCs secreting high levels of TGF-beta, IL-10, and NO can suppress T-cell proliferation both in vitro and in vivo. Furthermore, CD11b(hi)Ia(lo) DCs have the ability to potently suppress allo-DTH in vivo, indicating their preventive or therapeutic perspectives for some immunologic disorders. The inhibitory function of CD11b(hi)Ia(lo) DCs is mediated through NO but not through induction of regulatory T (Treg) cells or T-cell anergy. IL-10, which is secreted by endothelial splenic stroma, plays a critical role in the differentiation of the regulatory CD11b(hi)Ia(lo) DCs from HSCs. These results suggest that splenic microenvironment may physiologically induce regulatory DC differentiation in situ.

Animals↗

PubMed2006

Real-time telomeric repeat amplification protocol using the duplex scorpion and two reverse primers system: the high sensitive and accurate method for quantification of telomerase activity.

BACKGROUND: Real-time quantitative TRAP assays for detection of telomerase activity have been recently developed to eliminate complex post-PCR procedures. However, all of them use the conventional TRAP assay that possesses an unpredictable cascade of events in PCR amplification caused by stagger annealing, which may affect the accuracy of quantitation. METHODS: A novel RTQ-TRAP method was developed by combining the duplex scorpion with modified TP-TRAP assay that has high fidelity PCR amplification of the telomerase product (DS/TP-TRAP). The synthesized oligonucleotide that represents telomerase products is used to set up a standard curve. RESULTS: The DS/TP-TRAP method gives the standard curve a dynamic range of 6 orders of magnitude (R(2)=0.9992). It optimizes PCR amplification efficiency and determines telomerase activity in a lower threshold cycle number (Ct value). The method is both accurate and reproducible to measure telomerase activity in human tumor cell lines, and linearity from 1 to 1000 cells could be obtained (R(2)=0.9926). For tumor samples, the results determined by the DS/TP-TRAP assay are comparable to the data obtained with the conventional TRAP method. CONCLUSIONS: The DS/TP-TRAP assay provides a high sensitive and accurate method for real-time quantitative detection of telomerase activity. It is thus a potential robust tool for application in cancer molecular diagnostics.

Base Sequence↗

PubMed2006

Suppression of the phosphorylation of receptor tyrosine phosphatase-alpha on the Src-independent site tyrosine 789 by reactive oxygen species.

Oxidation of receptor protein tyrosine phosphatase-alpha (RPTPalpha) is emerging as an important yet poorly characterized regulatory mechanism for RPTPalpha signaling in cells. RPTPalpha has been shown to be reversibly oxidized and inhibited by reactive oxygen species. However, it is not known whether oxidative stress could regulate the phosphorylation of Tyr789, a critical tyrosine residue for RPTPalpha signaling that modulates the function of Grb2 and the activation of Src family kinases. In the present study, we have taken advantage of a phosphospecific antibody against Tyr789-phosphorylated RPTPalpha and characterized the phosphorylation of RPTPalpha Tyr789 in various cultured cells, including SYF cells lacking all three ubiquitously expressed members (Src, Yes, and Fyn) of Src family kinases. We have obtained substantial evidence indicating that the phosphorylation of RPTPalpha Tyr789 is regulated predominantly by an Src kinase inhibitor, protein phosphatase 1 (PP1)-sensitive but Src/Yes/Fyn-independent tyrosine kinase, in cells. We further reported a novel finding that, besides the inhibition of RPTPalpha's activity, H(2)O(2) at low to moderate concentrations (50-250 microM) markedly suppressed the phosphorylation of RPTPalpha Tyr789 and the association of RPTPalpha with Grb2 in cultured cells, which may result from inhibition of such a PP1-sensitive but Src/Yes/Fyn-independent tyrosine kinase. Because Tyr789 plays an important role in RPTPalpha signaling, our findings may provide new insights into the functional regulation of RPTPalpha by oxidative stress in cells.

Cells, Cultured↗

PubMed2006

An oligonucleotide decoy for Stat3 activates the immune response of macrophages to breast cancer.

Tumor-associated macrophages (TAMs) have the potential to induce both immune activation and immune tolerance. Recent studies have indicated that in breast cancers the pro-tumor role of TAMs is dominant. We induced rat peritoneal macrophages with rat breast cancer cell-conditioned medium and analyzed signal transducer and activators of transcription 3 (Stat3) activities of the cells. Then these cells were transfected with Stat3 decoy oligonucleotides (ODNs) and were stimulated by lipopolysaccharide (LPS). The results demonstrate that induced macrophages displayed a reduction of cytotoxicity and antigen-presenting function in comparison with control but transfection with Stat3 decoy ODNs enhanced cytotoxicity and antigen-presenting function of the macrophages. Furthermore, injection of induced macrophages promoted tumor growth accompanied by immunosuppression in the rat tumor models, but injection of induced macrophages transfected with Stat3 decoy ODNs led to retarded tumor growth accompanied by immune activation. The data suggest that immunosuppressive activities of TAMs correlate with over-activated Stat3 signaling of the cells and disruption of Stat3 activity of TAMs can enhance rat immune response to breast cancer.

Animals↗

PubMed2006

The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication.

The extent of molecular differentiation between domesticated animals or plants and their wild relatives is postulated to be small. The availability of the complete genome sequences of two subspecies of the Asian rice, Oryza sativa (indica and japonica) and their wild relatives have provided an unprecedented opportunity to study divergence following domestication. We observed significantly more amino acid substitutions during rice domestication than can be expected from a comparison among wild species. This excess is disproportionately larger for the more radical kinds of amino acid changes (e.g. Cys<-->Tyr). We estimate that approximately a quarter of the amino acid differences between rice cultivars are deleterious, not accountable by the relaxation of selective constraints. This excess is negatively correlated with the rate of recombination, suggesting that 'hitchhiking' has occurred. We hypothesize that during domestication artificial selection increased the frequency of many deleterious mutations.

Crops, Agricultural↗