Consistent Direction Of Effect Research Articles

Abstract 1446: Genetic risk factors for the development of multiple primary cancers

Abstract Introduction: Individuals with one cancer are at greater risk of new primary cancers than the general population. While several hereditary cancer syndromes are known, genetic risk factors for multiple primary cancers in an individual are not well understood. Identification of susceptibility variants to multiple primary tumors could enhance screening for subsequent cancers among those at highest risk. Methods: We conducted a pan-cancer genome-wide association study (GWAS) of multiple primary cancers among participants from 2 prospective cohorts: Kaiser Permanente and the UK Biobank. The primary GWAS within cohorts used logistic regression to estimate associations for diagnosis with ≥2 invasive or in situ primary cancers other than non-melanoma skin (N=11,773, 8,928 invasive only) compared to cancer-free controls (N=420,101). Case-case analyses were conducted to distinguish associations with multiple cancers from single-cancer (N=90,576) susceptibility signals. Regression models were adjusted for age, sex, first 10 genetic ancestry principal components, and array. Cohort-specific GWAS results were meta-analyzed. We highlight genome-wide significant (p<5×10-8) results with consistent effect direction across the 2 studies. Results: We identified 8 variants associated with multiple primary cancers. Discussion: To our knowledge, rs192703567 has no previous cancer associations. Three identified variants are in known cancer predisposition genes (rs2293607 in TERC, rs6983267 in CASC8, rs35850753 in TP53). Three variants (rs34379047, rs612611, and rs9419958) are previously associated with multiple cancers, 2 (rs2293607 and rs6983267) with cancer pleiotropy, and 2 (rs283732 and rs35850753) with individual cancers. Most variants from the cancer-free control analyses had consistent effects in the single-cancer case-case analyses, suggesting pleiotropic mechanisms. Our preliminary findings offer insight into genetic risk factors associated with developing multiple primary cancers. Multiple vs. none Multiple invasive vs. none Multiple vs. single Multiple invasive vs. single Chr Position rsID A1 A2 Gene OR P OR P OR P OR P 3 169482335 rs2293607 T C TERC 1.11 1.0×10-9 1.10 2.2×10-7 1.06 2.0×10-3 1.05 0.01 8 128281644 rs283732 C T Intergenic 1.09 2.3×10-7 1.11 9.2×10-9 1.06 3.8×10-4 1.09 3.9×10-5 8 128413305 rs6983267 G T CASC8 POU5F1B CCAT2 PCAT1 1.08 4.1×10-7 1.09 2.9×10-8 1.00 0.83 1.02 0.34 10 105644473 rs34379047 T A OBFC1 1.16 8.5×10-12 1.19 6.0×10-11 1.19 2.3×10-4 1.10 4.0×10-4 10 105675946 rs9419958 T C STN1 1.14 1.8×10-11 1.16 4.5×10-11 1.08 3.1×10-4 1.09 2.8×10-4 11 69307463 rs612611 G A Intergenic 1.11 3.7×10-8 1.10 5.3×10-6 1.06 9.6×10-4 1.05 0.02 17 7578671 rs35850753 T C TP53 1.27 4.9×10-7 1.34 1.6×10-8 1.16 2.8×10-3 1.24 8.8×10-5 22 40738280 rs192703567 C T Intergenic 1.37 5.2×10-8 1.37 1.8×10-6 1.43 4.9×10-9 1.43 2.8×10-7 Chr=Chromosome; A1=Effect allele; A2=Other allele; OR=Odds ratio. Citation Format: Jovia L. Nierenberg, Linda Kachuri, Taylor B. Cavazos, Rebecca E. Graff, Thomas J. Hoffmann, Jie Zhang, Stacey Alexeeff, Laurel Habel, Douglas Corley, Stephen Van Den Eeden, Elad Ziv, Lori C. Sakoda, John S. Witte. Genetic risk factors for the development of multiple primary cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1446.

Genetically predicted fasting blood glucose level plays a causal role in intraocular pressure: A Mendelian randomisation study.

This study aimed to examine possible causal associations between various components of metabolic syndrome and glaucoma-related phenotypes. A two-sample Mendelian randomisation study was conducted with the models of inverse-variance weighted (IVW), maximum likelihood, weighted median and MR-Egger regression. We accessed data from publicly available genome-wide association studies for individual parameters of metabolic syndrome as the exposures and the data for glaucoma and its endophenotypes as the outcomes. Among 11 exposures and 6 outcomes examined in this Mendelian randomisation study, only fasting blood glucose level showed evidence of a causal influence on intraocular pressure. Results analysed by the IVW model suggested that each one-SD increase in genetically predicted fasting blood glucose level was significantly associated with 0.80 SD elevation in intraocular pressure (β: 0.80, 95% CI: 0.38-1.22, p: 2.12e-4). The maximum likelihood model (β: 0.82, 95% CI: 0.39-1.25, p: 1.616e-4) also supported a significant causal effect. The weighted median model (β: 0.78, 95% CI: 0.17-1.39, p: 0.012) showed a nominally significant effect whereas the MR-Egger model (β: 0.63, 95% CI: -0.32-1.59, p: 0.212) showed a consistent direction of effect but was not statistically significant. Several sensitivity analyses indicated no evidence of directional horizontal pleiotropy that would bias the result. This Mendelian randomisation study provides evidence for a causal role for genetically determined higher fasting blood glucose level in the development of increased intraocular pressure. This finding could be considered in the monitoring and control of intraocular pressure and may be instrumental in prevention strategies for ocular hypertension.

Genetic variants of PKLR are associated with acute pain in sickle cell disease

AbstractAcute pain, the most prominent complication of sickle cell disease (SCD), results from vaso-occlusion triggered by sickling of deoxygenated red blood cells (RBCs). Concentration of 2,3-diphosphoglycerate (2,3-DPG) in RBCs promotes deoxygenation by preferentially binding to the low-affinity T conformation of HbS. 2,3-DPG is an intermediate substrate in the glycolytic pathway in which pyruvate kinase (gene PKLR, protein PKR) is a rate-limiting enzyme; variants in PKLR may affect PKR activity, 2,3-DPG levels in RBCs, RBC sickling, and acute pain episodes (APEs). We performed a candidate gene association study using 2 cohorts: 242 adult SCD-HbSS patients and 977 children with SCD-HbSS or SCD-HbSβ0 thalassemia. Seven of 47 PKLR variants evaluated in the adult cohort were associated with hospitalization: intron 4, rs2071053; intron 2, rs8177970, rs116244351, rs114455416, rs12741350, rs3020781, and rs8177964. All 7 variants showed consistent effect directions in both cohorts and remained significant in weighted Fisher's meta-analyses of the adult and pediatric cohorts using P < .0071 as threshold to correct for multiple testing. Allele-specific expression analyses in an independent cohort of 52 SCD adults showed that the intronic variants are likely to influence APE by affecting expression of PKLR, although the causal variant and mechanism are not defined.

A236 ASSOCIATION OF STOOL METABOLOMIC PROFILE AND MICROBIOME COMPOSITION RISK SCORE WITH FUTURE ONSET OF CROHN’S DISEASE

BackgroundMicrobial composition-based risk score (MRS) was recently developed and validated to predict future risk of developing Crohn’s disease (CD) among healthy first-degree relatives (FDR) of CD patients. We hypothesized that stool metabolomic profiles, some of which are linked to the gut microbiome, are associated with future risk of CD.AimsTo assess the association of stool metabolomic profile with onset of CD and to determine the correlation between stool metabolites and the MRSMethodsHealthy FDR of CD patients were recruited as part of the nested case-control cohort of the CCC-GEM Project. Healthy FDRs who later developed CD (n=56) were matched approximately 1:1 by age, sex, follow-up duration, and geographical location with control FDRs remaining healthy (n=66). Stool metabolomics were assessed using the Metabolon’s DiscoveryHD4™ platform, and the stool microbiome characterised by 16s rDNA amplicon sequencing. We fitted a multivariable conditional logistic regression model on the disease status as a function of individual stool metabolites. We additionally performed Spearman correlation between each stool metabolite and the MRS.ResultsAmong 1,029 stool metabolites that were analyzed, 79 were associated with future risk of CD (p<0.05); however, none remained significant after multiple testing correction (FDR correction). Considering the exploratory nature of this study with limited sample size, we focused on the top seven metabolites associated with CD onset (p<0.01). Of these, two stool metabolites (dimethylglycine, methylmyristate) were associated with increased risk of CD onset while five (cytosine, guanine, cytidine, hydroxyglutarate, nervonate) were associated with decreased risk of developing CD. The two metabolites positively associated with CD onset were positively correlated with the MRS, while the five metabolites negatively associated with CD onset, were negatively correlated with the MRS. Meanwhile, 24 stool metabolites had significant correlation with MRS (FDR-corrected p<0.2). Among those, a total of four stool metabolites (cytosine, guanine, methymyristate, cytidine) overlapped with the top seven stool metabolites associated with CD onset.ConclusionsStool metabolite profiles may predict future risk of CD. A subset of these metabolites have significant correlation with the MRS with consistent direction of effect. This may suggest that stool metabolites mediate the putative effect of the gut microbiome on CD risk. Further validation in the full GEM cohort is warranted.Funding AgenciesCCC, CIHRThe Leona M. and Harry B. Helmsley Charitable Trust; Kenneth Croitoru is the recipient of the Canada Research Chair in Inflammatory Bowel Diseases; Sun-Ho Lee is a recipient of the Imagine/ CIHR/CAG Fellowship Award; Sun-Ho Lee, Juan Antonio Raygoza Garay, and Williams Turpin are recipients of fellowship awards from the Department of Medicine, Mount Sinai Hospital, Toronto, Canada.

A157 DEFINITIONS OF MEDITERRANEAN DIET INCONSISTENTLY ASSOCIATE WITH MARKERS OF GUT BARRIER FUNCTION OR SUBCLINICAL INFLAMMATION IN A POPULATION-BASED COHORT

BackgroundThe Mediterranean Diet (MD) is proposed to reduce the risk of Crohn’s disease (CD) onset in cohort studies, with inconsistent results. This inconsistency may be due to heterogeneity in defining MD scores. Additionally, relationships between MD compliance and intestinal permeability or sub-clinical inflammation are not defined.AimsWe examined correlations between different MD scores, and determined associations between MD compliance and intestinal permeability or subclinical inflammation in a cohort of first degree relatives of CD patients.MethodsWe used food frequency questionnaire data from 2,112 subjects of the Crohn’s Colitis Canada- Genes, Environment, Microbial (CCC-GEM) project. We obtained 12 MD definitions from the literature and calculated daily percent compliance, we further compared MD scores via pairwise correlations (Kendall’s Tau). We measured intestinal permeability via urinary fractional excretion ratio of lactulose to mannitol (LMR) (LMR≥0.03 defined abnormal), and subclinical inflammation via fecal calprotectin (FCP) measured with BÜHLMANN fCAL® ELISA (FCP≥250 defined abnormal). We fit multivariable regression models between MD compliance and abnormal LMR and FCP, respectively. Two-sided p<0.05 defined significance.ResultsThere was large variation in cross-correlations among MD scores, from nil (t=0.0, p=0.54) to highly significant (t=0.97, p<2.2e-16). Associations of MD compliance and abnormal LMR or FCP were in both directions of effect, largely non-significant. Of the 12 MD scores, none associated with abnormal LMR, while 4 associated with abnormal FCP-Odds Ratios =1.22, 1.23, 1.24, and 1.30; p=0.02, 0.02, 0.01, and 0.009, and 95% Confidence Intervals = [1.03,1.45], [1.04,1.45], [1.05,1.47], and [1.07,1.59] respectively. No diet remained significant after correcting for multiple testing.ConclusionsCurrently MD definitions vary widely. Despite discrepancies, we expected consistent directions of effect for MD compliance on LMR or FCP. The largely non-significant associations between MDs suggest limitations in definition, interpretation, and relation to biological outcomes.Submitted on behalf of the CCC-GEM consortium.Funding AgenciesCIHRCrohn’s and Colitis Canada Genetics Environment Microbial (CCC-GEM) III;The Leona M. and Harry B. Helmsley Charitable Trust; Justine Timpano is a recipient of a fellowship award from Mount Sinai Hospital; Kenneth Croitoru is the recipient of the Canada Research Chair in Inflammatory Bowel Diseases

P700 The GEM Project: Stool metabolomic profile is associated with microbiome risk score and with future onset of Crohn’s disease in healthy first-degree relatives

Abstract Background We recently developed and validated a microbial composition-based risk score (MRS) that predicts future risk of Crohn’s disease (CD) development among healthy first-degree relatives (FDR) of CD patients. We hypothesized that stool metabolomic profiles may mediate the effect of microbiome-based risk on future onset of CD. Methods Healthy FDRs of CD patients were recruited as part of the CCC-GEM Project. Stool metabolomics data were available in the nested case-control cohort (a subset of CCC-GEM cohort) whereby FDRs who later developed CD (n=56) were matched approximately 1:1 by age, sex, follow-up duration, and geographical location with control FDRs remaining healthy (n=66). Stool metabolomics were assessed using the Metabolon’s DiscoveryHD4™ platform, and the stool microbiome characterized by 16s rDNA amplicon sequencing. A multivariable conditional logistic regression model was evaluated on the disease development as a function of individual stool metabolites. Spearman correlation evaluated the rank values between stool metabolites and the MRS. Results 122 healthy FDRs (median age 15 years, 60% female) were followed for a median 5.2 years. Among 1,029 stool metabolites that were analyzed, 79 were associated with future risk of CD (p&amp;lt;0.05); however, none remained significant after adjustment for false-discovery rate. Considering the exploratory nature of this study with limited sample size, we focused on the top seven metabolites associated with CD onset (p&amp;lt;0.01). Of these, two stool metabolites (dimethylglycine, methylmyristate) were associated with increased risk of CD onset while five (cytosine, guanine, cytidine, hydroxyglutarate, nervonate) were associated with decreased risk of CD development. The two metabolites positively associated with CD onset were also positively correlated with the MRS, while the five metabolites negatively associated with CD onset, were also negatively correlated with the MRS. Meanwhile, 24 stool metabolites had significant correlation with MRS (false-discovery rate-corrected p&amp;lt;0.2). Among those, a total of four stool metabolites (cytosine, guanine, methymyristate, cytidine) overlapped with the top seven stool metabolites associated with CD onset. Conclusion Changes in stool metabolite profiles may predict future risk of CD. A subset of these metabolites has significant correlation with the MRS with consistent direction of effect. This may suggest that these particular stool metabolites mediate the putative effects of the gut microbiome on CD risk. Further validation in the entire GEM cohort is warranted.

The association of weight loss with changes in the gut microbiota diversity, composition, and intestinal permeability: a systematic review and meta-analysis

ABSTRACT The gut microbiome may be a mediator between obesity and health outcomes. However, it is unclear how intentional weight loss changes the gut microbiota and intestinal permeability. We aimed to systematically review and quantify this association. We searched Medline, Embase, CINAHL, Cochrane databases, and trial registries until June 2020 (PROSPERO: CRD42020205292). We included trials of weight loss interventions (energy-restricted diets, pharmacotherapy, bariatric surgery) reporting on the microbiome. Two reviewers independently completed screening, extraction, and risk assessment with the ROBINS-I tool. Pooled standardized mean differences (SMDs) were obtained from random-effects meta-analyses. Forty-seven trials with 1,916 participants (81% female) and a median follow-up of 6 months (range: 2–24) were included. Based on imprecise evidence but with fairly consistent direction of effect, weight loss was associated with a statistically significant increase in α-diversity [SMD: 0.4 (95% CI: 0.2, 0.6], p < .0001, I2 = 70%, n = 30 studies) and a statistically significant reduction in intestinal permeability [SMD: −0.7 (95% CI: −0.9, −0.4), p < .0001, I2 = 83%, n = 17 studies]. Each kg of weight loss was associated with a 0.012 (95% CI: 0.0003, 0.024, p = .045) increase in α-diversity and a −0.017 (95% CI: −0.034, −0.001, p = .038) reduction in intestinal permeability. There was clear evidence of increases in the relative abundance of Akkermansia, but no clear evidence of changes in individual phyla, species, or fecal short-chain fatty acids. Restricting the analyses to the studies with lower risk of bias did not materially alter the estimates. Increasing weight loss is positively associated with increases in gut microbiota α-diversity and reductions in intestinal permeability.

Profiling the metabolic landscape of AD

Metabolic dysfunction, including perturbations in lipid, neurotransmitter, and polyamine metabolism, is an early indicator of cognitive impairment and Alzheimer disease (AD) risk. Further investigation is needed to elucidate the role of genetic heterogeneity in these metabolic disturbances. Here, we interrogate metabolomic signatures in the brains of carriers of pathological mutations in APP, PSEN1, and PSEN2 (Autosomal Dominant AD; ADAD), risk variants in TREM2, non-carrier sporadic AD cases (sAD), individuals with neuropathology but without clinical symptoms (Presymptomatic), and neuropathology-free controls (CO). Metabolomic data from parietal brain tissue of donors to the Knight Alzheimer Disease Research Center and the Dominantly Inherited Alzheimer Network (ADAD, n=25; TREM2, n=21; sAD, n=305; Presymptomatic, n=15; CO, n=27) were generated using the Metabolon global metabolomics platform. A total of 627 metabolites passed our QC process. Differential abundance between AD strata and controls was tested using linear regression corrected for sex, age, and post-mortem interval. Age was excluded from ADAD models. Benjamini-Hochberg multiple testing correction was applied, and pathway analysis was performed with MetaboAnalyst and IMPaLA. In total, we identified 138 metabolites associated with distinct genetic strata (FDR q-value<0.05). For sAD, these included tryptophan betaine (β=-0.55) and N-acetylputrescine (β=-0.14). Metabolites associated with both sAD and ADAD were ergothioneine (β=-0.22 and -0.26 respectively) and serotonin (β=-0.34 and -0.57). TREM2 and ADAD showed association with α-tocopherol (β=-0.12 and -0.12). β-citrylglutamate abundance decreased in sAD, ADAD, and TREM2 versus controls (β=-0.14; -0.22; and -0.29). Pathways identified included glutamate, vitamin, and antioxidant metabolism. A 16-metabolite subset showed consistent direction of effect among the genetic strata with the magnitude of effect of ADAD greater than that of TREM2, in turn greater than sAD. A representation of these (eigengene) is associated with disease duration in sAD (p=5.65x10-03 ), possibly driven by tau accumulation. Hierarchical clustering identified 41 "early stage" sAD individuals with Braak tau stage similar to Presymptomatic (p=0.35), but lower than other sAD individuals (β=-0.56, p=3.09x10-04 ) (Figure 1). Our findings suggest distinct and characteristic metabolic perturbations in ADAD and TREM2 brains. Investigation of these differentially abundant metabolites may lead to greater insight into the metabolic etiology of AD and its impact on clinical presentation.

Long Non-Coding RNAs Involved in Progression of Non-Alcoholic Fatty Liver Disease to Steatohepatitis.

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease and is characterized by different stages varying from benign fat accumulation to non-alcoholic steatohepatitis (NASH) that may progress to cirrhosis and liver cancer. In recent years, a regulatory role of long non-coding RNAs (lncRNAs) in NAFLD has emerged. Therefore, we aimed to characterize the still poorly understood lncRNA contribution to disease progression. Transcriptome analysis in 60 human liver samples with various degrees of NAFLD/NASH was combined with a functional genomics experiment in an in vitro model where we exposed HepG2 cells to free fatty acids (FFA) to induce steatosis, then stimulated them with tumor necrosis factor alpha (TNFα) to mimic inflammation. Bioinformatics analyses provided a functional prediction of novel lncRNAs. We further functionally characterized the involvement of one novel lncRNA in the nuclear-factor-kappa B (NF-κB) signaling pathway by its silencing in Hepatoma G2 (HepG2) cells. We identified 730 protein-coding genes and 18 lncRNAs that responded to FFA/TNFα and associated with human NASH phenotypes with consistent effect direction, with most being linked to inflammation. One novel intergenic lncRNA, designated lncTNF, was 20-fold up-regulated upon TNFα stimulation in HepG2 cells and positively correlated with lobular inflammation in human liver samples. Silencing lncTNF in HepG2 cells reduced NF-κB activity and suppressed expression of the NF-κB target genes A20 and NFKBIA. The lncTNF we identified in the NF-κB signaling pathway may represent a novel target for controlling liver inflammation.

Quantifying the contribution of Neanderthal introgression to the heritability of complex traits

Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.

Genome-wide association study of body fat distribution traits in Hispanics/Latinos from the HCHS/SOL.

Central obesity is a leading health concern with a great burden carried by ethnic minority populations, especially Hispanics/Latinos. Genetic factors contribute to the obesity burden overall and to inter-population differences. We aimed to identify the loci associated with central adiposity measured as waist-to-hip ratio (WHR), waist circumference (WC) and hip circumference (HIP) adjusted for body mass index (adjBMI) by using the Hispanic Community Health Study/Study of Latinos (HCHS/SOL); determine if differences in associations differ by background group within HCHS/SOL and determine whether previously reported associations generalize to HCHS/SOL. Our analyses included 7472 women and 5200 men of mainland (Mexican, Central and South American) and Caribbean (Puerto Rican, Cuban and Dominican) background residing in the USA. We performed genome-wide association analyses stratified and combined across sexes using linear mixed-model regression. We identified 16 variants for waist-to-hip ratio adjusted for body mass index (WHRadjBMI), 22 for waist circumference adjusted for body mass index (WCadjBMI) and 28 for hip circumference adjusted for body mass index (HIPadjBMI), which reached suggestive significance (P < 1 × 10−6). Many loci exhibited differences in strength of associations by ethnic background and sex. We brought a total of 66 variants forward for validation in cohorts (N = 34 161) with participants of Hispanic/Latino, African and European descent. We confirmed four novel loci (P < 0.05 and consistent direction of effect, and P < 5 × 10−8 after meta-analysis), including two for WHRadjBMI (rs13301996, rs79478137); one for WCadjBMI (rs3168072) and one for HIPadjBMI (rs28692724). Also, we generalized previously reported associations to HCHS/SOL, (8 for WHRadjBMI, 10 for WCadjBMI and 12 for HIPadjBMI). Our study highlights the importance of large-scale genomic studies in ancestrally diverse Hispanic/Latino populations for identifying and characterizing central obesity susceptibility that may be ancestry-specific.

DNAm-based signatures of accelerated aging and mortality in blood are associated with low renal function

BackgroundThe difference between an individual's chronological and DNA methylation predicted age (DNAmAge), termed DNAmAge acceleration (DNAmAA), can capture life-long environmental exposures and age-related physiological changes reflected in methylation status. Several studies have linked DNAmAA to morbidity and mortality, yet its relationship with kidney function has not been assessed. We evaluated the associations between seven DNAm aging and lifespan predictors (as well as GrimAge components) and five kidney traits (estimated glomerular filtration rate [eGFR], urine albumin-to-creatinine ratio [uACR], serum urate, microalbuminuria and chronic kidney disease [CKD]) in up to 9688 European, African American and Hispanic/Latino individuals from seven population-based studies.ResultsWe identified 23 significant associations in our large trans-ethnic meta-analysis (p < 1.43E−03 and consistent direction of effect across studies). Age acceleration measured by the Extrinsic and PhenoAge estimators, as well as Zhang’s 10-CpG epigenetic mortality risk score (MRS), were associated with all parameters of poor kidney health (lower eGFR, prevalent CKD, higher uACR, microalbuminuria and higher serum urate). Six of these associations were independently observed in European and African American populations. MRS in particular was consistently associated with eGFR (β = − 0.12, 95% CI = [− 0.16, − 0.08] change in log-transformed eGFR per unit increase in MRS, p = 4.39E−08), prevalent CKD (odds ratio (OR) = 1.78 [1.47, 2.16], p = 2.71E-09) and higher serum urate levels (β = 0.12 [0.07, 0.16], p = 2.08E−06). The “first-generation” clocks (Hannum, Horvath) and GrimAge showed different patterns of association with the kidney traits. Three of the DNAm-estimated components of GrimAge, namely adrenomedullin, plasminogen-activation inhibition 1 and pack years, were positively associated with higher uACR, serum urate and microalbuminuria.ConclusionDNAmAge acceleration and DNAm mortality predictors estimated in whole blood were associated with multiple kidney traits, including eGFR and CKD, in this multi-ethnic study. Epigenetic biomarkers which reflect the systemic effects of age-related mechanisms such as immunosenescence, inflammaging and oxidative stress may have important mechanistic or prognostic roles in kidney disease. Our study highlights new findings linking kidney disease to biological aging, and opportunities warranting future investigation into DNA methylation biomarkers for prognostic or risk stratification in kidney disease.

The First Genome-Wide Association Study for Type 2 Diabetes in Youth: The Progress in Diabetes Genetics in Youth (ProDiGY) Consortium.

The prevalence of type 2 diabetes in youth has increased substantially, yet the genetic underpinnings remain largely unexplored. To identify genetic variants predisposing to youth-onset type 2 diabetes, we formed ProDiGY, a multiethnic collaboration of three studies (TODAY, SEARCH, and T2D-GENES) with 3,006 youth case subjects with type 2 diabetes (mean age 15.1 ± 2.9 years) and 6,061 diabetes-free adult control subjects (mean age 54.2 ± 12.4 years). After stratifying by principal component–clustered ethnicity, we performed association analyses on ∼10 million imputed variants using a generalized linear mixed model incorporating a genetic relationship matrix to account for population structure and adjusting for sex. We identified seven genome-wide significant loci, including the novel locus rs10992863 in PHF2 (P = 3.2 × 10−8; odds ratio [OR] = 1.23). Known loci identified in our analysis include rs7903146 in TCF7L2 (P = 8.0 × 10−20; OR 1.58), rs72982988 near MC4R (P = 4.4 × 10−14; OR 1.53), rs200893788 in CDC123 (P = 1.1 × 10−12; OR 1.32), rs2237892 in KCNQ1 (P = 4.8 × 10−11; OR 1.59), rs937589119 in IGF2BP2 (P = 3.1 × 10−9; OR 1.34), and rs113748381 in SLC16A11 (P = 4.1 × 10−8; OR 1.04). Secondary analysis with 856 diabetes-free youth control subjects uncovered an additional locus in CPEB2 (P = 3.2 × 10−8; OR 2.1) and consistent direction of effect for diabetes risk. In conclusion, we identified both known and novel loci in the first genome-wide association study of youth-onset type 2 diabetes.

The Effect of the Mediterranean Diet on Metabolic Health: A Systematic Review and Meta-Analysis of Controlled Trials in Adults.

The Mediterranean diet (MD) may provide metabolic benefits but no systematic review to date has examined its effect on a multitude of outcomes related to metabolic health. This systematic review with meta-analysis (International Prospective Register of Systematic Reviews, PROSPERO; number CRD42019141459) aimed to examine the MD’s effect on metabolic syndrome (MetSyn) incidence, components and risk factors (primary outcomes), and incidence and/or mortality from MetSyn-related comorbidities and receipt of pharmacologic treatment for MetSyn components and comorbidities (secondary outcomes). We searched Pubmed, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Web of Science for controlled trials published until June 2019, comparing the MD with no treatment, usual care, or different diets in adults. Studies not published in English and not promoting the whole MD were excluded. Two authors independently extracted data and assessed risk of bias using the Cochrane Collaboration’s and Risk of Bias in non-randomised studies (ROBINS-I) tools. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Random-effects meta-analyses, subgroup analyses and meta-regressions were performed, and heterogeneity was quantified using the I2 statistic. We identified 2654 reports and included 84 articles reporting 57 trials (n = 36,983). In random effects meta-analyses, the MD resulted in greater beneficial changes in 18 of 28 MetSyn components and risk factors (body weight, body mass index, waist circumference, systolic and diastolic blood pressure, glucose, insulin, homeostatic model assessment of insulin resistance (HOMA-IR) index, total-, low-density lipoprotein (LDL)- and high-density lipoprotein (HDL)-cholesterol, triglycerides, alanine transaminase, hepatic fat mass, C-reactive protein, interleukin-6, tumour necrosis factor-a, and flow-mediated dilatation) and lower risk of cardiovascular disease incidence (risk ratio (RR) = 0.61, 95% confidence intervals (CI) 0.42–0.80; I2 = 0%), and stroke (RR = 0.67, 95% CI 0.35–0.98; I2 = 0%). Only six studies reported effects on pharmacotherapy use, and pooled analysis indicated no differences between diet groups. Lack of consistency in comparator groups and other study characteristics across studies resulted in high heterogeneity for some outcomes, which could not be considerably explained by meta-regressions. However, a consistent direction of beneficial effect of the MD was observed for the vast majority of outcomes examined. Findings support MD’s beneficial effect on all components and most risk factors of the MetSyn, in addition to cardiovascular disease and stroke incidence. More studies are needed to establish effects on other clinical outcomes and use of pharmacotherapy for MetSyn components and comorbidities. Despite the high levels of heterogeneity for some outcomes, this meta-analysis enabled the comparison of findings across studies and the examination of consistency of effects. The consistent direction of effect, suggesting the MD’s benefits on metabolic health, supports the need to promote this dietary pattern to adult populations.

Drug therapies for chronic conditions and risk of Alzheimer's disease and related dementias: A scoping review.

Most older Americans use drug therapies for chronic conditions. Several are associated with risk of Alzheimer's disease and related dementias (ADRD). A scoping review was used to identify drug classes associated with increasing or decreasing ADRD risk. We analyzed size, type, and findings of the evidence. We identified 29 drug classes across 11 therapeutic areas, and 404 human studies. Most common were studies on drugs for hypertension (93) or hyperlipidemia (81). Fewer than five studies were identified for several anti-diabetic and anti-inflammatory drugs. Evidence was observational only for beta blockers, proton pump inhibitors, benzodiazepines, and disease-modifying anti-rheumatic drugs. For 13 drug classes, 50% or more of the studies reported consistent direction of effect on risk of ADRD. Future research targeting drug classes with limited/non-robust evidence, examining sex, racial heterogeneity, and separating classes by molecule, will facilitate understanding of associated risk, and inform clinical and policy efforts to alleviate the growing impact of ADRD.

Abstract 46: Whole Genome Sequence Analysis Of Blood Pressure Phenotypes In The Trans-omics For Precision Medicine And Centers For Common Disease Genomics Programs

Background: Although genome-wide association studies (GWAS) have made important strides in localizing genomic regions associated with blood pressure (BP) phenotypes, the causal mechanisms underlying the vast majority of identified signals remain to be elucidated. Whole genome sequencing (WGS) provides an opportunity for novel genomic discoveries and high-resolution refinement of identified GWAS signals. Methods: This multi-stage genomic study of BP was conducted in an ancestrally diverse sample of up to 735,905 participants from 20 cohorts. In the discovery stage WGS study, variants with minor allele counts &gt;10 were tested for association with systolic BP (SBP), diastolic BP (DBP), and hypertension (HTN) among 50,755 participants from the Trans-Omics for Precision Medicine and Centers for Common Disease Genomics programs using the Analysis Commons cloud based platform. Variants achieving suggestive genome-wide significance (P&lt;1х10 -6 ) were tested for replication among UK Biobank (N=383,145) and Million Veterans Program (N=318,891) participants with GWAS data imputed to the TOPMed and 1000 Genomes reference panels, respectively. Results: Discovery stage analyses identified 63 novel loci suggestively associated with BP. As expected, most of these variants (81%) had minor allele frequencies (MAFs)&lt;1%. Although none achieved genome-wide significance (P&lt;5х10 -8 ) in joint analyses of discovery and replication stages, two rare variants had consistent effect directions and achieved nominal significance in replication analyses, including one for DBP at CHL1 (rs932205533; MAF=1.2х10 -4 ; joint β=18.0; joint P=7.4х10 -8 ) and one for SBP at MACROD2 (rs752530366; MAF=8.6х10 -4 ; joint β=-5.1; joint P=3.8х10 -6 ). A total of 44 novel variants from previously reported loci (r 2 &lt;0.1 with previously reported variants) were also identified in the discovery stage analyses, including 31 rare variants with large effect sizes (70%). Nine common variants from these loci achieved genome-wide significance in joint analyses. Variants for SBP included ones at NPPB (rs12406089; MAF=0.34; joint β=-0.58; joint P=2.7х10 -79 ), AC137675.1 (rs2643826; MAF=0.56; joint β=0.56; joint P=1.5х10 -45 ), NEIL2 (rs804264; MAF=0.35; joint β=0.28; joint P=4.7х10 -20 ), CACNB2 (rs11014204; MAF=0.21; joint β=-0.53; joint P=6.8х10 -57 ), OVOL1 (rs557675; MAF=0.43; joint β=-0.25; joint P=1.9х10 -17 ), RP11-654D12.2 (rs8014582; MAF=0.05; joint β=-0.52; joint P=6.7х10 -13 ), and ATXN2 (rs35350651; MAF=0.67; joint β=-0.39; joint P=3.4х10 -38 ). Novel variants for DBP at INSR (rs36150639; MAF=0.45; joint β=-0.29; joint P=2.5х10 -27 ) and HTN at TBX3 (rs2891546; MAF=0.17; joint OR=0.95; joint P=3.1х10 -14 ) were also identified. Conclusion: WGS studies in large multi-ancestry samples can identify novel signals at previously reported GWAS loci, helping to localize causal genes and variants for BP.

Effect direction meta-analysis of GWAS identifies extreme, prevalent and shared pleiotropy in a large mammal

In genome-wide association studies (GWAS), variants showing consistent effect directions across populations are considered as true discoveries. We model this information in an Effect Direction MEta-analysis (EDME) to quantify pleiotropy using GWAS of 34 Cholesky-decorrelated traits in 44,000+ cattle with sequence variants. The effect-direction agreement between independent bull and cow datasets was used to quantify the false discovery rate by effect direction (FDRed) and the number of affected traits for prioritised variants. Variants with multi-trait p < 1e–6 affected 1∼22 traits with an average of 10 traits. EDME assigns pleiotropic variants to each trait which informs the biology behind complex traits. New pleiotropic loci are identified, including signals from the cattle FTO locus mirroring its bystander effects on human obesity. When validated in the 1000-Bull Genome database, the prioritized pleiotropic variants consistently predicted expected phenotypic differences between dairy and beef cattle. EDME provides robust approaches to control GWAS FDR and quantify pleiotropy.

Pseudouridine and N-formylmethionine associate with left ventricular mass index: Metabolome-wide association analysis of cardiac remodeling

BackgroundHeart failure (HF) is the fastest growing form of cardiovascular disease both nationally and globally, underlining a need to phenotype subclinical HF intermediaries to improve primary prevention. ObjectivesWe aimed to identify novel metabolite associations with left ventricular (LV) remodeling, one upstream HF intermediary, among a community-based cohort of individuals. MethodsWe examined 1052 Bogalusa Heart Study participants (34.98% African American, 57.41% female, aged 33.6–57.5 years). Measures of LV mass and relative wall thickness (RWT) were obtained using two-dimensional-guided echocardiographic measurements via validated eqs. LV mass was indexed to height2.7 to calculate left ventricular mass index (LVMI). Untargeted metabolomic analysis of fasting serum samples was conducted. In combined and ethnicity-stratified analyses, multivariable linear and multinomial logistic regression models tested the associations of metabolites with the continuous LVMI and RWT and categorical LV geometry phenotypes, respectively, after adjusting for demographic and traditional cardiovascular disease risk factors. ResultsPseudouridine (B = 1.38; p = 3.20 × 10−5) and N-formylmethionine (B = 1.65; 3.30 × 10−6) were significantly associated with LVMI in the overall sample as well significant in Caucasians, with consistent effect direction and nominal significance (p < .05) in African Americans. Upon exclusion of individuals with self-report myocardial infarction or congestive HF, we similarly observed a 1.33 g/m2.7 and 1.52 g/m2.7 higher LVMI for each standard deviation increase in pseudouridine and N-formylmethionine, respectively. No significant associations were observed for metabolites with RWT or categorical LV remodeling outcomes. ConclusionsThe current analysis identified novel associations of pseudouridine and N-formylmethionine with LVMI, suggesting that mitochondrial-derived metabolites may serve as early biomarkers for LV remodeling and subclinical HF.

An untargeted metabolomics study of blood pressure: findings from the Bogalusa Heart Study.

To identify novel and confirm previously reported metabolites associated with SBP, DBP, and hypertension in a biracial sample of Bogalusa Heart Study (BHS) participants. We employed untargeted, ultra-high performance liquid chromatography tandem mass spectroscopy metabolomics profiling among 1249 BHS participants (427 African-Americans and 822 whites) with BP and covariable data collected during the 2013 to 2016 visit cycle. A total of 1202 metabolites were tested for associations with continuous and binary BP phenotypes using multiple linear and logistic regression models, respectively, in overall and race-stratified analyses. A total of 24 novel metabolites robustly associated with BP, achieving Bonferroni-corrected P less than 4.16 × 10 in the overall analysis and consistent effect sizes across race groups. The identified metabolites included three amino acid and nucleotide metabolites from histidine, pyrimidine, or tryptophan metabolism sub-pathways, seven cofactor and vitamin or xenobiotic metabolites from the ascorbate and aldarate metabolism, bacterial/fungal, chemical, and food component sub-pathways, 10 lipid metabolites from the eicosanoid, phosphatidylcholine, phosphatidylethanolamine, and sphingolipid metabolism sub-pathways, and four still unnamed metabolites. Six previously described metabolites were robustly confirmed by our study (Bonferroni-corrected P < 4.95 × 10 and consistent effect directions across studies). Furthermore, previously reported metabolites for SBP, DBP, and hypertension demonstrated 5.92-fold, 4.77-fold, and 4.54-fold enrichment for nominally significant signals in the BHS (P = 3.08 × 10, 5.93 × 10, and 2.30 × 10, respectively). In aggregate, our study provides new information about potential molecular mechanisms underlying BP regulation. We also demonstrate reproducibility of findings across studies despite differences in study populations and metabolite profiling methods.

Serum metabolites associate with lipid phenotypes among Bogalusa Heart Study participants.

Dyslipidemia has been identified as a major risk factor for cardiovascular disease. We aimed to identify metabolites and metabolite modules showing novel association with lipids among Bogalusa Heart Study (BHS) participants using untargeted metabolomics. Untargeted ultrahigh performance liquid chromatography-tandem mass spectroscopy was used to quantify serum metabolites of 1 243 BHS participants (816 whites and 427 African-Americans). The association of single metabolites with lipids was assessed using multiple linear regression models to adjust for covariables. Weighted correlation network analysis was utilized to identify modules of co-abundant metabolites and examine their covariable adjusted correlations with lipids. All analyses were conducted according to race and using Bonferroni-corrected α-thresholds to determine statistical significance. Thirteen metabolites with known biochemical identities showing novel association achieved Bonferroni-significance, p<1.04×10-5, and showed consistent effect directions in both whites and African-Americans. Twelve were from lipid sub-pathways including fatty acid metabolism (arachidonoylcholine, dihomo-linolenoyl-choline, docosahexaenoylcholine, linoleoylcholine, oleoylcholine, palmitoylcholine, and stearoylcholine), monohydroxy fatty acids (2-hydroxybehenate, 2-hydroxypalmitate, and 2-hydroxystearate), and lysoplasmalogens [1-(1-enyl-oleoyl)-GPE (P-18:1) and 1-(1-enyl-stearoyl)-GPE (P-18:0)]. The gamma-glutamylglutamine, peptide from the gamma-glutamyl amino acid sub-pathway, were also identified. In addition, four metabolite modules achieved Bonferroni-significance, p<1.39×10-3, in both whites and African-Americans. These four modules were largely comprised of metabolites from lipid sub-pathways, with one module comprised of metabolites which were not identified in the single metabolite analyses. The current study identified 13 metabolites and 4 metabolite modules showing novel association with lipids, providing new insights into the physiological mechanisms regulating lipid levels.