Biomedical subjects

Xing Chen

Publications and source records attributed to Xing Chen.

At least 19 recordsLinked to original sources

PubMed2026

Single-nucleus transcriptomics reveals cell type-specific remodeling and epilepsy-associated microglia.

Temporal lobe epilepsy (TLE) is the most common acquired epilepsy, causing refractory seizures and cognitive deficits. We performed single-nucleus RNA sequencing on hippocampal tissue from mice 3 and 6 weeks following pilocarpine-induced status epilepticus, a robust model of TLE. Epilepsy samples showed reductions in Cck and Lamp5-Lhx6 interneuron subclusters, alongside increases in Cajal-Retzius cells, dentate granule (DG) cell precursors, and a mature DG cell subcluster. Among glia, an astrocyte subcluster and a markedly expanded microglia sublcuster were increased. We term this microglia population epilepsy-associated microglia (EAM). The transcriptomic profile of EAM overlaps with microglia described in models of Alzheimer's disease and traumatic brain injury, including enrichment of Myo1e and Igf1. EAM display amoeboid morphology, can be found in clumps around pyramidal and granule cell body layers, and exhibit enlarged vesicles and mitochondria. Cell-cell interaction analysis predicts DG cells as their primary interaction partners. This dataset defines transcriptomic programs underlying key cellular alterations in TLE, enabling mechanistic dissection of epileptogenesis.

TLE↗

PubMed2026

An oxidative stress - and immunotherapy-related six-gene signature defines immune subtypes and predicts prognosis and immunotherapy response in hepatocellular carcinoma.

BACKGROUND: Oxidative stress and the tumor immune microenvironment jointly shape hepatocellular carcinoma (HCC) progression and response to immunotherapy, yet integrated biomarkers linking these processes are lacking. METHODS: Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to identify oxidative stress- and immunotherapyrelated differentially expressed genes (OSIRDEGs). Functional enrichment, weighted gene co-expression network analysis (WGCNA) and LASSO-Cox regression were used to construct a prognostic signature. Consensus clustering, TIDE, CIBERSORT and ssGSEA characterized immune phenotypes. Somatic mutation, copy-number and drug-response data were integrated to assess genomic alterations and drug sensitivity. Expression of model genes was validated by qRT-PCR and western blotting in HCC cell lines. RESULTS: We identified 24 OSIRDEGs enriched in cell-cycle and mitotic pathways. WGCNA intersection yielded 18 module genes, from which a six-gene signature (BUB1B, CDKN2A, CENPE, HMMR, PTTG1, SPP1) was derived. The signature robustly stratified patients into high- and low-risk groups with significantly different progression-free and disease-free survival in both TCGA-LIHC and GSE14520. Based on signature expression, two molecular subtypes were defined, exhibiting distinct survival, immune landscapes and predicted immunotherapy responsiveness. Model genes harbored recurrent alterations and showed significant correlations with anticancer agents. All six genes were upregulated at mRNA and protein levels in metastatic HCC cell lines versus normal hepatocytes. CONCLUSIONS: We systematically explored the landscape of OSIRDEGs in HCC, and proposed a validated six-gene signature that refines prognostic stratification, delineates immunerelevant HCC subtypes and highlights candidate biomarkers for therapeutic selection and mechanistic investigation.

Humans↗

PubMed2026

Amino-acids-mTORC1-driven DDA1 phosphorylation promotes DNA repair and glioblastoma progression.

BACKGROUND: DDA1 is a protein involved in protein degradation, cell cycle regulation, and DNA damage repair. Although its expression varies across tumor types, the precise role of DDA1 in gliomagenesis remains unclear. METHODS: We investigated the function of DDA1 in multiple glioblastoma cell models using biochemical assays, phosphorylation analysis, subcellular localization studies, and integrated genomic and transcriptomic profiling to determine its signaling interactions and downstream effects. RESULTS: We identified a physical association between cytoplasmic DDA1 and Raptor, a core component of lysosome-associated mTORC1. Amino acid stimulation triggered phosphorylation of DDA1 at serine 33 promoting its nuclear translocation and involvement in DNA damage repair. Integrated transcriptomic analyses revealed that the mTORC1-DDA1S33-DNA repair axis regulates the expression of a subset of metabolic genes, including ENO2, CA12, and NMRK1. Functional assays further suggested that these genes contribute to the survival capacity of glioblastoma cells, particularly under DDA1-deficient conditions. Consistently, DDA1 deficiency markedly impaired glioblastoma growth and induced compensatory upregulation of metabolic activity. CONCLUSION: Our findings identify DDA1 as a previously unrecognized phosphorylation target downstream of mTORC1 and a critical mediator of the mTORC1 driven DNA damage response. Through its involvement in DNA repair and metabolic gene regulation, DDA1 appears to support glioblastoma progression, providing mechanistic insight into mTORC1 related gliomagenesis and suggesting potential therapeutic relevance.

Glioblastoma↗

PubMed2025

Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes.

Heart failure (HF) is a major contributor to global morbidity and mortality. While distinct clinical subtypes, defined by etiology and left ventricular ejection fraction, are well recognized, their genetic determinants remain inadequately understood. In this study, we report a genome-wide association study of HF and its subtypes in a sample of 1.9 million individuals. A total of 153,174 individuals had HF, of whom 44,012 had a nonischemic etiology (ni-HF). A subset of patients with ni-HF were stratified based on left ventricular systolic function, where data were available, identifying 5,406 individuals with reduced ejection fraction and 3,841 with preserved ejection fraction. We identify 66 genetic loci associated with HF and its subtypes, 37 of which have not previously been reported. Using functionally informed gene prioritization methods, we predict effector genes for each identified locus, and map these to etiologic disease clusters through phenome-wide association analysis, network analysis and colocalization. Through heritability enrichment analysis, we highlight the role of extracardiac tissues in disease etiology. We then examine the differential associations of upstream risk factors with HF subtypes using Mendelian randomization. These findings extend our understanding of the mechanisms underlying HF etiology and may inform future approaches to prevention and treatment.

Humans↗

PubMed2006

A selective cyclooxygenase-2 inhibitor decreases transforming growth factor-beta1 synthesis and matrix production in human peritoneal mesothelial cells.

High glucose concentration, which provides the chief driving force in peritoneal dialysis, has been considered to be an important initial factor that contributes to peritoneal thickening and fibrosis. Human peritoneal mesothelial cells (HPMCs) and the expansion of extracellular matrix (ECM) play important roles in the pathological process of peritoneal fibrosis. Peritoneal matrix accumulation is a characteristic of peritoneal fibrosis (PF). Continuous ambulatory peritoneal dialysis (CAPD) patients with upregulation of transforming growth factor-beta1 (TGF-beta1) in their drained effluent show an increased risk of PF. Inhibition of TGF-beta1 expression in human peritoneal mesothelial cells (HPMCs) may provide a potential treatment for PF. sc58236, a highly selective cyclooxygenase-2 (COX-2) inhibitor, reduces proteinuria and mRNA expression of TGF-beta1 and collagen III and IV in the remnant kidney, but their effects on ECM turnover in HPMCs are unknown. The aims of this study were to investigate the effects of sc58236 on TGF-beta1 expression and matrix production in HPMCs. HPMCs were cultured from human omentum by an enzyme digestion method. To examine the effect of sc58236 on TGF-beta1 and ECM secretion, HPMC were incubated in medium F12 with high concentration of D-glucose (4.25%) in the presence and absence of 20 microM sc58236. The mRNA expression of COX-2, TGF-beta1 and collagen I (Col I) were determined by semi-quantification reverse transcription PCR (RT-PCR). Prostaglandin E2 (PGE2) concentration in the culture medium was measured by enzyme-linked immunosorbent assay (ELISA). The protein of TGF-beta1 was determined by ELISA and the activity of TGF-beta1 present in the conditioned media was measured using the mink lung epithelial cell (MLEC) growth inhibition assay. Proteins of COX-2 and Col were determined by Western blot. The results showed that primary cultures of HPMCs do express the mRNA for COX-2 and stimulation of these cells with 4.25% D-glucose induced a marked increase in COX-2 mRNA expression and protein. PGE2 expression was obviously up-regulated with stimulation by 4.25% D-glucose. Addition of 20 microM sc58236 significantly inhibited PGE2 release into the culture medium. mRNA expression and bioactive and total protein of TGF-beta1 and Col I were significantly increased in HPMCs stimulated with 4.25% D-glucose compared to the control group with F12 media, which was reversed in the presence of sc58236 (20 microM). An obvious decrease in TGF-beta1 mRNA expression and bioactive and total protein were found in sc58236 treated groups compared to the group stimulated with 4.25% D-glucose. Exposure of HPMCs to sc58236 reduced Col I secretion. Sc58236 reduces the expression of TGF-beta1 in HPMCs stimulated by 4.25% D-glucose and reduces ECM production through PGE2 production. These studies suggest that sc58236, a highly selective cyclooxygenase-2 (COX-2) inhibitor, may have a specific role in ameliorating the course of progressive peritoneal fibrosis under long-term peritoneal dialysis states.

Cell Division↗

PubMed2006

Expression and function of periostin-like factor in vascular smooth muscle cells.

In injured blood vessels activated vascular smooth muscle cells (VSMCs) migrate from the media to the intima, proliferate and synthesize matrix proteins. This results in occlusion of the lumen and detrimental clinical manifestations. We have identified a novel isoform of the periostin family of proteins referred to as periostin-like factor (PLF). PLF expression in VSMCs was increased following treatment with mitogenic compounds, suggesting that PLF plays a role in VSMC activation. Correspondingly, proliferation of the cells was significantly reduced with anti-PLF antibody treatment. PLF expression increased VSMC migration, an essential cellular process leading to vascular restenosis after injury. PLF protein was localized to neointimal VSMC of rat and swine balloon angioplasty injured arteries, as well as in human arteries with transplant restenosis, supporting the hypothesis that PLF is involved in VSMC activation and vascular proliferative diseases. Taken together, these data suggest a role for PLF in the regulation of vascular proliferative disease.

Angioplasty, Balloon, Coronary↗

PubMed2006

Electronic spectra of linear isoelectronic clusters C2n+1S and C2n+1Cl+ (n = 0-4): an ab initio study.

Structures and stabilities of linear carbon chains C2n+1S and C2n+1Cl+ (n=0-4) in their ground states have been investigated by the CCSD and B3LYP approaches. The CASSCF calculations have been used to determine geometries of selected excited states of both isoelectronic series. Linear C2n+1S cluster has a cumulenic carbon framework, whereas its isoelectronic C2n+1Cl+ has a dominant character of acetylenic structure in the vicinity of terminal Cl. The vertical excitation energies of low-lying excited states have been calculated by the CASPT2 method. Calculations show that the excitation energies have nonlinear size dependence. The 2(1)Sigma+<--X1Sigma+ transition energy in C2n+1S has a limit of 1.78 eV, as the chain size is long enough. The predicted vertical excitation energies for relatively strong 1(1)Pi<--X1Sigma+ and 2(1)Sigma+<--X1Sigma+ transitions are in reasonable agreement with available experimental values. The spin-orbit effect on the spin-forbidden transition in both series is generally small, and the enhancement of the spin-forbidden transition by spin-orbit coupling exhibits geometrical and electronic structural dependence.

Journal Article↗

PubMed2006

Extracellular targeting of endoplasmic reticulum chaperone glucose-regulated protein 170 enhances tumor immunity to a poorly immunogenic melanoma.

We have demonstrated previously that immunization with tumor-derived endoplasmic reticulum (ER) chaperone glucose-regulated protein 170 (grp170) elicits potent antitumor immunity. In the present study, we determine the impact of extracellular targeting grp170 by molecular engineering on tumor immunogenicity and potential use of grp170-secreting tumor cells as a cancer vaccine. grp170 depleted of ER retention sequence "KNDEL," when secreted by B16 tumor cells, maintained its highly efficient chaperoning activities and was significantly superior to both hsp70 and gp96. The continued secretion of grp170 dramatically reduced the tumorigenicity of B16 tumor cells in vivo, although the modification did not alter its transformation phenotype and cell growth rate. C57BL/6 mice that rejected grp170-secreting B16 tumor cells (B16-sgrp170) developed a strong CTL response recognizing melanocyte differentiation Ag TRP2 and were resistant to subsequent tumor challenge. B16-sgrp170 cells also stimulated the production of proinflammatory cytokines by cocultured dendritic cells. Depletion studies in vivo indicate that NK cells play a primary role in elimination of viable B16-sgrp170 tumor cells inoculated into the animals, whereas both NK cells and CD8(+) T cells are required for a long-term protection against wild-type B16 tumor challenge. Both the secreted and endogenous grp170, when purified from the B16 tumor, exhibited potent tumor-protective activities. However, the B16-sgrp170 cell appears to be more effective than tumor-derived grp170. Thus, molecular engineering of tumor cell to release the largest ER chaperone grp170 is capable of eliciting innate as well as adaptive immune responses, which may provide an effective cell-based vaccination approach for cancer immunotherapy.

Animals↗

PubMed2006

Interfacing carbon nanotubes with living cells.

We developed a polymer coating for carbon nanotubes (CNTs) that mimics the mucin glycoprotein coating of mammalian cells. CNTs coated with these mucin mimic polymers have two novel properties: they can bind to carbohydrate receptors, providing a means for biomimetic interactions with cell surfaces, and, importantly, they are rendered nontoxic to cells.

Animals↗

PubMed2006

Chaperoning function of stress protein grp170, a member of the hsp70 superfamily, is responsible for its immunoadjuvant activity.

When used as vaccines, tumor-derived stress proteins can elicit antitumor immune responses. For members of the hsp70 superfamily, like grp170, this seems to be due to (a) the chaperoning of antigenic peptide by the stress protein and (b) the binding of the stress protein to receptor(s) on antigen-presenting cells (APC) and subsequent antigen presentation. This suggests that domains exist on the stress protein for each function. In this study, we determine the ability of grp170 and its structural domains to (a) bind to and present melanoma-associated antigen gp100 to the immune system and (b) to bind to receptors on APCs. A direct correlation between chaperone function, binding to APCs in a receptor-like manner, and antitumor immunity was observed. Two mutants that share no common sequence, yet are both effective in their antitumor activities, compete with one another for APC binding. Studies of other members of the hsp70 superfamily, hsp110 and hsp70, or their domain deletion mutants, further confirmed that APC binding segregates with chaperoning function and not sequence. Therefore, these studies suggest that molecular chaperoning is involved in stress protein interactions with APCs, antigen binding, and in eliciting antitumor immunity, thus bridging this ancient function of stress proteins in prokaryotes to their ability to elicit immunity in higher organisms.

Animals↗

PubMed2006

A rigid poly(dimethylsiloxane) sandwich electrophoresis microchip based on thin-casting method.

We present a novel concept of glass/poly(dimethylsiloxane) (PDMS)/glass sandwich microchip and developed a thin-casting method for fabrication. Unlike the previously reported casting method for fabricating PDMS microchip, several drops of PDMS prepolymer were first added on the silanizing SU-8 master, then another glass plate was placed over the prepolymer as a cover plate, and formed a glass plate/PDMS prepolymer/SU-8 master sandwich mode. In order to form a thin PDMS membrane, a weight was placed on the glass plate. After the whole sandwich mode was cured at 80 degrees C for 30 min, the SU-8 master was easily peeled and the master microstructures were completely transferred to the PDMS membrane which was tightly stuck to the glass plate. The microchip was subsequently assembled by reversible sealing with the glass cover plate. We found that this PDMS sandwich microchip using the thin-casting method could withstand internal pressures of >150 kPa, more than 5 times higher than that of the PDMS hybrid microchip with reversible sealing. In addition, it shows an excellent heat-dissipating property and provides a user-friendly rigid interface just like a glass microchip, which facilitates manipulation of the microchip and fix tubing. As an application, PDMS sandwich microchips were tested in the capillary electrophoresis separation of fluorescein isothiocyanate-labeled amino acids.

Amino Acids↗

PubMed2006

Relationship between clinical predictors and tubulointerstitial damage in adult-onset primary nephrotic syndrome.

BACKGROUND: Tubulointerstitial damage (TID) is an important mediator in the progression of chronic proteinuric nephropathies. Our aim in this study was to evaluate the relationship between several clinical predictors and TID in adult-onset primary nephrotic syndrome in China. METHODS: One hundred ninety-five adult inpatients who were diagnosed with primary nephrotic syndrome based on clinical presentation and biopsy results were enrolled in this study from March 2003 to September 2005. The degree of TID was graded by a semiquantitative method including <2 score and >or=2 score. RESULTS: In all patients, the rate of glomerulosclerosis was correlated with the severity of TID. Serum creatinine and uric acid (r = 0.183, p = 0.012 and r = 0.377, p = 0.00001, respectively) but not serum lipid or total 24-h urinary protein were related with TID. In 64 patients, urinary excretion of IgG (r = 0.443, p = 0.00001) but not of albumin, transferrin, retinal-binding protein, or alpha1-microglobulin were significantly associated with the extent of TID. Proteinuria selectivity index based upon IgG also correlated significantly with the extent of TID (p = 0.0001) (score 0-1 vs. score >or=2). CONCLUSIONS: These results showed that serum creatinine and uric acid, the excretion of urinary IgG and proteinuria selectivity index based upon IgG, were highly correlated with the severity of TID in adult-onset primary nephrotic syndrome. These clinical parameters might be useful for predicting the development and progression of proteinuric nephropathy as independent risk factors.

Adolescent↗

PubMed2006

[High-level expression of phenylalanine ammonia-lyase in Lactococcus Lactis via synthesized sequence based on bias codons].

To construct a safer and more efficient gene engineering Lactococcus Lactis for expressing phenylalaine ammonia lyase (PAL) which will be benefit for PKU therapy, pal cDNA of Parsly and synthesized sequence based on Lactococcus Lactis bias codons were recombined into two Lactococcus Lactis NICE systems. The activities of the expressed PAL were detected, and the effect of Lactococcus Lactis bias codons on the expression of exterior protein was analyzed. The results showed that the expression level of PAL was increased by using Lactococcus Lactis bias codons in both Lactococcus Lactis NICE systems. Through which several safer andmore efficient strains of the gene engineering Lactococcus Lactis were obtained.

Cloning, Molecular↗

PubMed2006

Inhibition of TGF-beta1 expression in human peritoneal mesothelial cells by pcDU6 vector-mediated TGF-beta1 shRNA.

BACKGROUND AND AIM: Transforming growth factor-beta(1) (TGF-beta(1)) is an important mediator of the fibrosis process. High expression of TGF-beta(1) is closely related to peritoneal fibrosis. RNA interference using short hairpin RNA (shRNA) can mediate sequence-specific inhibition of gene expression in mammalian cells. The aim of this study was to assess the effect of shRNA targeting TGF-beta(1) on the expression of TGF-beta(1) in human peritoneal mesothelial cells (HPMC). METHODS: TGF-beta(1) specific shRNA expression vectors were constructed and introduced to HPMC stimulated with 4.25% D-glucose (Gs) and 10 microg/mL of lipopolysaccharide (LPS). Expression of TGF-beta(1) mRNA was assessed by semiquantification reverse transcription polymerase chain reaction (RT-PCR). The TGF-beta(1) protein level in the culture supernatant was determined by sandwich enzyme-linked immunosorbent assay. RESULTS: The expression of TGF-beta(1) was upregulated significantly in HPMC stimulated with 4.25% D-Gs and 10 microg/mL LPS P < 0.01. TGF-beta(1) expression in pcDU6 plasmid vector-mediated TGF-beta(1) shRNA groups were obviously downregulated when compared to the 4.25% D-Gs and 10 microg/mL LPS group (P < 0.01) and the pcDU6 void vector group (P < 0.05), with no significant difference among pcDU6 plasmid vector -mediated TGF-beta(1) shRNA groups (P > 0.05). No significant difference was found between teh pcDNA3.1(-) vector plasmid-mediated TGF-beta(1) antisense RNA group and pcDU6 void vector group (P > 0.05). The expression of TGF-beta(1) in pcDU6 plasmid vector-mediated TGF-beta(1) shRNA groups were obviously downregulated when compared to the pcDNA3.1(-) plasmid vector-mediated TGF-beta(1) antisense RNA group (P < 0.05). CONCLUSION: TGF-beta(1)-specific shRNA can significantly inhibit the expression of TGF-beta(1) in HPMC stimulated with 4.25% D-Gs and 10 microg/mL LPS in HPMC. These results suggest the possible application of TGF-beta(1)-specific shRNA in preventing peritoneal fibrosis in patients receiving peritoneal dialysis.

Epithelial Cells↗

PubMed2006

Troglitazone inhibits synthesis of transforming growth factor-beta1 and reduces matrix production in human peritoneal mesothelial cells.

AIM: Peritoneal matrix accumulation is a characteristic of peritoneal fibrosis (PF). Continuous ambulatory peritoneal dialysis (CAPD) patients with up-regulation of transforming growth factor-beta1 (TGF-beta1) in their drained effluent show an increased risk of PF. Inhibition of TGF-beta1 expression in human peritoneal mesothelial cells (HPMC) may provide a potential treatment for PF. Peroxisome proliferator-activated receptor-gamma (PPAR-gamma) agonists are increasingly used in patients with diabetes, but their effects on extracellular matrix (ECM) turnover are unknown. The aims of this study were to investigate the effects of the PPAR-gamma agonist troglitazone on TGF-beta1 expression and matrix production in HPMC. METHODS: Human peritoneal mesothelial cells were cultured from human omentum by an enzyme digestion method, grown in a medium containing 30 mmol/L D-glucose. TGF-beta1 expression and matrix production and turnover were measured in HPMC in the presence and absence of 15 micromol/L troglitazone. The mRNA expressions of TGF-beta(1), Collagen I (Col I) and fibronectin (FN) were determined by semiquantification reverse-transcriptive polymerase chain reaction (RT-PCR). The protein of TGF-beta1 was determined by ELISA and proteins of Col I, FN were determined by western blot. RESULTS: The mRNA expression and protein of TGF-beta(1), Col I, FN were significantly increased in HPMC stimulated with 30 mmol/L D-glucose compared to the control group with F12 media (P < 0.01), which was reversed in the presence of troglitazone (15 micromol/L). Obvious decrease of TGF-beta(1) was found in troglitazone-treated groups as compared to groups stimulated with GS (P < 0.05). Exposure of HPMC to troglitazone reduced collagen I secretion (P < 0.05), and fibronectin secretion (P < 0.05). CONCLUSION: Troglitazone reduce the expression of TGF-beta(1) in HPMC stimulated by 30 mmol/L D-glucose, and reduces ECM production. These studies suggest that the PPAR-gamma agonists may have a specific role in ameliorating the course of progressive peritoneal fibrosis under long-term peritoneal dialysis states.

Blotting, Western↗

PubMed2006

Multiple mechanisms underlie resistance of leukemia cells to Apo2 Ligand/TRAIL.

Targeting death receptors with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has the remarkable potential to selectively kill malignant cells whereas normal cells are largely unaffected by this treatment. However, some tumor cells, including leukemia cells, exhibit resistance to this molecule. To investigate the basis for resistance of leukemia cells to the zinc-bound form of Apo2 ligand (Apo2L)/TRAIL, which is currently being evaluated in clinical trial, we isolated several resistant HL60 clones from parental HL60 cells by selection using the recombinant Apo2L/TRAIL. Differing resistance mechanisms were identified and characterized in these Apo2L/TRAIL-resistant clones. In one case, the level of the cell-surface death receptor DR4, but not DR5, was significantly decreased. However, these cells did undergo apoptosis in response to another form of recombinant TRAIL, histidine-tagged TRAIL, suggesting differing contributions of DR4 and DR5 in the response to these two forms of TRAIL. In the case of other clones, expression of procaspase-8 protein was lost and this was associated with a novel Leu(22)-->Phe(22) point mutation in CASP-8 gene. These results show that cells within a given tumor can have widely distinct mechanisms underlying resistance to Apo2L/TRAIL.

Amino Acid Substitution↗

PubMed2005

Angioblast-mesenchyme induction of early kidney development is mediated by Wt1 and Vegfa.

Most studies on kidney development have considered the interaction of the metanephric mesenchyme and the ureteric bud to be the major inductive event that maintains tubular differentiation and branching morphogenesis. The mesenchyme produces Gdnf, which stimulates branching, and the ureteric bud stimulates continued growth of the mesenchyme and differentiation of nephrons from the induced mesenchyme. Null mutation of the Wt1 gene eliminates outgrowth of the ureteric bud, but Gdnf has been identified as a target of Pax2, but not of Wt1. Using a novel system for microinjecting and electroporating plasmid expression constructs into murine organ cultures, it has been demonstrated that Vegfa expression in the mesenchyme is regulated by Wt1. Previous studies had identified a population of Flk1-expressing cells in the periphery of the induced mesenchyme, and adjacent to the stalk of the ureteric bud, and that Vegfa was able to stimulate growth of kidneys in organ culture. Here it is demonstrated that signaling through Flk1 is required to maintain expression of Pax2 in the mesenchyme of the early kidney, and for Pax2 to stimulate expression of Gdnf. However, once Gdnf stimulates branching of the ureteric bud, the Flk1-dependent angioblast signal is no longer required to maintain branching morphogenesis and induction of nephrons. Thus, this work demonstrates the presence of a second set of inductive events, involving the mesenchymal and angioblast populations, whereby Wt1-stimulated expression of Vegfa elicits an as-yet-unidentified signal from the angioblasts, which is required to stimulate the expression of Pax2 and Gdnf, which in turn elicits an inductive signal from the ureteric bud.

Animals↗

PubMed2005

Visualization-based discovery and analysis of genomic aberrations in microarray data.

BACKGROUND: Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data. RESULTS: We have developed ChARMView, a visualization and analysis system for guided discovery of chromosomal abnormalities from microarray data. Our system facilitates manual or automated discovery of aneuploidies through dynamic visualization and integrated statistical analysis. ChARMView can be used with array CGH and gene expression microarray data, and multiple experiments can be viewed and analyzed simultaneously. CONCLUSION: ChARMView is an effective and accurate visualization and analysis system for recognizing even small aneuploidies or subtle expression biases, identifying recurring aberrations in sets of experiments, and pinpointing functionally relevant copy number changes. ChARMView is freely available under the GNU GPL at http://function.princeton.edu/ChARMView.

Algorithms↗