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1.  Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes 
Science (New York, N.y.)  2011;334(6052):105-108.
Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
doi:10.1126/science.1208344
PMCID: PMC3368382  PMID: 21885731
2.  Metabolic Syndrome, Components, and Cardiovascular Disease Prevalence in Chronic Kidney Disease: Findings from the Chronic Renal Insufficiency Cohort (CRIC) Study 
American Journal of Nephrology  2011;33(6):477-484.
Background/Aims
Metabolic syndrome may increase the risk for incident cardiovascular disease (CVD) and all-cause mortality in the general population. It is unclear whether, and to what degree, metabolic syndrome is associated with CVD in chronic kidney disease (CKD). We determined metabolic syndrome prevalence among individuals with a broad spectrum of kidney dysfunction, examining the role of the individual elements of metabolic syndrome and their relationship to prevalent CVD.
Methods
We evaluated four models to compare metabolic syndrome or its components to predict prevalent CVD using prevalence ratios in the Chronic Renal Insufficiency Cohort (CRIC) Study.
Results
Among 3,939 CKD participants, the prevalence of metabolic syndrome was 65% and there was a significant association with prevalent CVD. Metabolic syndrome was more common in diabetics (87.5%) compared with non-diabetics (44.3%). Hypertension was the most prevalent component, and increased triglycerides the least prevalent. Using the bayesian information criterion, we found that the factors defining metabolic syndrome, considered as a single interval-scaled variable, was the best of four models of metabolic syndrome, both for CKD participants overall and for diabetics and non-diabetics separately.
Conclusion
The predictive value of this model for future CVD outcomes will subsequently be validated in longitudinal analyses.
doi:10.1159/000327618
PMCID: PMC3095834  PMID: 21525746
Cardiovascular disease; Chronic kidney disease; Chronic Renal Insufficiency Cohort (CRIC) Study; Metabolic syndrome
3.  Risk of Bladder Cancer Among Diabetic Patients Treated With Pioglitazone 
Diabetes Care  2011;34(4):916-922.
OBJECTIVE
Some preclinical in vivo studies and limited human data suggest a possible increased risk of bladder cancer with pioglitazone therapy. This is an interim report of an ongoing cohort study examining the association between pioglitazone therapy and the risk of bladder cancer in patients with diabetes.
RESEARCH DESIGN AND METHODS
This study includes 193,099 patients in the Kaiser Permanente Northern California diabetes registry who were ≥40 years of age between 1997 and 2002. Those with prior bladder cancer were excluded. Ever use of each diabetes medication (defined as two or more prescriptions within 6 months) was treated as a time-dependent variable. Cox regression–generated hazard ratios (HRs) compared pioglitazone use with nonpioglitazone use adjusted for age, sex, race/ethnicity, diabetes medications, A1C, heart failure, household income, renal function, other bladder conditions, and smoking.
RESULTS
The group treated with pioglitazone comprised 30,173 patients. There were 90 cases of bladder cancer among pioglitazone users and 791 cases of bladder cancer among nonpioglitazone users. Overall, ever use of pioglitazone was not associated with risk of bladder cancer (HR 1.2 [95% CI 0.9–1.5]), with similar results in men and women (test for interaction P = 0.8). However, in the a priori category of >24 months of therapy, there was an increased risk (1.4 [1.03–2.0]). Ninety-five percent of cancers diagnosed among pioglitazone users were detected at early stage.
CONCLUSIONS
In this cohort of patients with diabetes, short-term use of pioglitazone was not associated with an increased incidence of bladder cancer, but use for more than 2 years was weakly associated with increased risk.
doi:10.2337/dc10-1068
PMCID: PMC3064051  PMID: 21447663
4.  FGF23, PTH and Phosphorus Metabolism in the Chronic Renal Insufficiency Cohort 
Kidney international  2011;79(12):1370-1378.
Fibroblast growth factor 23 (FGF23) regulates phosphorus metabolism and is a strong predictor of mortality in dialysis patients. FGF23 has been proposed as an early biomarker of disordered phosphorus metabolism in earlier stages of chronic kidney disease (CKD), but data from large, well-characterized CKD cohorts are lacking. We measured FGF23 in baseline samples from 3,879 participants in the Chronic Renal Insufficiency Cohort study, a nationally representative, diverse CKD cohort with mean (± sd) estimated glomerular filtration rate (eGFR) of 42.8 ± 13.5 ml/min/1.73m2. Serum phosphate (3.7 ± 0.7 mg/dl) and parathyroid hormone (PTH; median 54, interquartile range [IQR] 35 – 89 pg/ml) levels were in the normal range, but FGF23 (median 145, IQR 96 – 239 RU/ml) was markedly greater than in healthy populations and increased significantly with decreasing eGFR. FGF23 excess, defined as ≥ 100 RU/ml, was more common than secondary hyperparathyroidism (≥ 65 pg/ml) and hyperphosphatemia (≥ 4.6 mg/dl) in all strata of eGFR, and the eGFR threshold at which the slope of FGF23 increased (57.8; 95%CI: 55.4 – 60.8 ml/min/1.73m2) was higher than the corresponding threshold for PTH (46.9; 95%CI: 45.5 – 51.4 ml/min/1.73m2). Thus, increased FGF23 is a common manifestation of CKD that develops earlier than increases in phosphate or PTH. These findings provide additional support for use of FGF23 as a sensitive early screening test to identify disordered phosphorus metabolism in CKD patients with normal serum phosphate levels.
doi:10.1038/ki.2011.47
PMCID: PMC3134393  PMID: 21389978
5.  FGF23 induces left ventricular hypertrophy 
The Journal of Clinical Investigation  2011;121(11):4393-4408.
Chronic kidney disease (CKD) is a public health epidemic that increases risk of death due to cardiovascular disease. Left ventricular hypertrophy (LVH) is an important mechanism of cardiovascular disease in individuals with CKD. Elevated levels of FGF23 have been linked to greater risks of LVH and mortality in patients with CKD, but whether these risks represent causal effects of FGF23 is unknown. Here, we report that elevated FGF23 levels are independently associated with LVH in a large, racially diverse CKD cohort. FGF23 caused pathological hypertrophy of isolated rat cardiomyocytes via FGF receptor–dependent activation of the calcineurin-NFAT signaling pathway, but this effect was independent of klotho, the coreceptor for FGF23 in the kidney and parathyroid glands. Intramyocardial or intravenous injection of FGF23 in wild-type mice resulted in LVH, and klotho-deficient mice demonstrated elevated FGF23 levels and LVH. In an established animal model of CKD, treatment with an FGF–receptor blocker attenuated LVH, although no change in blood pressure was observed. These results unveil a klotho-independent, causal role for FGF23 in the pathogenesis of LVH and suggest that chronically elevated FGF23 levels contribute directly to high rates of LVH and mortality in individuals with CKD.
doi:10.1172/JCI46122
PMCID: PMC3204831  PMID: 21985788
6.  Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags 
BMC Microbiology  2010;10:206.
Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80°C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method.
doi:10.1186/1471-2180-10-206
PMCID: PMC2921404  PMID: 20673359
7.  Use of the Non-invasive Components of the Mayo Score to Assess Clinical Response in Ulcerative Colitis 
Inflammatory bowel diseases  2008;14(12):1660-1666.
Background
The Mayo score and a non-invasive 9-point partial Mayo score are used as outcome measures for clinical trials assessing therapy for ulcerative colitis. There are limited data assessing what defines a clinically relevant change in these indices. We sought to assess what constitutes a clinically meaningful change in these indices using data from a recently completed placebo-controlled clinical trial.
Methods
105 patients were enrolled in a 12 week randomized, placebo-controlled trial assessing rosiglitazone for treatment of mild to moderate ulcerative colitis. We compared the change in the Mayo score, the partial Mayo score, and a 6 point score composed just of the stool frequency and bleeding components of the Mayo score to the patient’s perception of disease activity at week 0 and week 12. Optimal cut points were calculated as the maximal product of sensitivity and specificity.
Results
Each index was strongly correlated with the patient’s rating of disease activity at week 12 (Spearman correlations from 0.61 to 0.71, p<0.0001 for all correlations). The maximal product of sensitivity and specificity to identify patient reported improvement of disease activity was achieved using cut points for change of 2.5 for the Mayo score (sensitivity 88%, specificity 80%), 2.5 for the partial Mayo score (sensitivity 88%, specificity 87%), and 1.5 for the 6 point score (sensitivity 88%, specificity 80%).
Conclusion
The partial Mayo score and the 6 point score composed solely of the stool frequency and bleeding components performed as well as the full Mayo score to identify patient perceived clinical response.
doi:10.1002/ibd.20520
PMCID: PMC2597552  PMID: 18623174
8.  Rosiglitazone for Active Ulcerative Colitis 
Gastroenterology  2007;134(3):688-695.
Background
Thiazolidinedione ligands for the gamma subtype of peroxisome proliferator-activated receptors (PPARγ), widely used to treat type 2 diabetes mellitus, have been proposed as novel therapies for ulcerative colitis.
Methods
This multicenter randomized, double blind, placebo-controlled clinical trial compared the efficacy of rosiglitazone (Avandia™) 4 mg orally twice daily versus placebo twice daily for 12 weeks in 105 patients with mild to moderately active UC. Disease activity was measured with the Mayo Score. The primary endpoint was clinical response (≥ 2 point reduction) at week 12. Clinical remission (Mayo Score ≤2), endoscopic remission, and quality of life were secondary outcomes.
Results
After 12 weeks of therapy, 23 patients (44%) treated with rosiglitazone and 12 patients (23%) treated with placebo achieved clinical response (p=0.04). Remission was achieved in 9 patients (17%) treated with rosiglitazone and 1 patient (2%) treated with placebo (p=0.01). Endoscopic remission was uncommon in either treatment arm (8% rosiglitazone vs. 2% placebo, p=0.34). Clinical improvement was evident as early as 4 weeks (p=0.049). Quality of life was significantly improved at week 8 (p=0.01) but not at week 4 (p=0.48) or 12 (p=0.14). Serious adverse events were rare.
Conclusions
Rosiglitazone was efficacious in the treatment of mild to moderately active ulcerative colitis.
doi:10.1053/j.gastro.2007.12.012
PMCID: PMC2276587  PMID: 18325386

Results 1-8 (8)