Biomedical subjects

Dung-Tsa Chen

Publications and source records attributed to Dung-Tsa Chen.

14 recordsLinked to original sources

PubMed2005

Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates.

MOTIVATION: One major area of interest in analyzing oligonucleotide gene array data is identifying differentially expressed genes. A challenge to biostatisticians is to develop an approach to summarizing probe-level information that adequately reflects the true expression level while accounting for probe variation, chip variation and interaction effects. Various statistical tools, such as MAS and RMA, have been developed to address this issue. In these approaches, the probe level expression data are summarized into gene level data, which are then used for downstream statistical analysis. Since probe variation is often larger than chip variation and there is also a potential interaction effect between probe affinity and treatment effect, strategies such as a gene level analysis, may not be optimal. In this study, we propose a procedure to analyze probe level data for selecting differentially expressed genes under two treatment conditions (groups) with a small number of replicates. The probe level discrepancy between two groups can be measured by a difference of the percentiles of probe perfect-match (PM) ranks or of probe PM weighted ranks. The difference is then compared with a pre-specified threshold to determine differentially expressed genes. The probe level approach takes into account non-homogenous treatment effects and reduces possible cross-hybridization effects across a set of probes. RESULTS: The proposed approach is compared with MAS and RMA using two benchmark gene array datasets. Positive predictivity and sensitivity are used for evaluation. Results show the proposed approach has higher positive predictivity and higher sensitivity. AVAILABILITY: Available on request from the authors. CONTACT: dtchen@uab.edu.

Algorithms↗

PubMed2005

Safety and immunogenicity of adenovirus-vectored nasal and epicutaneous influenza vaccines in humans.

The increasing number and density of the human population, the emergence of lethal influenza strains, and the potential use of designer influenza virus as a bioweapon, collectively highlight a critical need for more rapid production of influenza vaccines and less invasive means of delivery. We have developed a nonreplicative adenovirus-vectored influenza vaccine that can be produced without the prerequisite of growing influenza virus. This new class of vaccines can be administered as a nasal spray or skin patch by personnel without medical training. We report here that adenovirus-vectored nasal and epicutaneous influenza vaccines were well tolerated by human volunteers. The nasal vaccine was more potent than its epicutaneous counterpart under the adjuvant-free experimental condition. These results provide the foundation for further human testing of needleless vectored vaccines as promising alternatives to current vaccines.

Adenoviridae↗

PubMed2004

Sample size for gene expression microarray experiments.

MOTIVATION: Microarray experiments often involve hundreds or thousands of genes. In a typical experiment, only a fraction of genes are expected to be differentially expressed; in addition, the measured intensities among different genes may be correlated. Depending on the experimental objectives, sample size calculations can be based on one of the three specified measures: sensitivity, true discovery and accuracy rates. The sample size problem is formulated as: the number of arrays needed in order to achieve the desired fraction of the specified measure at the desired family-wise power at the given type I error and (standardized) effect size. RESULTS: We present a general approach for estimating sample size under independent and equally correlated models using binomial and beta-binomial models, respectively. The sample sizes needed for a two-sample z-test are computed; the computed theoretical numbers agree well with the Monte Carlo simulation results. But, under more general correlation structures, the beta-binomial model can underestimate the needed samples by about 1-5 arrays. CONTACT: jchen@nctr.fda.gov.

Algorithms↗

PubMed2004

Laboratory tests to determine the cause of hypokalemia and paralysis.

BACKGROUND: Hypokalemia and paralysis may be due to a short-term shift of potassium into cells in hypokalemic periodic paralysis (HPP) or due to a large deficit of potassium in non-HPP. Failure to make a distinction between HPP and non-HPP may lead to improper management. Therefore, we evaluated the diagnostic value of spot urine tests in patients with hypokalemia and paralysis during 3 years. METHODS: Before therapy, the urine potassium concentration, potassium-creatinine ratio, and transtubular potassium concentration gradient were determined in a second voided urine sample. RESULTS: Forty-three patients with hypokalemia and paralysis were identified: 30 had HPP and 13 had non-HPP. There was no significant difference in the plasma potassium or bicarbonate concentrations and in the pH of arterial blood between the 2 groups. All but 2 patients in the non-HPP group had urine potassium concentration values less than 20 mmol/L. Although the potassium concentration was significantly lower in the HPP group, there was some overlap. In contrast, the transtubular potassium concentration gradient and potassium-creatinine ratio differentiated patients with HPP vs non-HPP. Although only a mean +/- SD of 63 +/- 36 mmol of potassium chloride was administered in the patients with HPP, rebound hyperkalemia (>5 mmol/L) occurred in 19 (63%) of these 30 patients. CONCLUSIONS: Calculating the transtubular potassium concentration gradient and potassium-creatinine ratio provided a simple and reliable test to distinguish HPP from non-HPP. Minimal potassium chloride supplementation should be given to avoid rebound hyperkalemia in patients with HPP.

Adult↗

PubMed2004

Gene selection for oligonucleotide array: an approach using PM probe level data.

MOTIVATION: Analysis of oligonucleotide array data, especially to select genes of interest, is a highly challenging task because of the large volume of information and various experimental factors. Moreover, interaction effect (i.e. expression changes depend on probe effects) complicates the analysis because current methods often use an additive model to analyze data. We propose an approach to address these issues with the aim of producing a more reliable selection of differentially expressed genes. The approach uses the rank for normalization, employs the percentile-range to measure expression variation, and applies various filters to monitor expression changes. RESULTS: We compare our approach with MAS and Dchip models. A data set from an angiogenesis study is used for illustration. Results show that our approach performs better than other methods either in identification of the positive control gene or in PCR confirmatory tests. In addition, the invariant set of genes in our approach provides an efficient way for normalization.

Algorithms↗

PubMed2004

A novel time-course cDNA microarray analysis method identifies genes associated with the development of cisplatin resistance.

In recent years, most cDNA microarray studies of chemotherapeutic drug resistance have not considered the temporal pattern of gene expression. The objective of this study was to examine systematically changes in gene expression of NCI-H226 and NCI-H2170 lung cancer cells treated weekly with IC10 doses of cisplatin. NCI-H226 lung cancer cells were treated weekly with an IC10 dose of cisplatin. Candidate genes with a fold change of 2.0 or more were identified from this study. A second experiment was conducted by exposing NCI-H2170 cells to cisplatin doses that were increased in week 4 and decreased in week 5. Overall, 44 genes were differentially expressed in both the NCI-H226 and NCI-H2170 cell lines. In the NCI-H2170 cell line, 24 genes had a twofold gene expression change from weeks 3 to 4. Real-time PCR found a significant correlation of the gene expression changes for seven genes of interest. This small time-ordered series identified novel genes associated with cisplatin resistance. This kind of analysis should be viewed as a first step towards building gene-regulatory networks.

Antineoplastic Agents↗

PubMed2004

Clinical signs and symptoms in a large hereditary spastic paraparesis pedigree with a novel spastin mutation.

The most common form of autosomal dominant hereditary spastic paraparesis (HSP), SPG4, is caused by mutations in the spastin gene on chromosome 2p. This disease is characterized by intra- and interfamilial phenotypic variation. To determine the predictive values of clinical signs and symptoms in SPG4, we examined 43 members of a large pedigree with autosomal dominant HSP. We then identified the genetic etiology of the disorder in this family, a novel nonsense mutation in exon 1 of spastin, carried by 24 of the examined family members. The best clinical predictors of positive gene status were the presence of hyperreflexia in the lower extremities, >2 beats of ankle clonus, pes cavus, bladder symptoms and increased tone in the legs. The mean age of onset was 32.2 +/- 7.4 years, but the age of onset was earlier in children from 10 of 12 child-parent gene-positive pairs, with a mean difference of 10.8 +/- 3.3 years. The finding of leg weakness was especially common in older-onset affected family member with leg hyperreflexia. These results suggest that specific clinical signs and symptoms may be of value in differentiating individuals affected with SPG4 from family members with nonspecific neurological findings.

Adenosine Triphosphatases↗

PubMed2004

A graphical approach for quality control of oligonucleotide array data.

In studies of quality control of oligonucleotide array data, one objective is to screen out ineligible arrays. Incomparable arrays (one type of ineligible arrays) arise as the experimental factors are poorly controlled. Due to the high volume of data in gene arrays, examination of array comparability requires special treatments to reduce data dimension without distortion. This paper proposes a graphical approach to address these issues. The proposed approach uses percentile methods to group data, and applies the 2D image plot to display the grouped data. Moreover, an invariant band is employed to quantify degrees of array comparability. We use two publicly available oligonucleotide array datasets from Affymetrix GeneChip System for evaluation. The results demonstrate the utility of our approach to examine data quality and also as an exploratory tool to verify differentially expressed genes selected by vigorous statistical methods.

Algorithms↗

PubMed2004

Effect of methotrexate therapy on bone mineral density and body composition in rat adjuvant arthritis.

OBJECTIVE: To test whether methotrexate (MTX) therapy of rat adjuvant arthritis (AA) prevents loss of bone mineral density (BMD) and loss of adipose and lean body mass compared to pair-fed controls with untreated rat AA (positive controls) and rats without AA (negative controls). METHODS: AA was induced by a Mycobacterium butyricum injection at the base of the tail of 5-week-old female Lewis rats. The MTX-treated group was injected with adjuvant and then treated twice weekly with MTX (1.0 mg/kg/wk intraperitoneally). To control for the effects of AA on appetite and weight, food given to control animals and MTX-treated rats with AA was limited to that consumed by rats with untreated AA. At 42 days post-adjuvant injection, the animals were sacrificed and tibial BMD was measured. Body composition was analyzed for percentage fat, protein, ash, and water. RESULTS: There was no difference in ankle edema score or ankle width between the negative controls and MTX-treated group at necropsy. BMD was significantly higher in the negative controls versus positive controls and MTX-treated and in MTX-treated versus positive controls. There was significantly less body fat and protein and greater body water in the positive controls and MTX group compared to the negative controls. CONCLUSION: MTX prevents loss of BMD in the tibia in the rat AA model compared to positive controls. While MTX is effective in lowering inflammation in rat AA, there are still significant losses in BMD and body composition, which may have implications for rheumatoid arthritis.

Animals↗

PubMed2003

Detecting the expression of human endogenous retrovirus E envelope transcripts in human prostate adenocarcinoma.

BACKGROUND: The expression of human endogenous retrovirus (HERV) mRNA and proteins was associated recently with diseases that include human malignancies. The authors report that, in the current study, transcripts encoding the envelope region of an HERV family, HERV-E, were expressed in human prostate carcinoma. METHODS: RNA was isolated from various prostate tissues and was tested for the expression of various HERV envelope (env) genes by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis, RNA in situ hybridization (ISH), and Northern blot analysis. Variants of HERV that appeared in prostate carcinoma tissues were sequenced, and HERV-E was expressed in prokaryotic and eukaryotic systems. RESULTS: In the current study, the authors found that the mRNA of the env gene of one particular family of HERVs, HERV-E, was expressed in some prostate carcinoma tissues (38.8% positive; n = 49 specimens) but not in normal prostate tissues using RT-PCR, RNA ISH, and Northern blot assays. The expression of HERV-E transcripts in prostate tumor epithelial cells was confirmed further by ISH using an HERV-E specific antisense probe. Approximately 50% of the cDNA of HERV-E obtained from prostate carcinoma specimens contained no stop codon and expressed proteins in prokaryotic or eukaryotic expression systems. Furthermore, the expression of both HERV-E and ERV3 (another class of HERV) was detected in the same prostate carcinoma tissues. CONCLUSIONS: The expression and distribution of multiple HERV-E endogenous retroviral elements in prostate carcinoma, but not in normal control specimens, suggests that they may serve as novel tumor markers for the early diagnosis and immunotherapy of patients with prostate carcinoma.

Blotting, Northern↗

PubMed2003

Antitumor activity of the 16-kDa prolactin fragment in prostate cancer.

The 16-kDa prolactin (PRL), derived from the proteolytic cleavage of wild-type 23-kDa PRL, has been shown to have antiangiogenic activity. Such an antiangiogenic activity may have an effect on tumor growth in vivo. Here we examined the effect of 23-kDa and 16-kDa PRL on tumor growth, and the potential of using recombinant 16-kDa human PRL for prostate cancer therapy. The effects of 23-kDa PRL and 16-kDa PRL on the tumorigenicity of prostate cancer cells in vivo were studied. Using an adenovirus transfer vector to achieve high efficiency 23-kDa and 16-kDa PRL transfection in DU145 and PC-3 human prostate carcinoma cell lines, we demonstrated that expression of 16-kDa PRL in the prostate cancer cells markedly reduced their ability to form tumors in a xenograft animal model. These studies established that the 16-kDa PRL has antitumor activity in vivo, presumably as a result of its antiangiogenic effect. Interestingly, 23-kDa PRL showed a weak and transient suppression of prostate tumor growth. The weak antitumor activity of 23-kDa PRL may be because of the production of 16-kDa PRL from 23-kDa PRL by the tumor cells. Thus, the apparent effect of 23-kDa PRL on the growth of DU145 and PC-3 cells in vivo may result from the combined effects of 23-kDa PRL and 16-kDa PRL. These results suggest that the 16-kDa PRL has potential as a treatment agent in prostate cancer.

Adenoviridae↗

PubMedDate not supplied

Treatment of refractory urothelial carcinoma with alternating paclitaxel, methotrexate, cisplatin (TMP) and 5-fluorouracil, alpha-interferon, cisplatin (FAP).

We assessed the activity and safety of a biochemotherapy regimen in which courses of paclitaxel, methotrexate, and cisplatin were alternated with courses of 5-fluorouracil, alpha-interferon, and cisplatin in the treatment of refractory urothelial carcinoma. Forty patients were enrolled in the study. In the phase I portion, 15 patients were treated according to an escalating dosage regimen designed to determine the maximum tolerated dose. A total of 30 patients received treatment according to the maximum tolerated dose regimen: methotrexate (30 mg/m(2)) given iv on days 1 and 22; paclitaxel (175 mg/m(2)) given iv over 3 h on day 1; cisplatin (70 and 25 mg/m(2)) administered iv on days 1 and 22, respectively; 5-fluorouracil (400 mg/m(2)) given iv by continuous infusion daily for 5 days beginning on day 22; and alpha-interferon (4 mIU/m(2)) given SC daily for 5 days simultaneously with the 5-fluorouracil infusions. The regimen was repeated at 42-day intervals. The 40 treated patients had an overall response rate of 43%, a complete response rate of 18%, and a median survival time of 44 weeks. Most of the toxic effects were hematologic: Grade 4 neutropenia occurred in 30% of patients (12 patients) and Grade 3 thrombocytopenia in 20% (8 patients). Even though this alternating biochemotherapy regimen was active for patients with refractory urothelial carcinoma, its activity was not better than that of certain single cytotoxic agents. Furthermore, the complicated dosing schedule and toxic effects of the regimen precluded its routine use in the treatment of urothelial carcinoma.

Aged↗

PubMedDate not supplied

Synthesis and biological evaluation of paclitaxel-C225 conjugate as a model for targeted drug delivery.

Tumor-targeted drug delivery is an attractive strategy in cancer treatment. We have previously reported a paclitaxel model conjugate using a bombesin receptor-recognizing peptide in which the drug cytotoxicity against H1299 human nonsmall cell lung cancer was enhanced compared to unconjugated taxol. In an effort to expand the development of tumor-recognizing taxanes, paclitaxel (PTX, taxol) was conjugated to the anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibody (MAb) Erbitux (C225) to serve as a model MAb-mediated drug delivery compound. Thus, paclitaxel was derivatized at its 2'-hydroxy function by introduction of a succinate linker, and the carboxyl group of the latter was covalently attached to C225 through amide bond formation. The final product conjugate (PTXC225) was analyzed mass spectrometrically for assessment of the drug-to-antibody ratios. Cytotoxicity screening of the drug-antibody conjugate against A431, UM-SCC-1, and UM-SCC-6 cells indicated an enhancement in cytocidal effect of paclitaxel as compared to those of the free drug, the intact antibody, and a physical mixture of the two (the controls). In A431 cells, the conjugate showed 25.2% +/- 2.2% of apoptosis induction as compared to little or no apoptosis caused by the controls. Biodistribution analysis of the PTXC225 in tumor-implanted nude mice and a tyrosine-kinase assay showed that conjugation of the drug did not interfere with the immunoreactivity of the antibody. The 24-h tumor uptake of C225 and PTXC225 were 11.7% +/- 6.0% and 7.1% +/- 3.6% of the injected dose per gram of tissue (%ID/g), respectively, which were not significantly different. Also, in A431-implanted nude mice, the conjugate and C225 showed tumor growth inhibition effects of 57.2% and 41.2%, respectively, against a saline-treated control, which were not significantly different from each other. This lack of difference in the in vivo antitumor activity of the MAb-delivered drug and free PTX may be due to either a relatively low dose of the antibody-delivered drug (346 microg/kg), or an untimely release of it, or both. The tumor growth inhibition pattern of the conjugate, however, was identical to that of C225, indicating that the attachment of PTX did not affect the antigen-binding and growth inhibitory features of the MAb. These preliminary results demonstrate the potential of tumor-targeted delivery of taxol as a promising strategy in cancer treatment and warrant further work to develop more suitable drug-MAb linkers as well as improved dosage and treatment protocols.

Algorithms↗

PubMedDate not supplied

Effectiveness of multiple internal standards: deuterated analogues of methylenedioxymethamphetamine, methylenedioxyamphetamine, methamphetamine, and amphetamine.

With the increasing abuse of methylenedioxymethamphetamine (MDMA) thereby requiring analysis, we have undertaken a systematic evaluation on parameters associated with the analysis of MDMA and related compounds, including methylenedioxyamphetamine (MDA), methamphetamine (MA), and amphetamine (AM). Parameters studied included three solid-phase adsorbents, five derivatization reagents, and four deuterated internal standards (IS). This report examines whether differences in quantitation data derived from the use of four ISs (one for each analyte) and two ISs (one for AM and MA, one for MDA and MDMA) are statistically significant. Two types of samples were included in this study. The first type (Type I) included four replicate sets of standard solutions prepared in urine matrix. All analytes (AM, MA, MDA, and MDMA) were included in all samples, and these analytes' concentrations in each set were at five levels (100, 250, 500, 1000, and 2000 ng/mL). Four deuterated analogues (MA-d(8), AM-d(8), MDMA-d(5), and MDA-d(5)) at 500 ng/mL were also included in all solutions. The second type of samples (Type II) included 25 case urine specimens. Most of these specimens contained MA/AM and/or MDMA/MDA. The specific objective of this study is to determine whether the 4-IS approach can indeed generate better quantitative data than a less-costly 2-IS. For Type I samples, where the true concentrations of the analytes are known, two-sample t-test is adapted to examine whether the two sets of prediction errors (i.e., known concentration minus calculated concentration) resulting from the 4-IS and the 2-IS approaches are statistically different. For Type II samples, where the analytes' true concentrations are unknown, one-sample t-test was adapted to determine whether the difference of the quantitation results derived from the 4-IS and the 2-IS approaches is statistically significant. Statistical analysis of quantitation data derived from Types I and II samples indicates that differences in MDA and MDMA concentrations resulting from the use of one (MDA-d(5) or MDMA-d(5)) or two (MDA-d(5) and MDMA-d(5)) are statistically nonsignificant. On the other hand, similar analysis on data derived from Type I samples indicate the use of the analytes' respective deuterated analogues as the ISs appear to generate better quantitative data for AM and MA.

3,4-Methylenedioxyamphetamine↗