Biomedical subjects

Kai Yu

Publications and source records attributed to Kai Yu.

At least 19 recordsLinked to original sources

PubMed2026

Identification of immune cell type-specific susceptibility genes in multiple cancers using transcriptome-wide association studies.

BACKGROUND: Transcriptome-wide association studies (TWAS) integrate gene expression and genome-wide association studies (GWAS) to identify disease susceptibility genes. Because gene expression varies substantially across cell types within tissues, cell type-specific prediction models may enhance the power of TWAS. METHODS: We conducted cell type-specific TWAS leveraging single-cell RNA sequencing data from the OneK1K cohort (14 immune cell types, 1.27 million cells) and GWAS summary statistics for 7 cancers (>290 000 cases in total). To improve prediction accuracy, we developed a modeling framework that incorporates shared gene expression effects across cell types. RESULTS: At a false discovery rate of 5%, we identified 106 (Bonferroni 5%: 13) previously unreported loci for breast cancer, 51 (4) loci for prostate cancer, 11 (4) loci for lung cancer, 39 (5) loci for melanoma, 9 (1) loci for ovarian cancer, and 2 (1) loci for diffuse large B-cell lymphoma, with most genes exhibiting cell type specificity. Gene set analyses confirmed joint associations of unreported genes with breast and prostate cancer risk in UK Biobank data. Additional lung tissue single-cell RNA sequencing data with 113 individuals validated 18 of 32 (56.3%) statistically significant genes for lung cancer. Across cancers, 139 statistically significant genes were shared by at least 2 cancer types and were primarily enriched in specific immune cell types. CONCLUSION: Cell type-specific TWAS improve the identification of novel cancer susceptibility loci and provide insights into the immune landscape of cancer etiology.

Humans↗

PubMed2025

miR-9-5p/HMMR regulates the tumorigenesis and progression of clear cell renal cell carcinoma through EMT and JAK1/STAT1 signaling pathway.

BACKGROUND: The most common malignant type of kidney cancer is clear cell renal cell carcinoma (ccRCC). The expression levels of hyaluronan-mediated motility receptor (HMMR) in many tumor types are significantly elevated. HMMR is closely associated with tumor-related progression, treatment resistance, and poor prognosis, and has yet to be fully investigated in terms of its expression patterns and molecular mechanisms of action in ccRCC. Further research is imperative to elucidate these aspects. METHODS: We used The Cancer Genome Atlas (TCGA) database to preliminarily investigate HMMR expression and function in ccRCC and the data for 19 samples from the NCBI GEO database (GSE207493) for single-cell analysis. We assessed the differential expression level of HMMR between ccRCC cancerous tissues and their matched non-tumor tissues. Subsequently, a series of in vivo and in vitro experiments were designed to elucidate the biological function of HMMR in ccRCC, including Transwell assays, CCK-8 assays, clone formation assays and subcutaneous xenograft experiments in nude mice. Through bioinformatics analysis, we identified potential microRNAs (miRNAs) that may regulate HMMR, as well as the possible signaling pathways involved. Finally, we conducted a series of cellular functional experiments to validate our hypotheses regarding the HMMR axis. RESULTS: HMMR expression was significantly up-regulated in tumor tissues of ccRCC patients, and elevated HMMR expression level showed a strong correlation with ccRCC progression and adverse prognoses of patients. Knocking down HMMR inhibited the proliferative and migratory abilities of ccRCC cells, while its overexpression amplified these oncogenic properties. In nude mice model, reduced HMMR expression inhibited ccRCC tumor proliferation in vivo. Furthermore, overexpression of an upstream transcriptional regulator, miR-9-5p, effectively downregulated HMMR expression and thus impeded ccRCC cells proliferation and migration. HMMR might influence ccRCC growth via the Epithelial-Mesenchymal Transition (EMT) pathway and the Janus Kinase 1/Signal Transducer and Activator of Transcription 1 (JAK1/STAT1) pathway. CONCLUSIONS: HMMR is overexpressed in ccRCC, and there is a significant link between high HMMR expression and tumor progression, as well as poor patient prognosis. Specifically, HMMR could be targeted and inhibited by miR-9-5p and might modulate the tumorigenesis and progression of ccRCC through both EMT and JAK1/STAT1 signaling pathway.

Carcinoma, Renal Cell↗

PubMed2007

Fibroblast growth factor receptor 2 tyrosine kinase is required for prostatic morphogenesis and the acquisition of strict androgen dependency for adult tissue homeostasis.

The fibroblast growth factor (FGF) family consists of 22 members and regulates a broad spectrum of biological activities by activating diverse isotypes of FGF receptor tyrosine kinases (FGFRs). Among the FGFs, FGF7 and FGF10 have been implicated in the regulation of prostate development and prostate tissue homeostasis by signaling through the FGFR2 isoform. Using conditional gene ablation with the Cre-LoxP system in mice, we demonstrate a tissue-specific requirement for FGFR2 in urogenital epithelial cells--the precursors of prostatic epithelial cells--for prostatic branching morphogenesis and prostatic growth. Most Fgfr2 conditional null (Fgfr2(cn)) embryos developed only two dorsal prostatic (dp) and two lateral prostatic (lp) lobes. This contrasts to wild-type prostate, which has two anterior prostatic (ap), two dp, two lp and two ventral prostatic (vp) lobes. Unlike wild-type prostates, which are composed of well developed epithelial ductal networks, the Fgfr2(cn) prostates, despite retaining a compartmented tissue structure, exhibited a primitive epithelial architecture. Moreover, although Fgfr2(cn) prostates continued to produce secretory proteins in an androgen-dependent manner, they responded poorly to androgen with respect to tissue homeostasis. The results demonstrate that FGFR2 is important for prostate organogenesis and for the prostate to develop into a strictly androgen-dependent organ with respect to tissue homeostasis but not to the secretory function, implying that androgens may regulate tissue homeostasis and tissue function differently. Therefore, Fgfr2(cn) prostates provide a useful animal model for scrutinizing molecular mechanisms by which androgens regulate prostate growth, homeostasis and function, and may yield clues as to how advanced-tumor prostate cells escape strict androgen regulations.

Androgens↗

PubMed2006

Measuring marker information content by the ambiguity of block boundaries observed in dense SNP data.

Recent studies have noted that the boundary of common haplotype blocks in hapmap constructions involve a certain degree of ambiguity, and so do the resulting "tagSNPs". Here, we report how to address this issue at the level of individual SNP markers. We introduce a measure called the marker ambiguity score (MAS), and evaluate its utility by simulation studies based on a real dataset of 2949 SNPs spanning a region of 56.1M bp. We show that the MAS method can be used to assess the level of boundary ambiguity caused by varying ethnic background, sample sizes for hapmap construction, and disease aggregation. We find a striking difference in overall patterns of block boundary distributions in two ethnic groups (blacks and whites), and subtle changes in block structures that agree with the evolutionary history of the two populations. Our analyses suggest that a sample size of 200 or more subjects is probably needed for "stable" hapmap constructions. In addition, we demonstrate that there are subtle changes in block boundaries in hapmaps constructed in disease populations versus normal controls. This approach can quantify the information content of individual markers in the context of highly dense SNP data, which may have important implications in designing efficient genome-wide association mapping projects.

Computer Simulation↗

PubMed2006

FGF signalling generates ventral telencephalic cells independently of SHH.

Sonic hedgehog (SHH) is required to generate ventral cell types throughout the central nervous system. Its role in directly specifying ventral cells, however, has recently been questioned because loss of the Shh gene has little effect on ventral development if the Gli3 gene is also mutant. Consequently, another ventral determinant must exist. Here, genetic evidence establishes that FGFs are required for ventral telencephalon development. First, simultaneous deletion of Fgfr1 and Fgfr3 specifically in the telencephalon results in the loss of differentiated ventromedial cells; and second, in the Fgfr1;Fgfr2 double mutant, ventral precursor cells are lost, mimicking the phenotype obtained previously with a loss of SHH signalling. Yet, in the Fgfr1;Fgfr2 mutant, Shh remains expressed, as does Gli1, the transcription of which depends on SHH activity, suggesting that FGF signalling acts independently of SHH to generate ventral precursors. Moreover, the Fgfr1;Fgfr2 phenotype, unlike the Shh phenotype, is not rescued by loss of Gli3, further indicating that FGFs act downstream of Shh and Gli3 to generate ventral telencephalic cell types.

Animals↗

PubMed2006

Circulating angiogenic factors and placental abruption.

OBJECTIVE: Abnormalities in circulating angiogenic factors have been reported in diseases of abnormal placentation, such as preeclampsia and intrauterine growth restriction. Our objective was to determine whether circulating angiogenic factors are altered in another placental vascular disease, abruptio placentae. METHODS: In a nested case-control study of nulliparous pregnancies, we examined levels of placental growth factor (PlGF) and soluble fms-like tyrosine kinase 1 (sFlt-1) in serum collected prospectively from 31 women who later developed placental abruption and from 31 normal control subjects. All serum specimens were collected before the onset of hypertension or abruption and before labor or delivery. Serum angiogenic factors were compared within 3 gestational age windows: early (20 weeks or less), middle (21-32 weeks), and late (33 weeks or more) pregnancy. RESULTS: During early pregnancy women who developed placental abruption had lower PlGF and higher sFlt-1 concentrations and higher sFlt-1/PlGF ratios than women with normal pregnancies. In mid-pregnancy these differences became greater, reaching statistical significance for PlGF concentration (431 versus 654 pg/mL, P<.01) and the sFlt-1/PlGF ratio (25.3 versus 2.5, P<.01). When the women with placental abruption were subdivided into those who did (n=10) and those who did not (n=21) develop preeclampsia or gestational hypertension, significant alterations in angiogenic factors were noted only in women who later developed hypertension in pregnancy. Among these women, PlGF concentrations were decreased in mid-pregnancy (160 versus 723 pg/mL, P<.001), and the mid-pregnancy sFlt-1/PlGF ratio was increased (70.1 versus 2.3, P=.001). CONCLUSION: Serum levels of the proangiogenic factor PlGF were decreased, and those of the antiangiogenic ratio sFlt-1/PlGF were increased in nulliparous women who subsequently developed hypertension and placental abruption.

Abruptio Placentae↗

PubMed2006

Assessing performance of prediction rules in machine learning.

INTRODUCTION: An important goal in machine learning is to assess the degree to which prediction rules are robust and replicable, since these rules are used for decision making and for planning follow-up studies. This requires an estimate of a prediction rule's true error rate, a statistic that can be estimated by resampling data. However, there are many possible approaches depending upon whether we draw observations with or without replacement, or sample once, repeatedly, or not at all, and the pros and cons of each are often unclear. This study illustrates and compares different methods for estimating true error with the aim of providing practical guidance to users of machine learning techniques. METHODS: We conducted Monte Carlo simulation studies using four different error estimators: bootstrap, split sample, resubstitution and a direct estimate of true error. Here, 'split sample' refers to a single random partition of the data into a pair of training and test samples, a popular scheme. We used stochastic gradient boosting as a learning algorithm, and considered data from two studies for which the underlying data mechanism was known to be complex: a library of 6000 tripeptide substrates collected for analysis of proteasome inhibition as part of anticancer drug design, and a cardiovascular study involving 600 subjects receiving antiplatelet treatment for acute coronary syndrome. RESULTS: There were important differences in the performance of the various error estimators examined. Error estimators for split sample and resubstitution, while being the most transparent in action and the simplest to apply, did not quantify the performance of prediction rules as accurately as the bootstrap. This was true for both types of study data, despite their highly different nature. CONCLUSIONS: The robustness and reliability of decisions based on analysis of genomics data could, in many cases, be improved by following best practices for prediction error estimation. For this, techniques such as bootstrap should be considered.

Algorithms↗

PubMed2006

Toxicogenomics strategies for predicting drug toxicity.

INTRODUCTION: The failure of pharmaceutical drug candidates due to toxicity, especially hepatotoxicity, is an important and continuing problem for drug development. The current manuscript explores new toxicogenomics approaches to better understand the hepatotoxic potential of human pharmaceutical compounds and to assess their toxicity earlier in the drug development process by means of a toxicity screen. RESOURCES: Data consisted of two commercial knowledgebases that employed a hybrid experimental design in which human drug toxicity information was extracted from the literature, dichotomized and merged with rat-based gene expression measures. One knowledgebase used gene expression from rat primary hepatocytes while the other employed whole rats. Approximately 100 compounds were used in each. METHODS: Toxicity classification rules were built using a stochastic gradient boosting machine learner, with classification error estimated using a modified bootstrap estimate of true error. Several types of clustering methods were also applied, some based on sets of compounds and others based on sets of genes. RESULTS: Robust classification rules were constructed for both in vitro (hepatocytes) and in vivo (liver) data, based on a high dose, 24-hour design. There appeared to be little overlap between the two classifiers, at least in terms of their gene lists. Robust classifiers could not be fitted when earlier timepoints and/or low dose data were included, indicating that experimental design is important for these systems. CONCLUSIONS: In light of these findings, a working compound screen based on these toxicity classifiers appears feasible, with classifier operating characteristics used to tune a screen for a specific implementation. To ensure robust and optimal performance, issues such as site variability of microarrays and generalizability of findings should be addressed as indicated.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed2005

Inhibition or activation of Apert syndrome FGFR2 (S252W) signaling by specific glycosaminoglycans.

Most Apert syndrome patients harbor a single amino acid mutation (S252W) in fibroblast growth factor (FGF) receptor 2 (FGFR2), which leads to abnormal FGF/FGFR2 signaling. Here we show that specific combinations of FGFs and glycosaminoglycans activate both alternative splice forms of the mutant but not of the wild-type FGF receptors. More importantly, 2-O- and N-sulfated heparan sulfate, prepared by a combined chemical and enzymatic synthesis, antagonized the over-activated FGFR2b (S252W) to basal levels at nanomolar concentrations. These studies demonstrated that specific glycosaminoglycans could be useful in treating ligand-dependent FGFR signaling-related diseases, such as Apert syndrome and cancer.

Acrocephalosyndactylia↗

PubMed2005

Decreased alloreactivity using donor cells from mice expressing a CD200 transgene under control of a tetracycline-inducible promoter.

BACKGROUND: CD200 delivers an immunsuppressive signal that augments allograft survival following interaction with its receptor, CD200R1. We hypothesized that mice overexpressing CD200 as a trangene would also show a diminished alloresponsiveness and decreased allograft rejection. METHODS: A transgenic mouse on a C57BL/6 background, expressing a murine CD200 cDNA genetically linked to a green fluorescent protein tag (GFP) under control of a tetracycline response element (TRE), was mated with a commercial transgenic mouse carrying the reverse tetracycline regulated transactivator gene under control of a human CMV promoter. F1 mice were examined for induction of alloimmunity in vivo/in vitro, and for their ability to reject skin allografts in vivo. RESULTS: The F1 hybrid expressed CD200 after exposure to doxycyline (DOX), as assessed both by enhanced GFP expression in multiple organs and CD200-GFP expression. Splenocytes from F1 mice stimulated with LPS or allogeneic cells in vitro in the presence/absence of DOX showed reduced production of TNFalpha, and of allospecific CTL. Splenocytes from F1 mice used as stimulator cells in allogeneic MLCs in the presence of DOX were inefficient at induction of cytokines or CTL in vitro from normal allogeneic responder cells. Skin grafts from transgenic mice were inefficient at induction of CTL in vivo. Transgenic mice receiving DOX showed prolonged acceptance of skin allografts, which was abolished by infusion of anti-CD200 mAb. CONCLUSIONS: Our data confirmed that overexpression of CD200 in transgenic mice, or in skin grafts from these mice, decreases alloimmunity. This has potential clinical utility in transplantation and other diseases.

Animals↗

PubMed2005

Abnormalities in cartilage and bone development in the Apert syndrome FGFR2(+/S252W) mouse.

Apert syndrome is an autosomal dominant disorder characterized by malformations of the skull, limbs and viscera. Two-thirds of affected individuals have a S252W mutation in fibroblast growth factor receptor 2 (FGFR2). To study the pathogenesis of this condition, we generated a knock-in mouse model with this mutation. The Fgfr2(+/S252W) mutant mice have abnormalities of the skeleton, as well as of other organs including the brain, thymus, lungs, heart and intestines. In the mutant neurocranium, we found a midline sutural defect and craniosynostosis with abnormal osteoblastic proliferation and differentiation. We noted ectopic cartilage at the midline sagittal suture, and cartilage abnormalities in the basicranium, nasal turbinates and trachea. In addition, from the mutant long bones, in vitro cell cultures grown in osteogenic medium revealed chondrocytes, which were absent in the controls. Our results suggest that altered cartilage and bone development play a significant role in the pathogenesis of the Apert syndrome phenotype.

Acrocephalosyndactylia↗

PubMed2005

Signaling through FGF receptor-2 is required for lens cell survival and for withdrawal from the cell cycle during lens fiber cell differentiation.

Fibroblast growth factors (FGFs) play important roles in many aspects of development, including lens development. The lens is derived from the surface ectoderm and consists of an anterior layer of epithelial cells and elongated, terminally differentiated fiber cells that form the bulk of the tissue. FGF signaling has been implicated in lens induction, proliferation, and differentiation. To address the role of FGFs in lens development, we inactivated FGF receptor-2 (Fgfr2) using a Cre transgene that is expressed in all prospective lens cells from embryonic day 9.0. Inactivation of Fgfr2 shows that signaling through this receptor is not required for lens induction or for the proliferation of lens epithelial cells. However, Fgfr2 signaling is needed to drive lens fiber cells out of the cell cycle during their terminal differentiation. It also contributes to the normal elongation of primary lens fiber cells and to the survival of lens epithelial cells.

Animals↗

PubMed2005

Global transmission/disequilibrium tests based on haplotype sharing in multiple candidate genes.

It is well recognized that multiple genes are likely contributing to the susceptibility of most common complex diseases. Studying one gene at a time might reduce our chance to identify disease susceptibility genes with relatively small effect sizes. Therefore, it is crucial to develop statistical methods that can assess the effect of multiple genes collectively. Motivated by the increasingly available high-density markers across the whole human genome, we propose a class of TDT-type methods that can jointly analyze haplotypes from multiple candidate genes (linked or unlinked). Our approach first uses a linear signed rank statistic to compare at an individual gene level the structural similarity among transmitted haplotypes against that among non-transmitted haplotypes. The results of the ranked comparisons from all considered genes are subsequently combined into global statistics, which can simultaneously test the association of the set of genes with the disease. Using simulation studies, we find that the proposed tests yield correct type I error rates in stratified populations. Compared with the gene-by-gene test, the new global tests appear to be more powerful in situations where all candidate genes are associated with the disease.

Haplotypes↗

PubMed2005

Endocardial and epicardial derived FGF signals regulate myocardial proliferation and differentiation in vivo.

The epicardium regulates growth and survival of the underlying myocardium. This activity depends on intrinsic retinoic acid (RA) and erythropoietin signals. However, these signals do not act directly on the myocardium and instead are proposed to regulate the production of an unidentified soluble epicardial derived mitogen. Here, we show that Fgf9, Fgf16, and Fgf20 are expressed in the endocardium and epicardium and that RA can induce epicardial expression of Fgf9. Using knockout mice and an embryonic heart organ culture system, we show that endocardial and epicardial derived FGF signals regulate myocardial proliferation during midgestation heart development. We further show that this FGF signal is received by both FGF receptors 1 and 2 acting redundantly in the cardiomyoblast. In the absence of this signal, premature differentiation results in cellular hypertrophy and newborn mice develop a dilated cardiomyopathy. FGFs thus constitute all or part of the epicardial signal regulating myocardial growth and differentiation.

Age Factors↗

PubMed2005

A haplotype similarity based transmission/disequilibrium test under founder heterogeneity.

Taking advantage of increasingly available high-density single nucleotide polymorphisms (SNP) markers across the genome, various types of transmission/disequilibrium tests (TDT) using haplotype information have been developed. A practical challenge arising in such studies is the possibility that transmitted haplotypes have inherited disease-causing mutations from different ancestral chromosomes, or do not bear any disease-causing mutations (founder heterogeneity). To reduce the loss of signal strength due to founder heterogeneity, we propose an SP-TDT test that combines a sequential peeling procedure with the haplotype similarity based TDT method. The proposed SP-TDT method is applicable to any size of nuclear family with or without ambiguous phase information. Simulation studies suggest that the SP-TDT method has the correct type I error rate in stratified populations, and enhanced power compared with some existing haplotype similarity based TDT methods. Finally, we apply the proposed method to study the association of the leptin gene with obesity from the National Heart, Lung, and Blood Institute Family Heart Study.

Algorithms↗

PubMed2005

Using tree-based recursive partitioning methods to group haplotypes for increased power in association studies.

Motivated by the increasing availability of high-density single nucleotide polymorphism (SNP) markers across the genome, various haplotype-based methods have been developed for candidate gene association studies, and even for genome-wide association studies. Although haplotype approaches dramatically reduce the multiple comparisons problem (as compared to single SNP analysis), even the number of existing haplotypes is relatively large, which increases the degrees of freedom and decreases the power for the corresponding test statistic. Grouping haplotypes is a way to reduce the degrees of freedom. We propose a procedure that uses a tree-based recursive partitioning algorithm to group haplotypes into a small number of clusters, and conducts the association test based on groups of haplotypes instead of individual haplotypes. The method can be used for both population-based and family-based association studies, with known or ambiguous phase information. Simulation studies suggest that the proposed method has the right type I error rate, and is more powerful than some existing haplotype-based tests.

Algorithms↗

PubMed2005

Power and sample size for clinical trials when efficacy is required in multiple endpoints: application to an Alzheimer's treatment trial.

BACKGROUND: When the efficacy of a treatment in a randomized controlled trial is required for multiple primary endpoints, trial design and analysis differ from trial requiring efficacy in only one of the multiple endpoints. METHODS: We consider a two-arm clinical trial requiring efficacy analysis for multiple primary endpoints, formulating the appropriate null and alternative hypotheses for the test of treatment efficacy. We study the significance level/statistical power of an intersection-union test (IUT) in this situation. We compare IUT with the intuitive approach (selecting the maximum sample size over those obtained from testing individual primary endpoints one by one) for determination of sample size. RESULTS: The proposed IUT reserves the same Type I error rate as shared by all endpoint-specific tests. The statistical power of the proposed IUT is no more than the minimum from the individual tests. The maximum sample size from multiple endpoint-specific tests is often inadequate for the test of treatment efficacy, especially when the standardized effect sizes are similar. Finally, the IUT can be applied to Alzheimer's disease treatment trials in which two primary endpoints are typically used. CONCLUSIONS: The IUT is a valid method for use in the design and analysis of clinical trials requiring efficacy at multiple primary endpoints.

Alzheimer Disease↗

PubMed2004

Mutations that cause osteoglophonic dysplasia define novel roles for FGFR1 in bone elongation.

Activating mutations in the genes for fibroblast growth factor receptors 1-3 (FGFR1-3) are responsible for a diverse group of skeletal disorders. In general, mutations in FGFR1 and FGFR2 cause the majority of syndromes involving craniosynostosis, whereas the dwarfing syndromes are largely associated with FGFR3 mutations. Osteoglophonic dysplasia (OD) is a "crossover" disorder that has skeletal phenotypes associated with FGFR1, FGFR2, and FGFR3 mutations. Indeed, patients with OD present with craniosynostosis, prominent supraorbital ridge, and depressed nasal bridge, as well as the rhizomelic dwarfism and nonossifying bone lesions that are characteristic of the disorder. We demonstrate here that OD is caused by missense mutations in highly conserved residues comprising the ligand-binding and transmembrane domains of FGFR1, thus defining novel roles for this receptor as a negative regulator of long-bone growth.

Adult↗