Stool Bacteriomic Profiling in Patients with Metastatic Renal Cell Carcinoma Receiving Vascular Endothelial Growth Factor-Tyrosine Kinase Inhibitors.

PURPOSE: Diarrhea occurs in approximately half of patients with metastatic renal cell carcinoma (mRCC) receiving vascular endothelial growth factor-tyrosine kinase inhibitors (VEGF-TKI). We evaluated the relationship between VEGF-TKI-related diarrhea and stool microbiota. EXPERIMENTAL DESIGN: Stool samples were collected from 20 mRCC patients receiving VEGF-TKIs. 16S rRNA sequencing was used to characterize the stool bacteriomic profiling of patients. Assay validation with Salmonella typhimurium spike-in experiments suggested greatest speciation with use of the V5 region. RESULTS: Higher levels of Bacteroides spp. and lower levels of Prevotella spp. were found in patients with diarrhea. In addition, patients receiving VEGF-TKIs with mRCC appeared to have less relative abundance of Bifidobacterium spp. as compared with previous reports based on healthy subjects. CONCLUSIONS: We have thus demonstrated interplay between microbiota and VEGF-TKI-induced diarrhea. Further studies are warranted to evaluate the potential causative role of preexisting dysbiosis in VEGF-TKI-related diarrhea.

Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families.

Monoallelic expression is an integral component of regulation of a number of essential genes and gene families. To probe for allele-specific expression in cells of CNS origin, we used next-generation sequencing (RNA-seq) to analyze four clonal neural stem cell (NSC) lines derived from Mus musculus C57BL/6 (B6)×Mus musculus molossinus (JF1) adult female mice. We established a JF1 cSNP library, then ascertained transcriptome-wide expression from B6 vs. JF1 alleles in the NSC lines. Validating the assay, we found that 262 of 268 X-linked genes evaluable in at least one cell line showed monoallelic expression (at least 85% expression of the predominant allele, p-value<0.05). For autosomal genes 170 of 7,198 genes (2.4% of the total) showed monoallelic expression in at least 2 evaluable cell lines. The group included eight known imprinted genes with the expected pattern of allele-specific expression. Among the other autosomal genes with monoallelic expression were five members of the glutathione transferase gene superfamily, which processes xenobiotic compounds as well as carcinogens and cancer therapeutic agents. Monoallelic expression within this superfamily thus may play a functional role in the response to diverse and potentially lethal exogenous factors, as is the case for the immunoglobulin and olfactory receptor superfamilies. Other genes and gene families showing monoallelic expression include the annexin gene family and the Thy1 gene, both linked to inflammation and cancer, as well as genes linked to alcohol dependence (Gabrg1) and epilepsy (Kcnma1). The annotated set of genes will provide a resource for investigation of mechanisms underlying certain cases of these and other major disorders.

Intraoperative spillage of favorable histology wilms tumor cells: influence of irradiation and chemotherapy regimens on abdominal recurrence. A report from the National Wilms Tumor Study Group.

PURPOSE: We undertook this study to determine (1) the frequency with which spilled tumor cells of favorable histology produced intra-abdominal disease in patients treated with differing chemotherapy regimens and abdominal radiation therapy (RT) and (2) the patterns of relapse and outcomes in such patients. METHODS AND MATERIALS: The influence of RT dose (0, 10, and 20 Gy), RT fields (flank, whole abdomen), and chemotherapy with dactinomycin and vincristine (2 drugs) vs. added doxorubicin (three drugs) on intra-abdominal tumor recurrence rates was analyzed by logistic regression in 450 patients. Each patient was considered at risk for two types of failure: flank and subdiaphragmatic beyond-flank recurrence, with the correlation between the two outcomes accounted for in the analyses. RESULTS: The crude odds ratio for the risk of recurrence relative to no RT was 0.35 (0.15-0.78) for 10Gy and 0.08 (0.01-0.58) for 20Gy. The odds ratio for the risk of recurrence for doxorubicin to two drugs after adjusting for RT was not significant. For Stage II patients (NWTS-4), the 8-year event rates with and without spillage, respectively, were 79% and 87% for relapse-free survival (p = 0.07) and 90% and 95% for overall survival (p = 0.04). CONCLUSIONS: Irradiation (10 Gy or 20 Gy) reduced abdominal tumor recurrence rates after tumor spillage. Tumor spillage in Stage II patients reduced relapse-free survival and overall survival, but only the latter was of statistical significance. These data provide a basis for assessing the risks vs. benefits when considering treatment for children with favorable histology Wilms tumor and surgical spillage.

A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis.

MicroRNAs regulate diverse cellular processes and play an integral role in cancer pathogenesis. Genomic variation within miRNA target sites may therefore be important sources for genetic differences in cancer risk. To investigate this possibility, we mapped HapMap single nucleotide polymorphisms (SNP) to putative miRNA recognition sites within genes dysregulated in estrogen receptor-stratified breast tumors and used local linkage disequilibrium patterns to identify high-ranking SNPs in the Cancer Genetic Markers of Susceptibility (CGEMS) breast cancer genome-wide association study for further testing. Two SNPs, rs1970801 and rs11097457, scoring in the top 100 from the CGEMS study, were in strong linkage disequilibrium with rs1434536, an SNP that resides within a miR-125b target site in the 3' untranslated region of the bone morphogenic receptor type 1B (BMPR1B) gene encoding a transmembrane serine/threonine kinase. We validated the CGEMS association findings for rs1970801 in an independent cohort of admixture-corrected cases identified from families with multiple case histories. Subsequent association testing of rs1434536 for these cases and CGEMS controls with imputed genotypes supported the association. Furthermore, luciferase reporter assays and overexpression of miR-125b-mimics combined with quantitative reverse transcription-PCR showed that BMPR1B transcript is a direct target of miR-125b and that miR-125b differentially regulates the C and T alleles of rs1434536. These results suggest that allele-specific regulation of BMPR1B by miR-125b explains the observed disease risk. Our approach is general and can help identify and explain the mechanisms behind disease association for alleles that affect miRNA regulation.

A transdimensional Bayesian model for pattern recognition in DNA sequences.

Identification of transcription factor binding sites (TFBSs) is essential to elucidate gene regulatory networks. This article is focused on the recognition of overpresented short patterns, called "motifs", that may correspond to regulatory binding sites in the DNA sequences upstream of genes. An integrated Bayesian model is proposed to incorporate all unknown characteristics in motif discovery, including the number of motifs, motif widths, motif compositions, the number of motif sites, and locations of motif sites. Reversible jump Markov chain Monte Carlo is used to obtain posterior inference in the transdimensional parameter space. We present a number of suggestions for graphical summarization of the posterior distribution over the complex parameter space. The basic model is extended using a third-order Markov structure for nonmotif bases and allowing positions within a motif to be switched between 2 types: "conserved" and "degenerate." We evaluate the prediction accuracy for the simulated data with 3 motifs and apply the model to upstream sequences in high signal-to-noise regions in a human ChIP-chip study. The performance of the Bayesian model is assessed using yeast data sets of various numbers of sequences and background structures, with and without true TFBSs. The performance is also compared to other computational methods, including 2 statistical approaches, AlignACE and multiple expectation maximization for motif elicitation, and 1 word numeration-based approach, yeast motif finder (YMF).

Wilcoxon-based group sequential designs for comparison of areas under two correlated ROC curves.

Clinical studies to evaluate the relative accuracies of two diagnostic modalities via their receiver operating characteristic (ROC) curves are currently conducted using fixed sample designs: cases are accrued until a predetermined sample size is achieved and, at that point, the areas under the ROC curves are computed and compared (Radiology 1982; 143:29-36; Radiology 1983; 148:839-843). In prospective ROC studies (Radiology 1990; 175:571-575), participants are recruited from a clinically defined cohort and diagnostic test information is obtained and interpreted in advance of ascertaining the definitive proof of diagnosis ('gold standard'). In retrospective studies, cases are selected from a set of patient records and their diagnostic tests are interpreted without knowledge of the 'gold standard'. The conduct of ROC studies requires considerable effort and resources, particularly for the collection of 'gold standard' information. Thus, it is highly desirable to search for designs which are more efficient than using a fixed sample. In this paper, we discuss the formulation and application of group sequential designs (GSDs) to comparative ROC studies based on non-parametric Wilcoxon estimators of the area under the ROC curves. The approach is applicable to comparisons of ROC curve areas of two tests measured on either continuous or ordinal scales on same cases ('paired' designs) with one reader. The adoption of GSDs may lead to substantial savings in the number of required cases, thus resulting in both time and resource use efficiency.

ITT analysis of randomized encouragement design studies with missing data.

In this paper, we considered a missing outcome problem in causal inferences for a randomized encouragement design study. We proposed both moment and maximum likelihood estimators for the marginal distributions of potential outcomes and the local complier average causal effect (CACE) parameter. We illustrated our methods in a randomized encouragement design study on the effectiveness of flu shots.

High telomerase RNA expression level is an adverse prognostic factor for favorable-histology Wilms' tumor.

PURPOSE: A primary objective of the fifth National Wilms Tumor Study (NWTS-5) was to identify prognostic indicators for patients with favorable-histology Wilms' tumor. The prognostic significance of telomerase expression level in primary tumor samples was assessed. PATIENTS AND METHODS: A case-cohort study was conducted involving 291 NWTS-5 registrants. Telomerase activity was measured using the telomeric repeat amplification protocol (TRAP). Expression levels of TERT mRNA (encoding the telomerase catalytic component) and TERC/hTR (the telomerase RNA template) were measured using quantitative real-time polymerase chain reaction. RESULTS: After excluding samples because of lack of viable tumor, RNA degradation, or insufficient clinical information, 244 patients remained for the final analysis (96 with relapse and 148 without relapse). Univariate analysis revealed a positive correlation between relative risk (RR) of relapse and levels of TERT mRNA and TERC expression. For each doubling in TERT mRNA and TERC level, the RR increased by a factor of 1.16 (95% CI, 1.04 to 1.29; P = .01) and 1.35 (95% CI, 1.11 to 1.64; P = .003), respectively. The one third of patients whose tumors had the highest TERC expression level had an RR of 2.06 (95% CI, 1.14 to 3.70; P = .02) compared with patients with the lowest level. TERC expression level remained a significant prognostic indicator in a multivariate analysis adjusting for TERT mRNA, tumor stage, and patient age. TRAP level did not correlate with RR of relapse. Telomerase expression levels were not predictive of overall survival. CONCLUSION: Telomerase RNA expression level may provide a clinically useful adjunct to the current risk classification schema for favorable-histology Wilms' tumor.

Cardiovascular fitness among U.S. adults: NHANES 1999-2000 and 2001-2002.

PURPOSE: To present information on cardiovascular fitness (estimated maximal oxygen uptake [VO2max] and cardiovascular fitness levels based on sex- and age-specific cut-points of estimated VO2max) among U.S. adults. METHODS: Analysis of data on 1978 adults (20-49 yr) who had completed a submaximal exercise test, from the National Health and Nutrition Examination Survey (1999-2000 and 2001-2002), a cross-sectional health survey of a nationally representative sample of the noninstitutionalized U.S. population RESULTS: Estimated VO2max was significantly lower (P < 0.01) in non-Hispanic black ([mean +/- standard error] 38.2 +/- 0.7 mL x min(-1) x kg(-1)) than Mexican-American and non-Hispanic white adults (41.5 +/- 0.6 and 40.6 +/- 0.4 mL x min(-1) x kg(-1), respectively). Estimated VO2max was also significantly lower (P < 0.001) in non-Hispanic black females (33.1 +/- 0.6 mL x min(-1) x kg(-1)) than in Mexican-American and non-Hispanic white females (37.0 +/- 0.7 and 36.4 +/- 0.4 mL x min(-1) x kg(-1), respectively). The proportion of low, moderate, and high cardiovascular fitness differed (P < 0.001) among race and race-sex groups. This difference was most striking among females, where 30.9% [95% confidence interval = 23.6-38.2%] of non-Hispanic black women had a low cardiovascular fitness level, compared with only 13.5% [10.0-17.0%] of non-Hispanic white and 18.9% [14.0-23.8%] of Mexican-American women. CONCLUSIONS: Adults of non-Hispanic black race have lower cardiovascular fitness than other major race groups in the United States. Nearly one third of non-Hispanic black women had a low cardiovascular fitness level, suggesting that this group in particular may be at increased health risk due to low cardiovascular fitness.

Age and kidney function are the primary correlates of fasting plasma total homocysteine levels in non-diabetic and diabetic adults. Results from the 1999-2002 National Health and Nutrition Examination Survey.

BACKGROUND: Plasma total homocysteine (tHcy) is commonly elevated in persons with diabetes. This may be due to effects of insulin and/or glucose and/or metabolic control on the metabolism or plasma levels of tHcy. This study examined the effects of fasting plasma glucose status on fasting tHcy levels among adults without diabetes, and diabetes per se among adults with a self-report history of diabetes. METHODS: Analysis of data on adults (> or = 20y) who had fasted at least 8 hours, from the National Health and Nutrition Examination Survey (1999-2000 and 2001-2002). Subjects with no self-report history of diabetes were grouped according to fasting plasma glucose status as normal (< 100 mg/dL = NFG, n = 2,244), impaired (> or = 100 < 126 mg/dL = IFG, n = 1,108), or a provisional diagnosis of diabetes (> or = 126 mg/dL = DFG, n = 133). Subjects with a self-report history of diabetes (n = 275) were examined separately. RESULTS: Fasting tHcy was higher (Ps < 0.01) among non-diabetic subjects with DFG and IFG, compared to NFG (median [95% confidence interval] = 8.6 [8.0-9.2], 8.3 [8.1-8.5], and 7.4 [7.3-7.5] micromol/L, respectively). Diabetic subjects had levels similar to non-diabetic subjects with DFG and IFG (8.3 [7.9-8.6] micromol/L). Age and estimated creatinine clearance were strong correlates of fasting tHcy among non-diabetic subjects (r = 0.38 to 0.44 and r = -0.35 to -0.46, respectively) and diabetic subjects (r = 0.41 and r = -0.46, respectively) (Ps < 0.001), while fasting glucose and glycohemoglobin (HbA1c) were weaker (but still significant) correlates of tHcy in non-diabetic and diabetic subjects. Fasting glucose status was not a significant independent predictor of fasting tHcy levels in non-diabetic subjects, and HbA1c was not a significant independent predictor of tHcy in diabetic subjects (Ps > 0.05). CONCLUSION: Fasting tHcy levels are elevated among non-diabetic adults with elevated fasting glucose levels, compared to persons with normal fasting glucose levels, and among diabetic adults. However, elevations in fasting tHcy appear to be mediated primarily by age and kidney function, and not by measures of glucose metabolism.

Prevalence and trends of a metabolic syndrome phenotype among u.s. Adolescents, 1999-2000.

OBJECTIVE: To determine the prevalence of a metabolic syndrome phenotype among U.S. adolescents using the most recent national data and to examine trends in metabolic syndrome prevalence. RESEARCH DESIGN AND METHODS: Analysis of data on 991 adolescents (aged 12-19 years) who had fasted for at least 6 h, from the National Health and Nutrition Examination Survey (NHANES 1999-2000). The metabolic syndrome was determined using the National Cholesterol Education Program (Adult Treatment Panel III) definition modified for age. RESULTS: The overall prevalence of a metabolic syndrome phenotype among U.S. adolescents increased from 4.2% in NHANES III (1988-1992) to 6.4% in NHANES 1999-2000 (P < 0.001). The syndrome was more prevalent (P < 0.01) in male than female adolescents (9.1 vs. 3.7%) and was found in 32.1% of overweight adolescents (BMI > or = 95th percentile for age and sex), compared with 7.1% of adolescents at risk for overweight (BMI between 85th and 95th percentiles) (P < 0.001). Based on population-weighted estimates, > 2 million U.S. adolescents currently have a metabolic syndrome phenotype. CONCLUSIONS: The prevalence of a metabolic syndrome phenotype has increased significantly over the past decade among U.S. adolescents and is particularly prevalent (> 30%) in overweight adolescents. These findings have important implications for public health because of the well-known health risks associated with the metabolic syndrome in adults.

Influence of radiation therapy delay on abdominal tumor recurrence in patients with favorable histology Wilms' tumor treated on NWTS-3 and NWTS-4: a report from the National Wilms' Tumor Study Group.

PURPOSE: This study was undertaken to determine whether radiation therapy (RT) delay of >or=10 days had an adverse impact on abdominal tumor recurrence among children with favorable histology (FH) Wilms' tumor enrolled in National Wilms' Tumor Study (NWTS) 3 and 4. METHODS AND MATERIALS: A total of 1226 patients with Stage II-IV FH tumors who received flank or abdominal RT in NWTS-3 and NWTS-4 were included in this analysis. Recurrent disease in the operative bed was classified as flank recurrence. Abdominal recurrence included all infradiaphragmatic tumor recurrences, including flank recurrences. This analysis included all flank/abdominal tumor recurrences, regardless of whether they might have been the initial or subsequent site of relapse. Based on the NWTS-1 results, RT delay was analyzed in two categories: 0-9 days and >or=10 days. RESULTS: The mean RT delay was 10.9 days; median delay was 9 days (range: 1-277 days). The RT delay was concentrated in a relatively narrow range of 8 to 12 days after nephrectomy in the majority of patients (59%). Univariate and multivariate analysis did not reveal RT delay of >or=10 days to significantly influence flank and abdominal tumor recurrence rates in NWTS-3 or NWTS-4. The 8-year flank tumor recurrence rates for 0-9 days and 10+ days RT delay were 1.9% and 1.2%, respectively (p value = 0.3). The 8-year abdominal tumor recurrence rates for 0-9 days and 10+ days RT delay were 4.8% and 5.3%, respectively (p value = 0.7). CONCLUSIONS: RT delay of >or=10 days did not significantly influence flank or abdominal tumor recurrence rates among children with FH tumors treated on NWTS-3 and NWTS-4. However, we were unable to test for a meaningful difference, because of the concentration of RT delay close to 10 days.