Citations

ABSTRACT Evaluating the association of multiple genetic variants with a trait of interest by use of kernel‐based methods has made a significant impact on how genetic association analyses are conducted. An advantage of kernel methods is that they tend to be robust when the genetic variants have effects that are a mixture of positive and negative effects, as well as when there is a small fraction of causal variants. Another advantage is that kernel methods fit within the framework of mixed models, providing flexible ways to adjust for additional covariates that influence traits. Herein, we review the basic ideas behind the use of kernel methods for genetic association analysis as well as recent methodological advancements for different types of traits, multivariate traits, pedigree data, and longitudinal data. Finally, we discuss opportunities for future research.

The lack of reliable, noninvasive methods to diagnose early nonalcoholic steatohepatitis (NASH) is a major unmet need. We aimed to determine the diagnostic accuracy of three‐dimensional magnetic resonance elastography (3D‐MRE), with shear stiffness measured at 60 Hz, damping ratio at 40 Hz, and magnetic resonance imaging proton density fat fraction (MRI‐PDFF) in the detection of NASH in individuals undergoing bariatric surgery. Obese adults at risk for NASH were enrolled between 2015 and 2017 (prospective cohort, n = 88) and 2010 and 2013 (retrospective cohort, n = 87). The imaging protocol consisted of multifrequency 3D‐MRE (mf3D‐MRE) with shear waves delivered at different frequencies to explore parameters that best correlated with histologic NASH, and MRI‐PDFF to estimate steatosis. The prospective cohort was used to establish the optimal mf3D‐MRE technical parameters for NASH detection. The two cohorts were then combined to derive predictive models of NASH and disease activity by nonalcoholic fatty liver disease activity score (NAS) using the three imaging parameters that correlated with NASH. A total of 175 patients (median age 45, 81% women, and 81 [46%] with histologic NASH) were used for model derivation. From the complex shear modulus output generated by mf3D‐MRE, the damping ratio at 40 Hz and shear stiffness at 60 Hz best correlated with NASH. The fat fraction obtained from MRI‐PDFF correlated with steatosis ( P < 0.05 for all). These three parameters were fit into a logistic regression model that predicted NASH with cross‐validated area under the receiver operating characteristic curve (AUROC) = 0.73, sensitivity = 0.67, specificity = 0.80, positive predictive value = 0.73 and negative predictive value = 0.74, and disease activity by NAS with cross‐validated AUROC = 0.82. Conclusion: The mf3D‐MRE allows identification of imaging parameters that predict early NASH and disease activity. This imaging biomarker represents a promising alternative to liver biopsy for NASH diagnosis and monitoring. The results provide motivation for further studies in nonbariatric cohorts.

Increased amino acids in the dysbiotic gut influences susceptibility to Clostridioides difficile infection in mice and humans.

Abstract Background: A number of cohort studies have collected Scope mouthwash samples by mail, which are being used for microbiota measurements. We evaluated the stability of Scope mouthwash samples at ambient temperature and determined the comparability of Scope mouthwash with saliva collection using the OMNIgene ORAL Kit. Methods: Fifty-three healthy volunteers from Mayo Clinic and 50 cohort members from Bangladesh provided oral samples. One aliquot of the OMNIgene ORAL and Scope mouthwash were frozen immediately and one aliquot of the Scope mouthwash remained at ambient temperature for 4 days and was then frozen. DNA was extracted and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the HiSeq. Intraclass correlation coefficients (ICC) were calculated. Results: The overall stability of the Scope mouthwash samples was relatively high for alpha and beta diversity. For example, the meta-analyzed ICC for the Shannon index was 0.86 (95% confidence interval, 0.76–0.96). Similarly, the ICCs for the relative abundance of the top 25 genera were generally high. The comparability of the two sample types was relatively low when measured using ICCs, but were increased by using a Spearman correlation coefficient (SCC) to compare the rank order of individuals. Conclusions: Overall, the Scope mouthwash samples appear to be stable at ambient temperature, which suggests that oral rinse samples received by the mail can be used for microbial analyses. However, Scope mouthwash samples were distinct compared with OMNIgene ORAL samples. Impact: Studies should try to compare oral microbial metrics within one sample collection type.

AbstractRecent research has highlighted the importance of the human microbiome in many human disease and health conditions. Most current microbiome association analyses focus on unrelated samples; such methods are not appropriate for analysis of data collected from more advanced study designs such as longitudinal and pedigree studies, where outcomes can be correlated. Ignoring such correlations can sometimes lead to suboptimal results or even possibly biased conclusions. Thus, new methods to handle correlated outcome data in microbiome association studies are needed. In this paper, we propose the correlated sequence kernel association test (CSKAT) to address such correlations using the linear mixed model. Specifically, random effects are used to account for the outcome correlations and a variance component test is used to examine the microbiome effect. Compared to existing genetic association tests for longitudinal and family samples, we implement a correction procedure to better calibrate the null distribution of the score test statistic to accommodate the small sample size nature of data collected from a typical microbiome study. Comprehensive simulation studies are conducted to demonstrate the validity and efficiency of our method, and we show that CSKAT achieves a higher power than existing methods while correctly controlling the Type I error rate. We also apply our method to a microbiome data set collected from a UK twin study to illustrate its potential usefulness. A free implementation of our method in R software is available at https://github.com/jchen1981/SSKAT.

BackgroundPreoperative prediction of tumor recurrence is important in the management of patients with hepatocellular carcinoma (HCC).PurposeTo investigate whether tumor stiffness derived by magnetic resonance elastography (MRE) could predict early recurrence of HCC after hepatic resection.Study TypeRetrospective.PopulationIn all, 99 patients with pathologically confirmed HCCs after surgical resection.Field Strength/Sequence3.0T; preoperative MRE with 60‐Hz mechanical vibrations using an active acoustic driver.AssessmentRegions of interest (ROIs) were manually drawn in the tumors to measure mean tumor stiffness. Surgical specimens were reviewed for histological grade, capsule, vascular invasion, and surgical margins. The early recurrence of HCC was defined as that occurring within 2 years after resection.Statistical TestsCox proportional hazard models were used to evaluate risk factors associated with the time to early recurrence.ResultsHCCs with recurrence had higher tumor stiffness, higher rate of advanced T stage, vascular invasion, lower rate of capsule formation, larger tumor size, higher aspartate aminotransferase (AST), and hepatitis B virus (HBV)‐DNA level and aspartate aminotransferase / alanine aminotransferase ratio (P = 0.031, 0.007, 0.01, <0.001, 0.015, 0.034, 0.01, and 0.014, respectively) than HCCs without recurrence. Vascular invasion (hazard ratio [HR] = 2.922; 95% confidence interval [CI]: [1.079, 7.914], P = 0.035) and mean tumor stiffness (HR = 1.163; 95% CI: [1.055, 1.282], P = 0.002) were risk factors associated with early recurrence. Each 1‐kPa increase in tumor stiffness was associated with a 16.3% increase in the risk for tumor recurrence.Data ConclusionThe mean stiffness of HCCs may be a useful, noninvasive, quantitative biomarker for the prediction of early HCC recurrence after hepatic resection.Level of Evidence: 4Technical Efficacy: Stage 5J. Magn. Reson. Imaging 2019;49:719–730.

Abstract Ovarian cancer (OC) is the most lethal gynecologic malignancy and the fifth leading cause of cancer death in the United States. Metformin, an antidiabetic drug, has been shown to decrease the risk of mortality in cancer patients, particularly those with OC. Though the drug acts through inhibition of the PI3K/mTOR/AKT pathway, which is commonly altered in OC, knockout of key proteins in the pathway does not attenuate metformin’s antidiabetic effects. Further, intravenous metformin administration is less effective than oral, implying that some crucial interaction takes place in the gut. The gut is home to some 1013 bacterial cells, collectively known as the microbiota. These bacteria play important roles in fermentation of fiber, producing short-chain fatty acids (SCFA) that have positive health benefits, including prevention of metabolic syndrome, bowel disorders, and certain cancers. Mechanistically, SCFAs inhibit the PI3K/mTOR/AKT pathway, similar to metformin. Conditions such as obesity, metabolic syndrome, and diabetes significantly alter gut microbiota composition, possibly leading to a reduction in beneficial SCFAs. However, in type II diabetes, treatment with metformin leads to an increase in SCFA-producing bacteria, suggesting that metformin may positively influence the microbiota to improve patient metabolic profiles. In OC, metformin may play a similar role in promoting the presence of SCFA-producing bacteria. We hypothesized that metformin increases the abundance of SCFA-producing bacteria in the gut, with which it acts synergistically to decrease growth of OC cells in combination with OC chemotherapy. To investigate our hypothesis, we have employed the OC patient-derived xenograft (PDX) mouse model established at Mayo Clinic. Immunocompromised SCID mice received OC cells from Mayo Clinic patients and the tumors were allowed to grow to an appropriate size before treatment was started. Cage mates were split into one of four treatment arms: a control (no treatment) group, metformin only, carboplatin/paclitaxel (CP) chemotherapy only, or CP with metformin. Mice received 2mg/ml metformin in their water continuously and/or 51mg/kg carboplatin and 15mg/kg paclitaxel intravenously weekly. Stool was collected weekly prior to tumor injection, during tumor growth, and through the four weeks of treatment. DNA was extracted from stool and bacterial 16S rRNA amplicon sequencing was used to determine microbiota profiles. Mice with chemosensitive tumors treated with only CP chemotherapy had significant reductions in tumor growth along with significantly less microbial gut diversity than pretumor and pretreatment mice. Chemosensitive mice treated with metformin alone did not lose significant microbial diversity but did not have significant reductions in tumor growth as compared to the control mice. CP in combination with metformin both reduced tumor growth and protected against loss of microbiota diversity. Further, mice treated with only metformin had significant increases in abundance in the Firmicutes genera Ruminococcus and Oscillospira, SCFA producers that are associated with leanness and health. Mice treated with both metformin and CP had significant increases in another SCFA-producing Firmicute, Moryella. Finally, mice with chemoresistant tumors showed improved tumor growth inhibition with combination CP/metformin therapy, suggesting that metformin-associated changes in the gut microbiota may increase sensitivity to CP. These data support the hypothesis that metformin protects against detrimental loss of gut microbiota diversity induced by chemotherapy treatment, enriching beneficial SCFA producers. This work implies a role for the gut microbiota in OC treatment and provides support for metformin’s potential use as a beneficial addition to chemotherapy treatment. Citation Format: Dana M. Walsh, Ismail Mert, Chen Jun, Xiaonan Hou, Saravut John Weroha, Marina Walther-Antonio. Metformin alters the gut microbiota of ovarian cancer patients treated with carboplatin/paclitaxel chemotherapy and enhances sensitivity in resistant tumors. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr A70.

ABSTRACT Intestinal barrier function and microbiota are integrally related and play critical roles in maintenance of host physiology. Sex is a key biologic variable for several disorders. Our aim was to determine sex‐based differences in response to perturbation and subsequent recovery of intestinal barrier function and microbiota in healthy humans. Twenty‐three volunteers underwent duodenal biopsies, mucosal impedance, and in vivo permeability measurement. Permeability testing was repeated after administration of indomethacin, then 4 to 6 wk after its discontinuation. Duodenal and fecal microbiota composition was determined using 16S rRNA amplicon sequencing. Healthy women had lower intestinal permeability and higher duodenal and fecal microbial diversity than healthy men. Intestinal permeability increases after indomethacin administration in both sexes. However, only women demonstrated decreased fecal microbial diversity, including an increase in Prevotella abundance, after indomethacin administration. Duodenal microbiota composition did not show sex‐specific changes. The increase in permeability and microbiota changes normalized after discontinuation of indomethacin. In summary, women have lower intestinal permeability and higher microbial diversity. Intestinal permeability is sensitive to perturbation but recovers to baseline. Gut microbiota in women is sensitive to perturbation but appears to be more stable in men. Sex‐based differences in intestinal barrier function and microbiome should be considered in future studies.—Edogawa, S., Peters, S. A., Jenkins, G. D., Gurunathan, S. V., Sundt, W. J., Johnson, S., Lennon, R. J., Dyer, R. B., Camilleri, M., Kashyap, P. C., Farrugia, G., Chen, J., Singh, R. J., Grover, M. Sex differences in NSAID‐induced perturbation of human intestinal barrier function and microbiota. FASEB J. 32, 6615–6625 (2018). www.fasebj.org

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero-inflation remain largely undeveloped. Here we propose geometric mean of pairwise ratios—a simple but effective normalization method—for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.