Biomedical subjects

Hongyu Zhao

Publications and source records attributed to Hongyu Zhao.

At least 109 records · Page 6Linked to original sources

PubMed2003

Urea signalling to immediate-early gene transcription in renal medullary cells requires transactivation of the epidermal growth factor receptor.

Signalling by physiological levels of urea (e.g. 200 mM) in cells of the mammalian renal medulla is reminiscent of activation of a receptor tyrosine kinase. The epidermal growth factor (EGF) receptor may be transactivated by a variety of G-protein-coupled receptors, primarily through metalloproteinase-dependent cleavage of a membrane-anchored EGF precursor. In the murine inner medullary collecting duct (mIMCD3) cell line, urea (200 mM) induced prompt (1-5 min) tyrosine phosphorylation of the EGF receptor. Pharmacological inhibition of EGF receptor kinase activity with AG1478 or PD153035 blocked urea-inducible transcription and expression of the immediate-early gene, Egr-1. AG1478 blocked, either fully or partially, other hallmarks of urea signalling including Elk-1 activation and extracellular signal-regulated kinase phosphorylation. EGF receptor kinase inhibition also blocked the cytoprotective effect of urea observed in the context of hypertonicity-inducible apoptosis. EGF receptor transactivation was likely to be attributable to metalloproteinase-dependent ectodomain shedding of an EGF receptor agonist because both specific and non-specific inhibitors of metalloproteinases blocked the urea effect. Heparin-binding EGF (HB-EGF), in particular, was implicated because the diphtheria toxin analogue and highly specific antagonist of HB-EGF, CRM197, also blocked urea-inducible transcription. In aggregate, these data indicate that signalling in response to urea in renal medullary cells requires EGF receptor transactivation, probably through autocrine action of HB-EGF.

Animals↗

PubMed2003

Regulation of a transient receptor potential (TRP) channel by tyrosine phosphorylation. SRC family kinase-dependent tyrosine phosphorylation of TRPV4 on TYR-253 mediates its response to hypotonic stress.

The recently identified transient receptor potential (TRP) channel family member, TRPV4 (formerly known as OTRPC4, VR-OAC, TRP12, and VRL-2) is activated by hypotonicity. It is highly expressed in the kidney as well as blood-brain barrier-deficient hypothalamic nuclei responsible for systemic osmosensing. Apart from its gating by hypotonicity, little is known about TRPV4 regulation. We observed that hypotonic stress resulted in rapid tyrosine phosphorylation of TRPV4 in a heterologous expression model and in native murine distal convoluted tubule cells in culture. This tyrosine phosphorylation was sensitive to the inhibitor of Src family tyrosine kinases, PP1, in a dose-dependent fashion. TRPV4 associated with Src family kinases by co-immunoprecipitation studies and confocal immunofluorescence microscopy, and this interaction required an intact Src family kinase SH2 domain. One of these kinases, Lyn, was activated by hypotonic stress and phosphorylated TRPV4 in an immune complex kinase assay and an in vitro kinase assay using recombinant Lyn and TRPV4. Transfection of wild-type Lyn dramatically potentiated hypotonicity-dependent TRPV4 tyrosine phosphorylation whereas dominant negative-acting Lyn modestly inhibited it. Through mutagenesis studies, the site of tonicity-dependent tyrosine phosphorylation was mapped to Tyr-253, which is conserved across all species from which TRPV4 has been cloned. Importantly, point mutation of Tyr-253 abolished hypotonicity-dependent channel activity. In aggregate, these data indicate that hypotonic stress results in Src family tyrosine kinase-dependent tyrosine phosphorylation of the tonicity sensor TRPV4 at residue Tyr-253 and that this residue is essential for channel function in this context. This is the first example of direct regulation of TRP channel function through tyrosine phosphorylation.

Amino Acid Sequence↗

PubMed2003

On the use of DNA pooling to estimate haplotype frequencies.

Genome-wide association studies may be necessary to identify genes underlying certain complex diseases. Because such studies can be extremely expensive, DNA pooling has been introduced, as it may greatly reduce the genotyping burden. Parallel to DNA pooling developments, the importance of haplotypes in genetic studies has been amply demonstrated in the literature. However, DNA pooling of a large number of samples may lose haplotype information among tightly linked genetic markers. Here, we examine the cost-effectiveness of DNA pooling in the estimation of haplotype frequencies from population data. When the maximum likelihood estimates of haplotype frequencies are obtained from pooled samples, we compare the overall cost of the study, including both DNA collection and marker genotyping, between the individual genotyping strategy and the DNA pooling strategy. We find that the DNA pooling of two individuals can be more cost-effective than individual genotypings, especially when a large number of haplotype systems are studied.

Algorithms↗

PubMed2003

On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals.

Although genetic association studies using unrelated individuals may be subject to bias caused by population stratification, alternative methods that are robust to population stratification such as family-based association designs may be less powerful. Recently, various statistical methods robust to population stratification were proposed for association studies, using unrelated individuals to identify associations between candidate markers and traits of interest (both qualitative and quantitative). Here, we propose a semiparametric test for association (SPTA). SPTA controls for population stratification through a set of genomic markers by first deriving a genetic background variable for each sampled individual through his/her genotypes at a series of independent markers, and then modeling the relationship between trait values, genotypic scores at the candidate marker, and genetic background variables through a semiparametric model. We assume that the exact form of relationship between the trait value and the genetic background variable is unknown and estimated through smoothing techniques. We evaluate the performance of SPTA through simulations both with discrete subpopulation models and with continuous admixture population models. The simulation results suggest that our procedure has a correct type I error rate in the presence of population stratification and is more powerful than statistical association tests for family-based association designs in all the cases considered. Moreover, SPTA is more powerful than the Quantitative Similarity-Based Association Test (QSAT) developed by us under continuous admixture populations, and the number of independent markers needed by SPTA to control for population stratification is substantially fewer than that required by QSAT.

Analysis of Variance↗

PubMed2003

Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data.

Although large-scale gene expression data have been studied from many perspectives, they have not been systematically integrated to infer the regulatory potentials of individual genes in specific pathways. Here we report the analysis of expression patterns of genes in the Calvin cycle from 95 Arabidopsis microarray experiments, which revealed a consistent gene regulation pattern in most experiments. This identified pattern, likely due to gene regulation by light rather than feedback regulations of the metabolite fluxes in the Calvin cycle, is remarkably consistent with the rate-limiting roles of the enzymes encoded by these genes reported from both experimental and modeling approaches. Therefore, the regulatory potential of the genes in a pathway may be inferred from their expression patterns. Furthermore, gene expression analysis in the context of a known pathway helps to categorize various biological perturbations that would not be recognized with the prevailing methods.

Arabidopsis↗

PubMed2003

Inactivating E2f1 reverts apoptosis resistance and cancer sensitivity in Trp53-deficient mice.

The E2f1 transcription factor, which regulates genes required for S-phase entry, also induces apoptosis by transcriptional and post-translational mechanisms. As E2f1 is inducible by DNA damage we investigated its importance in vivo in ultraviolet (UV)-induced apoptosis, a protective mechanism that prevents the epidermis from accumulating UV-induced mutations. Contrary to expectation, E2f1-/- mice demonstrated enhanced keratinocyte apoptosis after UVB exposure, whereas apoptosis was suppressed by epidermis-specific overexpression of human E2F1. Apoptosis induced by -radiation was also repressed by E2f1. E2f1-/-;Trp53-/- double knockout mice exhibited the elevated UVB-induced apoptosis of E2f1-/- alone, rather than the profound apoptosis defect seen in Trp53-/- mice, indicating that Trp53 (p53) lies functionally upstream of E2f1. Transfecting E2F1 into E2f1-/-;Trp53-/- primary fibroblasts suppressed UVB-induced apoptosis and this suppression was relieved by Trp53. The double knockout also reverted the abnormal sex ratio and early-onset tumours of Trp53-/- mice. These results imply that E2f1 functions as a suppressor of an apoptosis pathway that is initiated by DNA photoproducts and perhaps genetic abnormalities; p53 relieves this suppression.

Animals↗

PubMed2003

Genotyping error detection through tightly linked markers.

The identification of genotyping errors is an important issue in mapping complex disease genes. Although it is common practice to genotype multiple markers in a candidate region in genetic studies, the potential benefit of jointly analyzing multiple markers to detect genotyping errors has not been investigated. In this article, we discuss genotyping error detections for a set of tightly linked markers in nuclear families, and the objective is to identify families likely to have genotyping errors at one or more markers. We make use of the fact that recombination is a very unlikely event among these markers. We first show that, with family trios, no extra information can be gained by jointly analyzing markers if no phase information is available, and error detection rates are usually low if Mendelian consistency is used as the only standard for checking errors. However, for nuclear families with more than one child, error detection rates can be greatly increased with the consideration of more markers. Error detection rates also increase with the number of children in each family. Because families displaying Mendelian consistency may still have genotyping errors, we calculate the probability that a family displaying Mendelian consistency has correct genotypes. These probabilities can help identify families that, although showing Mendelian consistency, may have genotyping errors. In addition, we examine the benefit of available haplotype frequencies in the general population on genotyping error detections. We show that both error detection rates and the probability that an observed family displaying Mendelian consistency has correct genotypes can be greatly increased when such additional information is available.

Family↗

PubMed2003

Haplotype frequency estimation in the presence of genotyping errors.

Several statistical methods have been proposed to estimate haplotype frequencies, either based on unrelated individuals or based on families. These estimates may yield insights on population genetics as well as associations between candidate regions and disease of interest. One limitation of the existing methods is that all these methods make the implicit assumption that there are no genotyping errors. However, genotyping errors are unavoidable in practice. Numerous methods have been developed to incorporate genotyping errors in genetic studies, but none to date have addressed the issues of haplotype inference in the presence of genotyping errors. In this article, we develop statistical methods for haplotype inference incorporating genotyping errors. We describe how our methods can be applied to analyze unrelated individuals as well as nuclear families. Our simulation results show that the proposed methods perform well in the presence of genotyping errors.

Computer Simulation↗

PubMed2003

Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development.

Microarray gene expression profiling was used to examine the role of pleiotropic COP/DET/FUS loci as well as other partially photomorphogenic loci during Arabidopsis seedling development and genome expression regulation. Four types of lethal, pleiotropic cop/det/fus mutants exhibit qualitatively similar gene expression profiles, yet each has specific differences. Mutations in COP1 and DET1 show the most similar genome expression profiles, while the mutations in the COP9 signalosome (CSN) and COP10 exhibit increasingly diverged genome expression profiles in both darkness and light. The genome expression profiles of the viable mutants of COP1 and DET1 in darkness mimic those of the physiological light-regulated genome expression profiles, whereas the genome expression profiles of representative lethal mutants belong to another clade and significantly diverge from the normal light control of genome expression. Instead, these lethal pleiotropic mutants show genome expression profiles similar to those from seedlings growth under high light intensity stress. Distinct lethal pleiotropic cop/det/fus mutants also result in distinct expression profiles in the small portion of genes examined and exhibit similar relatedness in both light and darkness. The partial cop/det/fus mutants affected expression of both light regulated and non-light regulated genes. Our results suggest that pleiotropic COP/DET/FUS loci control is largely overlapping but also has separable roles in plant development. The partially photomorphogenic loci regulate a subset of photomorphogenic responses as well as other non-light regulated processes.

Arabidopsis↗

PubMed2003

Haplotype analysis in population genetics and association studies.

Several studies of haplotype structures in the human genome in various populations have been published recently. Such knowledge may provide valuable information on human evolutionary history and lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. In this review, we summarize the current understanding of haplotype structure, diversity, and distribution in the human genome, with a focus on statistical issues in using haplotypes for studies of population genetics and evolutionary history, as well as to identify genetic variants underlying complex human traits.

Evolution, Molecular↗

PubMed2003

Linkage and linkage disequilibrium mapping of genes influencing human obesity in chromosome region 7q22.1-7q35.

Linkage results suggest that the region of chromosome 7 containing the leptin gene cosegregates with extreme obesity; however, leptin coding region mutations are rare. To investigate whether the leptin flanking sequence and/or a larger 40-cM region (7q22.1-7q35) contributes to obesity, we genotyped individuals from 200 European American families segregating extreme obesity and normal weight (1,020 subjects) using 21 microsatellite markers and two single nucleotide polymorphisms (SNPs) and conducted nonparametric linkage (NPL) analyses. We also carried out transmission disequilibrium tests for 135 European American triads using 27 markers (including eight SNPs). Both quantitative (MERLIN-regress) and qualitative (GENEHUNTER and MERLIN-npl) analyses provided evidence for linkage for BMI (GENEHUNTER NPL = 2.98, 20 cM centromeric to leptin at the marker D7S692; MERLIN Z score = 3.56). Results for several other regions in 7q gave weak linkage. Transmission disequilibrium test (TDT) and quantitative TDT (and quantitative pedigree disequilibrium test) analyses suggest linkage disequilibrium near leptin and other regions of 7q. Our results suggested that there could be two or more genes in chromosome region 7q22.1-7q35 that influence obesity. A new region found by this study (D7S692-D7S523, 7q31.1) has the most consistent linkage results and could harbor obesity-related genes.

Adolescent↗

PubMed2002

Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity.

Obesity is a multigenic trait that has a substantial genetic component. Animal models confirm a role for gene-gene interactions, and human studies suggest that as much as one-third of the heritable variance may be due to nonadditive gene effects. To evaluate potential epistatic interactions among five regions, on chromosomes 7, 10, and 20, that have previously been linked to obesity phenotypes, we conducted pairwise correlation analyses based on alleles shared identical by descent (IBD) for independent obese affected sibling pairs (ASPs), and we determined family-specific nonparametric linkage (NPL) scores in 244 families. The correlation analyses were also conducted separately, by race, through use of race-specific allele frequencies. Conditional analyses for a qualitative trait (body mass index [BMI] >/=27) and hierarchical models for quantitative traits were used to further refine evidence of gene interaction. Both the ASP-specific IBD-sharing probability and the family-specific NPL score revealed that there were strong positive correlations between 10q (88-97 cM) and 20q (65-83 cM), through single-point and multipoint analyses with three obesity thresholds (BMI >/=27, >/=30, and >/=35) across African American and European American samples. Conditional analyses for BMI >/=27 found that the LOD score at 20q rises from 1.53 in the baseline analysis to 2.80 (empirical P=.012) when families were weighted by evidence for linkage at 10q (D10S1646) through use of zero-one weights (weight(0-1)) and to 3.32 (empirical P<.001) when proportional weights (weight(prop)) were used. For percentage fat mass, variance-component analysis based on a two-locus epistatic model yielded significant evidence for interaction between 20q (75 cM) and the chromosome 10 centromere (LOD = 1.74; P=.024), compared with a two-locus additive model (LOD = 0.90). The results from multiple methods and correlated phenotypes are consistent in suggesting that epistatic interactions between loci in these regions play a role in extreme human obesity.

Body Mass Index↗

PubMed2002

Finding genetic contributions to sporadic disease: a recessive locus at 12q24 commonly contributes to patent ductus arteriosus.

The causes of many sporadic diseases are unexplained; the contribution of recessive loci with reduced penetrance is one possibility that has been difficult to explore. We describe an approach to this problem by first searching for diseases with higher prevalence in populations with high rates of consanguinity, then determining whether disease cases are more commonly the product of consanguinous union than controls in such populations, followed by analysis of genetic linkage in consanguinous cases. We demonstrate the utility of this approach by investigation of congenital heart disease in Iran. We found that patent ductus arteriosus (PDA), a common congenital heart disease, accounts for a higher fraction of congenital heart disease in Iran (15%) than in the United States (2-7%). Moreover, Iranian PDA cases demonstrated a marked increase of parental consanguinity (63%), compared with the general Iranian population (25%) or control cases with tetralogy of Fallot (30%). The recurrence of PDA among siblings was 5%. A genomewide analysis of linkage in 21 unrelated consanguinous PDA cases demonstrated a multipoint logarithm of odds score of 6.27 in favor of linkage of PDA to a 3-centimorgan interval of chromosome 12q24, with 53% of kindreds linked. These findings together establish a recessive component to PDA and implicate a single locus, PDA1, in one third or more of all PDA cases in Iran; they further suggest a role for this locus in PDA worldwide. Finally, these results suggest a general approach to the identification of recessive contributions to sporadic diseases.

Chromosome Mapping↗

PubMed2002

Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease.

Autosomal dominant polycystic kidney disease (ADPKD) occurs by germline mutation in PKD1 or PKD2. Evidence of homozygous inactivation of either gene in human cyst lining cells as well as in mouse knockout models strongly supports a two-hit mechanism for cyst formation. Discovery of trans-heterozygous mutations in PKD1 and PKD2 in a minority of human renal cysts has led to the proposal that such mutations also can play a role in cyst formation. In the current study, we investigated the role of trans-heterozygous mutations in mouse models of polycystic kidney disease. In Pkd1(+/-), Pkd2 (+/-) and Pkd1(+/-) : Pkd2 (+/-) mice, the renal cystic lesion was mild and variable with no adverse effect on survival at 1 year. In keeping with the two-hit mechanism of cyst formation, approximately 70% of kidney cysts in Pkd2 (+/-) mice exhibited uniform loss of polycystin-2 expression. Cystic disease in trans-heterozygous Pkd1(+/-) : Pkd2 (+/-) mice, however, was notable for severity in excess of that predicted by a simple additive effect based on cyst formation in singly heterozygous mice. The data suggest a modifier role for the 'trans' polycystin gene in cystic kidney disease, and support a contribution from threshold effects to cyst formation and growth.

Animals↗

PubMed2002

A method for easily determining coupling constant values: an addendum to "A practical guide to first-order multiplet analysis in 1H NMR spectroscopy".

A systematic procedure to decipher first-order 1H NMR multiplets is described. This method is a very practical tool for extracting coupling constant values. It requires only that one (a) learn to identify each of the 2n (n = number of spin 1/2 nuclei to which the proton is coupled) "units of intensity" of a multiplet and (b) then apply a clearly delineated sequence of iterative steps that allows the J's to be assigned in order (from smallest to largest). The approach is even easier to use than one described previously (J. Org. Chem. 1994, 59, 4096-4103).

Algorithms↗

PubMed2002

Linkage disequilibrium mapping with genotype data.

Linkage disequilibrium mapping has proven a powerful tool for locating disease genes. Although all existing linkage disequilibrium mapping methods implicitly assume that individual haplotypes can be inferred, only genotypes are directly observable in practice, and haplotypes cannot always be uniquely resolved based on genotype data. In this article, we propose a likelihood-based linkage disequilibrium mapping approach to analyzing multilocus genotype data arising from case-control studies. Results from extensive simulation studies suggest that this approach may be a useful tool to fine map disease genes using case-control data.

Chromosome Mapping↗

PubMed2002

Association mapping, using a mixture model for complex traits.

Association mapping for complex diseases using unrelated individuals can be more powerful than family-based analysis in many settings. In addition, this approach has major practical advantages, including greater efficiency in sample recruitment. Association mapping may lead to false-positive findings, however, if population stratification is not properly considered. In this paper, we propose a method that makes it possible to infer the number of subpopulations by a mixture model, using a set of independent genetic markers and then testing the association between a genetic marker and a trait. The proposed method can be effectively applied in the analysis of both qualitative and quantitative traits. Extensive simulations demonstrate that the method is valid in the presence of a population structure.

Alleles↗

PubMed2002

Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.

Phytochrome A (phyA) is the primary photoreceptor responsible for various far-red (FR) light-mediated responses. Previous studies have identified multiple phyA signaling mutants, including both positive and negative regulators of the phyA-mediated responses. How these defined intermediates act to mediate FR light responses is largely unknown. Here a cDNA microarray was used to examine effects of those mutations on the far-red light control of genome expression. Clustering analysis of the genome expression profiles supports the notion that phyA signaling may entail a network with multiple paths, controlling overlapping yet distinct sets of gene expression. FHY1, FAR1 and FHY3 most likely act upstream in the phyA signaling network, close to the phyA photoreceptor itself. FIN219, SPA1 and REP1 most likely act somewhere more downstream in the network and control the expression of smaller sets of genes. Further, this study also provides genomics evidence for the partial functional redundancy between FAR1 and FHY3. These two homologous proteins control the expression of a largely overlapping set of genes, and likely act closely together in the phyA-mediated FR light responses.

Arabidopsis↗