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Cheng Li

Publications and source records attributed to Cheng Li.

At least 55 records · Page 3Linked to original sources
PubMed2004

In vitro study of cell-promoting multiple-armed peptides.

The purpose of this study was to compare the effectiveness of several linear and branch cell-binding peptides to promote cell growth in prosthetic vascular grafts. In this in vitro study, the peptides were covalently immobilized onto expanded polytetrafluoroethylene (ePTFE) vascular grafts. Cell-growth properties were studied using primary human umbilical vein endothelial cells (HUVECs) and primary human umbilical artery smooth muscle cells (HUASMCs). Linear peptides (P15 and P15') and multiple-armed peptides (MAP4-I and MAP4-II) were covalently bonded onto ePTFE grafts by an atmospheric plasma coating method. X-ray photoelectron spectroscopy and amino acid analysis were used to analyze the surface characteristics of the peptide-coated samples. Cell adhesion, proliferation, and morphology were evaluated by culturing HUVECs and HUASMCs onto the surfaces of different samples: ePTFE control, chemically activated ePTFE, P15-coated ePTFE, and MAP4-coated ePTFE. The cell culture experiments were repeated several times to obtain statistically reliable cell-growth data. Cell-growth data were statistically analyzed by the two-way statistical analysis of variance. The study showed that multiple-armed MAP4 peptides were significantly more effective in promoting endothelial cells than the structurally similar linear P15 peptides. There were 800% more HUVECs proliferated on the MAP4-coated ePTFE samples compared with the ePTFE control. MAP4 peptides were 80% more effective for promoting HUVECs than P15 peptides. In contrast, MAP4 peptides were significantly less effective for promoting HUASMCs than HUVECs. There were only about 100% more HUASMCs proliferated on the MAP4-coated ePTFE samples compared with the ePTFE control. MAP4 and P15 peptides had similar cell-promoting characteristics for SMCs.

Amino Acid Sequence↗
PubMed2004

Differential birefringence in Bragg gratings in multicore fiber under transverse stress.

We present experimental measurements of the peak splitting of the reflection spectra of fiber Bragg gratings as a result of birefringence induced by transverse loading of a multicore fiber. Measurements show that the splitting is a function of the applied load and the direction of the load relative to the azimuth of the fiber. A model for calculating the stress in the fiber that is due to an applied load is in good agreement with our experimental observations.

Journal Article↗
PubMed2004

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

Computational Biology↗
PubMed2004

A global expression-based analysis of the consequences of the t(4;14) translocation in myeloma.

PURPOSE: Our purpose in this report was to define genes and pathways dysregulated as a consequence of the t(4;14) in myeloma, and to gain insight into the downstream functional effects that may explain the different prognosis of this subgroup. EXPERIMENTAL DESIGN: Fibroblast growth factor receptor 3 (FGFR3) overexpression, the presence of immunoglobulin heavy chain-multiple myeloma SET domain (IgH-MMSET) fusion products and the identification of t(4;14) breakpoints were determined in a series of myeloma cases. Differentially expressed genes were identified between cases with (n = 5) and without (n = 24) a t(4;14) by using global gene expression analysis. RESULTS: Cases with a t(4;14) have a distinct expression pattern compared with other cases of myeloma. A total of 127 genes were identified as being differentially expressed including MMSET and cyclin D2, which have been previously reported as being associated with this translocation. Other important functional classes of genes include cell signaling, apoptosis and related genes, oncogenes, chromatin structure, and DNA repair genes. Interestingly, 25% of myeloma cases lacking evidence of this translocation had up-regulation of the MMSET transcript to the same level as cases with a translocation. CONCLUSIONS: t(4;14) cases form a distinct subgroup of myeloma cases with a unique gene signature that may account for their poor prognosis. A number of non-t(4;14) cases also express MMSET consistent with this gene playing a role in myeloma pathogenesis.

Alternative Splicing↗
PubMed2004

In vitro and in vivo activity of the maytansinoid immunoconjugate huN901-N2'-deacetyl-N2'-(3-mercapto-1-oxopropyl)-maytansine against CD56+ multiple myeloma cells.

HuN901 is a humanized monoclonal antibody that binds with high affinity to CD56, the neuronal cell adhesion molecule. HuN901 conjugated with the maytansinoid N(2')-deacetyl-N(2')-(3-mercapto-1-oxopropyl)-maytansine (DM1), a potent antimicrotubular cytotoxic agent, may provide targeted delivery of the drug to CD56 expressing tumors. Based on gene expression profiles of primary multiple myeloma (MM) cells showing expression of CD56 in 10 out of 15 patients (66.6%) and flow cytometric profiles of MM (CD38(bright)CD45(lo)) cells showing CD56 expression in 22 out of 28 patients (79%), we assessed the efficacy of huN901-DM1 for the treatment of MM. We first examined the in vitro cytotoxicity and specificity of huN901-DM1 on a panel of CD56(+) and CD56(-) MM cell lines, as well as a CD56(-) Waldenstrom's macroglobulinemia cell line. HuN901-DM1 treatment selectively decreased survival of CD56(+) MM cell lines and depleted CD56(+) MM cells from mixed cultures with a CD56(-) cell line or adherent bone marrow stromal cells. In vivo antitumor activity of huN901-DM1 was then studied in a tumor xenograft model using a CD56(+) OPM2 human MM cell line in SCID mice. We observed inhibition of serum paraprotein secretion, inhibition of tumor growth, and increase in survival of mice treated with huN901-DM1. Our data therefore demonstrate that huN901-DM1 has significant in vitro and in vivo antimyeloma activity at doses that are well tolerated in a murine model. Taken together, these data provide the framework for clinical trials of this agent to improve patient outcome in MM.

Animals↗
PubMed2004

Gene regulation and DNA damage in the ageing human brain.

The ageing of the human brain is a cause of cognitive decline in the elderly and the major risk factor for Alzheimer's disease. The time in life when brain ageing begins is undefined. Here we show that transcriptional profiling of the human frontal cortex from individuals ranging from 26 to 106 years of age defines a set of genes with reduced expression after age 40. These genes play central roles in synaptic plasticity, vesicular transport and mitochondrial function. This is followed by induction of stress response, antioxidant and DNA repair genes. DNA damage is markedly increased in the promoters of genes with reduced expression in the aged cortex. Moreover, these gene promoters are selectively damaged by oxidative stress in cultured human neurons, and show reduced base-excision DNA repair. Thus, DNA damage may reduce the expression of selectively vulnerable genes involved in learning, memory and neuronal survival, initiating a programme of brain ageing that starts early in adult life.

Adult↗
PubMed2004

Molecular diversity of astrocytes with implications for neurological disorders.

The astrocyte represents the most abundant yet least understood cell type of the CNS. Here, we use a stringent experimental strategy to molecularly define the astrocyte lineage by integrating microarray datasets across several in vitro model systems of astrocyte differentiation, primary astrocyte cultures, and various astrocyterich CNS structures. The intersection of astrocyte data sets, coupled with the application of nonastrocytic exclusion filters, yielded many astrocyte-specific genes possessing strikingly varied patterns of regional CNS expression. Annotation of these astrocyte-specific genes provides direct molecular documentation of the diverse physiological roles of the astrocyte lineage. This global perspective in the normal brain also provides a framework for how astrocytes may participate in the pathogenesis of common neurological disorders like Alzheimer's disease, Parkinson's disease, stroke, epilepsy, and primary brain tumors.

Animals↗
PubMed2004

Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.

Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however, limited by the paucity of genomic DNA available. Here we have tested the fidelity and genome representation of phi29 polymerase-based genome amplification (phi29MDA) using direct sequencing and high density oligonucleotide arrays probing >10,000 SNP alleles. Genome representation was comprehensive and estimated to be 99.82% complete, although six regions encompassing a maximum of 5.62 Mb failed to amplify. There was no degradation in the accuracy of SNP genotyping and, in direct sequencing experiments sampling 500,000 bp, the estimated error rate (9.5 x 10(-6)) was the same as in paired unamplified samples. The detection of cancer-associated loss of heterozygosity and copy number changes, including homozygous deletion and gene amplification, were similarly robust. These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis.

Alleles↗
PubMed2004

An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays.

Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic representations of breast and lung carcinoma cell line and lung tumor DNA to SNP arrays, and measuring locus-specific hybridization intensity, we detected both known and novel genomic amplifications and homozygous deletions in these cancer samples. Moreover, by combining genotyping with SNP quantitation, we could distinguish loss of heterozygosity events caused by hemizygous deletion from those that occur by copy-neutral events. The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis.

Alleles↗
PubMed2004

High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines.

Chromosomal loss of heterozygosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. Hybridization to single-nucleotide polymorphism (SNP) arrays is an efficient method to detect genome-wide cancer LOH. Here, we survey LOH patterns in a panel of 33 human lung cancer cell lines using SNP array hybridization containing 1500 SNPs. We compared the LOH patterns generated by SNP array hybridization to those previously obtained by 399 microsatellite markers and find a high degree of concordance between the two methods. A novel informatics platform, dChipSNP, was used to perform hierarchical tumor clustering based on genome-wide LOH patterns. We demonstrate that this method can separate non-small-cell and small-cell lung cancer samples based on their shared LOH. Furthermore, we analysed seven human lung cancer cell lines using a novel 10 000 SNP array and demonstrate that this is an efficient and reliable method of high-density allelotyping. Using this array, we identified small regions of LOH that were not detected by lower density SNP arrays or by standard microsatellite marker panels.

Biomarkers, Tumor↗
PubMed2004

dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.

MOTIVATION: Oligonucleotide microarrays allow genotyping of thousands of single-nucleotide polymorphisms (SNPs) in parallel. Recently, this technology has been applied to loss-of-heterozygosity (LOH) analysis of paired normal and tumor samples. However, methods and software for analyzing such data are not fully developed. RESULT: Here, we report automated methods for pooling SNP array replicates to make LOH calls, visualizing SNP and LOH data along chromosomes in the context of genes and cytobands, making statistical inference to identify shared LOH regions, clustering samples based on LOH profiles and correlating the clustering results to clinical variables. Application of these methods to prostate and breast cancer datasets generates biologically important results. AVAILABILITY: The software module dChipSNP implementing these methods is available at http://biosun1.harvard.edu/complab/dchip/snp/ SUPPLEMENTARY INFORMATION: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart.

Algorithms↗
PubMed2004

Telomerase inhibition and cell growth arrest after telomestatin treatment in multiple myeloma.

PURPOSE: The aim of this study was to test the efficacy of telomestatin, an intramolecular G-quadruplex intercalating drug with specificity for telomeric sequences, as a potential therapeutic agent for multiple myeloma. EXPERIMENTAL DESIGN: We treated ARD, ARP, and MM1S myeloma cells with various concentrations of telomestatin for 7 days and evaluated for telomerase activity. Myeloma cells were treated with the minimal effective telomestatin concentration for 3-5 weeks. Every 7(th) day the fraction of live cells was determined by trypan blue exclusion, aliquots of cells were removed for various molecular assays, and the remaining cells were replated at the same cell number and at the same concentration of telomestatin. Telomere length, apoptosis, and gene expression changes were monitored as described in detail in "Materials and Methods." RESULTS: Telomestatin treatment led to inhibition of telomerase activity, reduction in telomere length, and apoptotic cell death in ARD, MM1S, and ARP myeloma cells. Gene expression profile after 1 and 7 days of telomestatin treatment revealed >/==" BORDER="0">2-fold change in only 6 (0.027%) and 51 (0.23%) of 33,000 genes surveyed, respectively. No changes were seen in expression of genes involved in cell cycle, apoptosis, DNA repair, or recombination. CONCLUSIONS: These results demonstrate that telomestatin exerts its antiproliferative and proapoptotic effects in myeloma cells via inhibition of telomerase and subsequent reduction in telomere length. We conclude that telomerase is an important potential therapeutic target for multiple myeloma therapy, and G-quadruplex interacting agents with specificity for binding to telomeric sequences can be important agents for additional evaluation.

Apoptosis↗
PubMed2004

Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers.

Gene expression array profiles identify subclasses of breast cancers with different clinical outcomes and different molecular features. The present study attempted to correlate genomic alterations (loss of heterozygosity; LOH) with subclasses of breast cancers having distinct gene expression signatures. Hierarchical clustering of expression array data from 89 invasive breast cancers identified four major expression subclasses. Thirty-four of these cases representative of the four subclasses were microdissected and allelotyped using genome-wide single nucleotide polymorphism detection arrays (Affymetrix, Inc.). LOH was determined by comparing tumor and normal single nucleotide polymorphism allelotypes. A newly developed statistical tool was used to determine the chromosomal regions of frequent LOH. We found that breast cancers were highly heterogeneous, with the proportion of LOH ranging widely from 0.3% to >60% of heterozygous markers. The most common sites of LOH were on 17p, 17q, 16q, 11q, and 14q, sites reported in previous LOH studies. Signature LOH events were discovered in certain expression subclasses. Unique regions of LOH on 5q and 4p marked a subclass of breast cancers with "basal-like" expression profiles, distinct from other subclasses. LOH on 1p and 16q occurred preferentially in a subclass of estrogen receptor-positive breast cancers. Finding unique LOH patterns in different groups of breast cancer, in part defined by expression signatures, adds confidence to newer schemes of molecular classification. Furthermore, exclusive association between biological subclasses and restricted LOH events provides rationale to search for targeted genes.

Breast Neoplasms↗
PubMed2004

Temporal gene expression following prosthetic arterial grafting.

BACKGROUND: Following prosthetic arterial grafting, cytokines and growth factors released within the perianastomotic tissues stimulate smooth muscle cell proliferation and matrix production. While much in vitro work has characterized this response, little understanding exists regarding the sequential up- and down-regulation of genes following prosthetic arterial grafting. This study evaluates temporal gene expression at the distal anastomosis of prosthetic arterial grafts using microarray analysis. METHODS: Expanded polytetrafluoroethylene (ePTFE) carotid interposition grafts (n = 12) were surgically implanted into mongrel dogs. Distal anastomotic segments were harvested at 7, 14, 30, or 60 days. Contralateral carotid artery served as control. Total RNA was isolated from the anastomotic tissue and paired controls. Samples were probed with oligonucleotide microarrays consisting of approximately 10000 human genes to analyze differential gene expression at each time point. RESULTS: Forty-nine genes were found to be up-regulated and 37 genes were found to be down-regulated at various time points. Six genes were found to be consistently up-regulated at all time intervals, including collagen type 1 alpha-1 and alpha-2, 80K-L protein (MARCKS), and osteopontin. Six genes were found to be consistently down-regulated, including smoothelin and tropomyosin 2. RT-PCR and immunohistochemistry confirmed the microarray data. CONCLUSIONS: This study uses microarray analysis to identify genes that were temporally up- and down-regulated after prosthetic arterial grafting. Genes with similar patterns of expression have been identified, providing insights into related cellular pathways that may result in the formation of anastomotic intimal hyperplasia.

Anastomosis, Surgical↗
PubMed2004

Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis.

OBJECTIVE: Autologous vein is the conduit of choice for small artery reconstruction. Despite excellent patency, these conduits undergo remodeling over time. The purpose of this study was to identify temporal gene expression in vein grafts versus control veins through microarray analysis. METHOD: Cephalic vein grafts (n = 12) were used to bypass femoral arteries in canines. Vein grafts were harvested after 1, 7, 14, and 30 days. Normal contralateral cephalic vein served as control. Total RNA was isolated; its quantity and quality were confirmed with spectrophotometry and gel electrophoresis. Affymetrix U133A GeneChips, comprising approximately 15,000 genes, were used to analyze differential gene expression at each time point. Statistical analysis was performed with Affymetrix and dChip software to identify consistently upregulated and downregulated genes. Real-time, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to validate microarray data. RESULTS: Statistical analysis revealed that 49 genes were consistently upregulated and 31 genes were consistently downregulated in all three animals at various time points. qRT-PCR to quantitatively assess messenger RNA expression was performed on specific genes to validate the microarray data. Immunohistochemistry to qualitatively assess protein expression was used for further validation. Hierarchical clustering with dChip identified additional genes with similar temporal or functional expression patterns. CONCLUSIONS: This is the first study to use microarray analysis with confirmatory qRT-PCR to identify altered genes after vein bypass grafting. Oligonucleotide microarrays and hierarchical clustering are powerful tools to generate hypotheses as the basis for additional research on gene expression in vein graft remodeling. Ultimately, identification of a temporal sequence of differential gene expression may provide insights not preferred into the molecular mechanisms of vein graft remodeling, but also into the pathways leading to intimal hyperplasia.

Animals↗
PubMed2004

Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K array.

Currently, most analytical methods assume all observed genotypes are correct; however, it is clear that errors may reduce statistical power or bias inference in genetic studies. We propose procedures for estimating error rate in genetic analysis and apply them to study the GeneChip Mapping 10K array, which is a technology that has recently become available and allows researchers to survey over 10,000 SNPs in a single assay. We employed a strategy to estimate the genotype error rate in pedigree data. First, the "dose-response" reference curve between error rate and the observable error number were derived by simulation, conditional on given pedigree structures and genotypes. Second, the error rate was estimated by calibrating the number of observed errors in real data to the reference curve. We evaluated the performance of this method by simulation study and applied it to a data set of 30 pedigrees genotyped using the GeneChip Mapping 10K array. This method performed favorably in all scenarios we surveyed. The dose-response reference curve was monotone and almost linear with a large slope. The method was able to estimate accurately the error rate under various pedigree structures and error models and under heterogeneous error rates. Using this method, we found that the average genotyping error rate of the GeneChip Mapping 10K array was about 0.1%. Our method provides a quick and unbiased solution to address the genotype error rate in pedigree data. It behaves well in a wide range of settings and can be easily applied in other genetic projects. The robust estimation of genotyping error rate allows us to estimate power and sample size and conduct unbiased genetic tests. The GeneChip Mapping 10K array has a low overall error rate, which is consistent with the results obtained from alternative genotyping assays.

Computer Simulation↗
PubMed2004

Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K array.

Population-based association design is often compromised by false or nonreplicable findings, partially due to population stratification. Genomic control (GC) approaches were proposed to detect and adjust for this confounder. To date, the performance of this strategy has not been extensively evaluated on real data. More than 10 000 single-nucleotide polymorphisms (SNPs) were genotyped on subjects from four populations (including an Asian, an African-American and two Caucasian populations) using GeneChip Mapping 10 K array. On these data, we tested the performance of two GC approaches in different scenarios including various numbers of GC markers and different degrees of population stratification. In the scenario of substantial population stratification, both GC approaches are sensitive using only 20-50 random SNPs, and the mixed subjects can be separated into homogeneous subgroups. In the scenario of moderate stratification, both GC approaches have poor sensitivities. However, the bias in association test can still be corrected even when no statistical significant population stratification is detected. We conducted extensive benchmark analyses on GC approaches using SNPs over the whole human genome. We found GC method can cluster subjects to homogeneous subgroups if there is a substantial difference in genetic background. The inflation factor, estimated by GC markers, can effectively adjust for the confounding effect of population stratification regardless of its extent. We also suggest that as low as 50 random SNPs with heterozygosity >40% should be sufficient as genomic controls.

Chromosome Mapping↗