Biomedical subjects

William D Shannon

Publications and source records attributed to William D Shannon.

13 recordsLinked to original sources

PubMed2006

A high-resolution map of segmental DNA copy number variation in the mouse genome.

Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.

Animals↗

PubMed2006

Effect of yearly mass drug administration with diethylcarbamazine and albendazole on bancroftian filariasis in Egypt: a comprehensive assessment.

BACKGROUND: Egypt was one of the first countries to implement a national programme to eliminate lymphatic filariasis based on WHO's strategy of repeated rounds of mass drug administration (MDA) with diethylcarbamazine and albendazole (target population, 2.5 million in 181 localities). We assessed the effect of five yearly rounds of MDA on filariasis in four sentinel villages in Egypt. METHODS: We studied two areas with different infection rates before MDA: the Qalubyia study area had a low infection rate because of previous treatment with diethylcarbamazine; this was typical of most filariasis-endemic villages in Egypt before MDA. The Giza study area had a high baseline infection rate. We undertook repeated surveys in villages for treatment compliance and tests for microfilaraemia and circulating filarial antigenaemia, antibodies to filarial antigen Bm14 in schoolchildren, and infections in indoor-resting mosquitoes (assessed by PCR). FINDINGS: MDA compliance rates were excellent (>80%). In Giza after MDA, prevalence rates of microfilaraemia and circulating filarial antigenaemia fell from 11.5% to 1.2%, and from 19.0% to 4.8%, respectively (p<0.0001). Corresponding rates in Qalubyia fell from 3.1% to 0% and 13.6% to 3.1%, respectively (p<0.0001). Rates of antifilarial antibody and circulating filarial antigenaemia in schoolchildren (aged about 7-8 years), fell from 18.3% to 0.2% (p<0.0001) and from 10.0% to 0.4% (p<0.0001) in Giza, respectively, and from 1.7% to 0% and 1.7% to 0% (both p=0.13) in Qalubyia, respectively. Mosquito infection rates fell from 3.07% (95% CI 2.38-3.88) to 0.19% (0.08-0.38) in Giza and from 4.37% (3.07-5.99) to 0% (0-0.05) in Qalubyia. INTERPRETATION: MDA greatly affects variables related to infection (microfilaraemia and circulating filarial antigenaemia prevalence rates) and transmission (antifilarial antibodies in young children and mosquito infection rates). Our results suggest that after five rounds of MDA filariasis is likely to have been eliminated in most endemic localities in Egypt.

Albendazole↗

PubMed2005

Variance in the expression of 5-Fluorouracil pathway genes in colorectal cancer.

Although colorectal cancer has the third highest cancer mortality rate, the treatment remains far from optimized with patients showing variable responses to standard treatment. Molecular differences in pharmacologically relevant genes may contribute to the variability in response. This study used Taqman PCR to investigate the expression of 24 5-fluorouracil (5-FU) pathway genes in colorectal cancer using paired nontumor and tumor sample from 52 patients with Dukes' C colon cancer. In comparing tumor versus nonmalignant tissue, 14 of the 24 genes showed significant variation in gene expression. For 11 of these same genes (FPGS, DHFR, GGH, NME1, NME2, RRM2, UMPH2, UNG, UMPS, TP53, and TK1), a significant proportion of the patients showed an over expression of the particular gene in tumor tissue with a tumor-to-nonmalignant (T/N) ratio >1.2, whereas one gene (DPYD) showed the converse with a large number of patients showing a lower expression in the tumor tissue (T/N < 0.8). Multiple gene correlations for the genes of the 5-FU pathway were found with the Spearman rank correlation of >0.6 (all P > 0.001), suggesting possible coregulation mechanisms. Hierarchical clustering analysis created at least three groups of genes, which were consistent with groupings by the other statistical methods. Additionally, the hierarchical clustering showed two distinct groups of patients based on their gene expression. These variations in gene expression could provide valuable insights for optimizing treatment selection for patients with colorectal cancer.

Adult↗

PubMed2005

Gene expression profiling of the irinotecan pathway in colorectal cancer.

The exact mechanism responsible for large variation of response to chemotherapy remains unclear. This study profiled the gene expression for the entire irinotecan pathway to provide insights into individualized cancer therapy. The RNA expressions of 24 irinotecan pathway genes were measured in paired tumor and normal tissues from 52 patients with Dukes' C colorectal cancer using a real-time quantitative reverse transcription-PCR assay. The relative expression levels across the 24 pathway genes varied considerably, with a 441-fold range from highest to lowest expression levels for the tumor tissues and a 934-fold range for the normal tissues. Interpatient variability was also quite large, with a 33.6 median fold change in the tumor tissue genes and a 30.1 median fold change in the normal tissue genes. Six of the 24 irinotecan pathway genes had dramatically lower expression levels in the tumor samples than did the genes in the normal tissues (median range, 1.28-4.39 folds; P = 0.001-0.029). Eight genes had significantly higher levels (median range, 1.35-2.42 folds; P = 0.001-0.011). Using hierarchical clustering, three gene clusters and three patient groups were observed with high similarity indices by the RNA expressions in colorectal tumors. The three patient groups had no unique clinical pathologic features but could be differentiated by the statistically significant differences in RNA expression level of seven genes. Our study indicates that gene expression profiling could be valuable for predicting tumor response to chemotherapy and for tailoring therapy to individual cancer patients.

Antineoplastic Agents, Phytogenic↗

PubMed2005

Delirium as detected by the CAM-ICU predicts restraint use among mechanically ventilated medical patients.

OBJECTIVE: The first goal of this investigation was to identify individuals with delirium defined by the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU) among medical patients with respiratory failure. Our second goal was to compare clinical interventions including use of continuous sedation infusions, the number of ventilator-free days, ICU length of stay, hospital mortality, and use of physical restraints in mechanically ventilated patients with and without delirium. DESIGN: A prospective, single-center, observational cohort study. SETTING: The medical intensive care unit (19 beds) of an urban teaching hospital. PATIENTS: Adult, intubated, and mechanically ventilated patients. INTERVENTIONS: Daily evaluation with the CAM-ICU, outcomes assessment, and prospective data collection. MEASUREMENTS AND MAIN RESULTS: Among 93 patients evaluated using the CAM-ICU, 44 patients (47%) developed delirium (CAM-ICU+) for >/=1 day while in the intensive care unit. Twenty-two patients (24%) had no episodes of delirium recorded (CAM-ICU-), and 27 (29%) remained comatose until extubation or death. A statistically greater number of patients with delirium (CAM-ICU+) received continuous infusions of midazolam (59% vs. 32%, p < .05) or fentanyl (57% vs. 32%, p < .05) and physical soft-limb restraints (77% vs. 50%, p < .05) compared with patients without delirium (CAM-ICU-). CONCLUSIONS: The identification of delirium using the CAM-ICU was associated with greater use of continuous sedation infusions and physical restraints. Additional studies are required to determine how the use of these specific interventions influences the occurrence and the natural history of delirium among critically ill patients.

Adult↗

PubMed2005

Irinotecan pharmacokinetic and pharmacogenomic alterations induced by methylselenocysteine in human head and neck xenograft tumors.

The combination of methylselenocysteine and irinotecan (CPT-11) is synergistic against FaDu and A253 xenografts. Methylselenocysteine/CPT-11 increased tumor cure rate to 100% in FaDu and to 60% in A253. In this study, the effect of methylselenocysteine on pharmacokinetic and pharmacogenetic profiles of genes relevant to CPT-11 metabolic pathway was evaluated to identify possible mechanisms associated with the observed combinational synergy. Nude mice bearing tumors (FaDu and A253) were treated with methylselenocysteine, CPT-11, and a combination of methylselenocysteine/CPT-11. Samples were collected and analyzed for plasma and intratumor concentration of CPT-11 and 7-ethyl-10-hydroxyl-camptothecin (SN-38) by high-performance liquid chromatography. The intratumor relative expression of genes related to the CPT-11 metabolic pathway was measured by real-time PCR. After methylselenocysteine treatment, the intratumor area under the concentration-time curve of SN-38 increased to a significantly higher level in A253 than in FaDu and was associated with increased expression of CES1 in both tumors. Methylselenocysteine/CPT-11 treatment, compared with CPT-11 alone, resulted in a significant decrease in levels of ABCC1 and DRG1 in FaDu tumors and an increase in levels of CYP3A5 and TNFSF6 in A253 tumors. No statistically significant changes induced by methylselenocysteine/CPT-11 were observed in the levels of other investigated variables. In conclusion, the significant increase in the cure rate after methylselenocysteine/CPT-11 could be related to increased drug delivery into both tumors (CES1), reduced resistance to SN-38 (ABCC1 and DRG1) in FaDu, and induced Fas ligand apoptosis (TNFSF6) in A253. No correlation was observed between cure rate and other investigated variables (transporters, degradation enzymes, DNA repair, and cell survival/death genes) in either tumor.

Animals↗

PubMed2005

A mouse model for developing treatment for secondary liver tumors.

Metastatic colorectal cancer is the second most common cause of cancer mortality. The liver is a common site of metastasis and only a minority of patients with liver metastases are candidates for potentially curative surgical resection. The treatment of patients with unresectable liver tumors is a major clinical problem and survival remains low. Many animal models of hepatic metastasis do not result in disease which resembles the advanced cancer setting. The purpose of this study was to establish a murine model for use in the evaluation of therapy for secondary liver cancer. Human colon cancer cells were injected directly into the portal vein of nude mice. Magnetic resonance imaging (MRI), performed weekly, was used to follow the time-course and characteristics of tumor growth. As expected, tumor size increased proportionately with time, following inoculation, and the MRI images correlated well with gross pathology findings at necropsy with respect to both tumor size and location. The tumors retained important morphology and biological characteristics of human colon cancer. Mice bearing liver metastasis were treated with irinotecan or drug vehicle. MRI evaluation pre/post-therapy gave an objective measure of therapeutic response. Irinotecan therapy was able to double the survival (median 76-93 days) compared to vehicle alone (median 43-46 days). This murine model is reproducible, rapid, inexpensive and has an excellent success rate for the development of liver metastasis (100%). When used in conjunction with small animal MRI, this model allows the efficient evaluation of the therapeutics of liver metastasis without the use of repeated laparotomy or splenectomy and without requiring large numbers of animals undergoing terminal experiments.

Animals↗

PubMed2004

Genotypes associated with myocardial infarction risk are more common in African Americans than in European Americans.

OBJECTIVES: This study was designed to describe the frequencies of multiple myocardial infarction (MI) risk-associated genotypes among different racial groups. BACKGROUND: Racial disparities in the prevalence of cardiovascular disease (CVD) are well known. Recent large Japanese case-control studies identified connexin-37 (GJA-4), plasminogen activator inhibitor-1 (PAI-1), and stromelysin-1 (MMP-3) polymorphisms as risk factors for MI, but the prevalence of these genotypes among different racial groups in the U.S. needs to be determined. METHODS: Genomic deoxyribonucleic acid from 95 healthy African Americans (AA) and 95 healthy European Americans (EA) was used for genotyping. Deoxyribonucleic acid containing the region of interest was amplified using the polymerase chain reaction, followed by genotyping using pyrosequencing. RESULTS: All three MI-risk genotypes were observed in both populations and were in Hardy-Weinberg equilibrium. The frequencies of two of the three "risk-associated" genotypes were significantly higher in the AA population: GJA4 C1019T T/T: AA, 20%, EA, 7% (p = 0.053); MMP3 -1171delA A/A: AA, 78%, EA, 24% (p < 0.001); PAI-1 -668delG G/G: AA, 55%, EA, 16% (p < 0.001). The likelihood of two or more high-risk genotypes was 3.3% among EA subjects and 51% in the AA group (p < 0.001). We found that 9.1% of AA had all three high-risk genotypes, compared with 0% among the EA group (p = 0.0097). CONCLUSIONS: We found higher frequencies of disease-associated genotypes in AA than in EA. Our results also show that more AA than EA carry multiple risk-associated genotypes. Future studies need to assess whether such genetic profiles predict adverse outcomes in U.S. populations and contribute to racial disparities in CVD burden.

Black or African American↗

PubMed2004

The Ross procedure: long-term clinical and echocardiographic follow-up.

BACKGROUND: Progressive dilatation of the pulmonary autograft is the principal cause for reoperation following the Ross procedure when the root replacement technique is used. We examined the relation between enlargement of the pulmonary autograft and the development and progression of neo-aortic valve regurgitation, and the long-term clinical follow-up, including the need for reoperation, in patients followed for up to 13 years postoperatively. METHODS: A Ross procedure was performed on 119 older children and young adults (mean age: 31 years old), using the root replacement technique, between June 1989 and January 2002. Serial echocardiography studies were obtained in 108 patients and analyzed blinded to clinical data. The following variables were measured: diameter of annulus, sinuses of Valsalva, and supravalvular ridge; presence and severity of aortic regurgitation; and valve thickening. RESULTS: The 30 day and late mortality rates were 1.7% and 1.7% (2 patients each). Forty-one patients were followed for more than 5 years, 19 for more than 7 years, and 9 for more than 10 years. There was one thrombotic and no endocarditis events. The 10-year actuarial survival was 96%. Reoperation on the pulmonary autograft or the pulmonary allograft was required in 12 patients. The principal indication for operation on the pulmonary autograft in 11 patients was neo-aortic valve regurgitation (7), aneurysm formation (3), and false aneurysm (1). At 10 years, actuarial freedom from reoperation on the pulmonary autograft was 75%. At last follow-up, 8 of 97 patients without reoperation on the autograft had moderate and none had severe regurgitation of the neo-aortic valve. Independent predictors of progression of neo-aortic valve regurgitation were time from operation, dilatation of the supravalvular ridge, and neo-aortic valve thickening (all p < 0.0002). Freedom from reoperation in the pulmonary allograft at 10 years was 86%. CONCLUSIONS: Long-term follow-up of patients with the Ross procedure using the root replacement technique indicates excellent survival and low thromboembolic and endocarditis risk. The main limitation is the need for reoperation. The prevalence of severe neo-aortic valve regurgitation is low, however there is a progressive increase in regurgitation and in aortic root diameters. Periodic follow-up with echocardiography is recommended because of the continuing risk of progressive regurgitation of the neo-aortic valve and aneurysm formation.

Adolescent↗

PubMed2004

Expression profiling of murine acute promyelocytic leukemia cells reveals multiple model-dependent progression signatures.

Leukemia results from the expansion of self-renewing hematopoietic cells that are thought to contain mutations that contribute to disease initiation and progression. Studies of the gene expression profiles of human acute myeloid leukemia samples has allowed their classification based on the presence of translocations and French-American-British subtypes, but it is not yet clear whether their molecular signatures reflect the initiating mutations or mutations acquired during progression. To begin to address this question, we examined the expression profiles of normal murine promyelocyte-enriched samples, nontransformed murine promyelocytes expressing human promyelocytic leukemia-retinoic acid receptor alpha (PML-RARalpha) fusion gene, and primary acute promyelocytic leukemia cells. The expression profile of nontransformed cells expressing PML-RARalpha was remarkably similar to that of wild-type promyelocytes. In contrast, the expression profiles of fully transformed cells from three acute promyelocytic leukemia model systems were all different, suggesting that the expression signature of acute promyelocytic leukemia cells reflects the genetic changes that contributed to progression. To further evaluate these progression events, we compared two high-penetrance acute promyelocytic leukemia models that both commonly acquire an interstitial deletion of chromosome 2 during progression. The two models exhibited distinct gene expression profiles, suggesting that the dominant molecular signatures of murine acute promyelocytic leukemia can be influenced by several independent progression events.

Animals↗

PubMed2004

Single nucleotide polymorphism profiling across the methotrexate pathway in normal subjects and patients with rheumatoid arthritis.

Methotrexate (MTX) is a commonly used disease-modifying antirheumatic drug in rheumatoid arthritis (RA). Polymorphisms occur in several genes encoding key enzymes in the folic acid pathway, which is influenced by MTX, but have not been evaluated in patients with RA. The effect of race on allele frequency has also not been evaluated. In this study, the allele frequencies of polymorphisms in six key enzymes in the MTX-folate pathway in patients with RA and healthy controls, including several common racial groups were studied. European- and African-American patients with RA and European and African healthy controls were genotyped for 22 genetic loci in six genes in the MTX cellular pathway. Differences in genotype distributions between the different racial groups were evaluated using chi(2) tests. Allele frequencies were significantly different (p < 0.001) for eight single nucleotide polymorphisms between the European and African controls. The allele frequencies of two polymorphisms showed significant differences (p < 0.001) between the African- and European-American patients with RA. Thus, racial differences exist between the allele frequencies of several polymorphisms in enzymes in the MTX-folate pathway in patients with RA and healthy controls. Whether such differences contribute to a differential response to MTX in patients with RA deserves to be investigated.

Black or African American↗

PubMed2002

Mantel statistics to correlate gene expression levels from microarrays with clinical covariates.

Mantel statistics provide an additional step to standard approaches in the analysis of gene expression and covariate data, allow the calculation of standard statistics such as correlation, partial correlation, and regression coefficients, and, with permutation tests, provide P values for these statistics to relate the sample covariates to the expression levels. In this article we describe the Mantel statistics and illustrate their use and interpretation with data from a study of seven human oligodendrogliomas (brain tumors) where expression levels of 1013 genes and five covariates were previously analyzed using standard approaches. In the previous analysis of these data, qualitative relationships were found between gene expressions and two of the clinical covariates. We show in this article how the Mantel statistics are able to formally quantify and provide P values to determine statistical significance of these relationships. We also show how the Mantel statistics can be used to rank subsets of genes, found using standard clustering methods, in terms of differential expression across samples.

Adult↗

PubMed2002

Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays.

OBJECTIVE: DNA microarrays allow genome-wide assessment of changes in relative messenger RNA abundance and thus can be used to monitor changes in gene expression. The aim of this series of experiments was to gain experience in sepsis gene expression profiling in a well-accepted model of murine polymicrobial abdominal sepsis and begin characterizing (in the parlance of genomics) the sepsis "transcriptome." DESIGN: Prospective animal study. SETTING: University-based animal research facility.SUBJECTS C57BL/6 mice. INTERVENTIONS: After induction of general anesthesia, cecal ligation and puncture were performed to induce peritonitis and polymicrobial sepsis. The control group had sham laparotomy only. Three samples of spleen and liver were collected from septic and sham animals at 24 hrs after laparotomy. Changes in expression were measured for 588 annotated mouse genes by using a commercially available complementary DNA microarray kit. MEASUREMENTS AND MAIN RESULTS: Broad-scale gene expression profiles were characterized for septic liver and spleen and compared with sham controls. The analytical tools used included commercially available software packages and a novel analysis program. Very little overlap was observed in the septic gene expression profiles of these two organs. Most of the genes identified have previously been linked to regulation of the inflammatory response; importantly, however, some have not. In addition, hierarchical cluster analysis showed that cecal ligation and puncture at 24 hrs induced coordinate expression of genes that alter cell signaling and survival pathways in spleen, consistent with previously published reports of sepsis-induced splenocyte apoptosis. The current limitations of microarray analysis as reflected in these studies are also discussed. CONCLUSIONS: Microarray technology provides a powerful new tool for rapidly analyzing tissue-specific changes in gene expression induced by sepsis in animal models. To our knowledge, these data constitute the first report on the use of microarrays to determine the sepsis transcriptome.

Animals↗