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1.
Front Immunol ; 15: 1415102, 2024.
Article in English | MEDLINE | ID: mdl-39007132

ABSTRACT

Human regulatory T cells (Treg) suppress other immune cells. Their dysfunction contributes to the pathophysiology of autoimmune diseases, including type 1 diabetes (T1D). Infusion of Tregs is being clinically evaluated as a novel way to prevent or treat T1D. Genetic modification of Tregs, most notably through the introduction of a chimeric antigen receptor (CAR) targeting Tregs to pancreatic islets, may improve their efficacy. We evaluated CAR targeting of human Tregs to monocytes, a human ß cell line and human islet ß cells in vitro. Targeting of HLA-A2-CAR (A2-CAR) bulk Tregs to HLA-A2+ cells resulted in dichotomous cytotoxic killing of human monocytes and islet ß cells. In exploring subsets and mechanisms that may explain this pattern, we found that CD39 expression segregated CAR Treg cytotoxicity. CAR Tregs from individuals with more CD39low/- Tregs and from individuals with genetic polymorphism associated with lower CD39 expression (rs10748643) had more cytotoxicity. Isolated CD39- CAR Tregs had elevated granzyme B expression and cytotoxicity compared to the CD39+ CAR Treg subset. Genetic overexpression of CD39 in CD39low CAR Tregs reduced their cytotoxicity. Importantly, ß cells upregulated protein surface expression of PD-L1 and PD-L2 in response to A2-CAR Tregs. Blockade of PD-L1/PD-L2 increased ß cell death in A2-CAR Treg co-cultures suggesting that the PD-1/PD-L1 pathway is important in protecting islet ß cells in the setting of CAR immunotherapy. In summary, introduction of CAR can enhance biological differences in subsets of Tregs. CD39+ Tregs represent a safer choice for CAR Treg therapies targeting tissues for tolerance induction.


Subject(s)
Apyrase , Receptors, Chimeric Antigen , T-Lymphocytes, Regulatory , Humans , Apyrase/immunology , Apyrase/metabolism , T-Lymphocytes, Regulatory/immunology , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/genetics , Receptors, Chimeric Antigen/metabolism , Cytotoxicity, Immunologic , Islets of Langerhans/immunology , Islets of Langerhans/metabolism , Diabetes Mellitus, Type 1/immunology , Diabetes Mellitus, Type 1/therapy , HLA-A2 Antigen/immunology , HLA-A2 Antigen/genetics , HLA-A2 Antigen/metabolism , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Insulin-Secreting Cells/immunology , Insulin-Secreting Cells/metabolism , Antigens, CD
2.
bioRxiv ; 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38948734

ABSTRACT

Comprehensive molecular and cellular phenotyping of human islets can enable deep mechanistic insights for diabetes research. We established the Human Islet Data Analysis and Sharing (HI-DAS) consortium to advance goals in accessibility, usability, and integration of data from human islets isolated from donors with and without diabetes at the Alberta Diabetes Institute (ADI) IsletCore. Here we introduce HumanIslets.com, an open resource for the research community. This platform, which presently includes data on 547 human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at the donor, islet and single-cell levels. As an example of the analytic capacity of this resource we show a dissociation between cell culture effects on transcript and protein expression, and an approach to correct for exocrine contamination found in hand-picked islets. Finally, we provide an example workflow and visualization that highlights links between type 2 diabetes status, SERCA3b Ca2+-ATPase levels at the transcript and protein level, insulin secretion and islet cell phenotypes. HumanIslets.com provides a growing and adaptable set of resources and tools to support the metabolism and diabetes research community.

3.
Diabetes Care ; 47(6): 1032-1041, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38608262

ABSTRACT

OBJECTIVE: To characterize high type 1 diabetes (T1D) genetic risk in a population where type 2 diabetes (T2D) predominates. RESEARCH DESIGN AND METHODS: Characteristics typically associated with T1D were assessed in 109,594 Million Veteran Program participants with adult-onset diabetes, 2011-2021, who had T1D genetic risk scores (GRS) defined as low (0 to <45%), medium (45 to <90%), high (90 to <95%), or highest (≥95%). RESULTS: T1D characteristics increased progressively with higher genetic risk (P < 0.001 for trend). A GRS ≥90% was more common with diabetes diagnoses before age 40 years, but 95% of those participants were diagnosed at age ≥40 years, and their characteristics resembled those of individuals with T2D in mean age (64.3 years) and BMI (32.3 kg/m2). Compared with the low-risk group, the highest-risk group was more likely to have diabetic ketoacidosis (low GRS 0.9% vs. highest GRS 3.7%), hypoglycemia prompting emergency visits (3.7% vs. 5.8%), outpatient plasma glucose <50 mg/dL (7.5% vs. 13.4%), a shorter median time to start insulin (3.5 vs. 1.4 years), use of a T1D diagnostic code (16.3% vs. 28.1%), low C-peptide levels if tested (1.8% vs. 32.4%), and glutamic acid decarboxylase antibodies (6.9% vs. 45.2%), all P < 0.001. CONCLUSIONS: Characteristics associated with T1D were increased with higher genetic risk, and especially with the top 10% of risk. However, the age and BMI of those participants resemble those of people with T2D, and a substantial proportion did not have diagnostic testing or use of T1D diagnostic codes. T1D genetic screening could be used to aid identification of adult-onset T1D in settings in which T2D predominates.


Subject(s)
Diabetes Mellitus, Type 1 , Veterans , Humans , Diabetes Mellitus, Type 1/genetics , Diabetes Mellitus, Type 1/epidemiology , Male , Middle Aged , Veterans/statistics & numerical data , Female , Adult , Aged , Genetic Predisposition to Disease , Diabetes Mellitus, Type 2/genetics , Diabetes Mellitus, Type 2/epidemiology , Risk Factors
5.
J Clin Epidemiol ; 153: 34-44, 2023 01.
Article in English | MEDLINE | ID: mdl-36368478

ABSTRACT

OBJECTIVES: We aimed to compare the performance of approaches for classifying insulin-treated diabetes within research datasets without measured classification biomarkers, evaluated against two independent biological definitions of diabetes type. STUDY DESIGN AND SETTING: We compared accuracy of ten reported approaches for classifying insulin-treated diabetes into type 1 (T1D) and type 2 (T2D) diabetes in two cohorts: UK Biobank (UKBB) n = 26,399 and Diabetes Alliance for Research in England (DARE) n = 1,296. The overall performance for classifying T1D and T2D was assessed using: a T1D genetic risk score and genetic stratification method (UKBB); C-peptide measured at >3 years diabetes duration (DARE). RESULTS: Approaches' accuracy ranged from 71% to 88% (UKBB) and 68% to 88% (DARE). When classifying all participants, combining early insulin requirement with a T1D probability model (incorporating diagnosis age and body image issue [BMI]), and interview-reported diabetes type (UKBB available in only 15%) consistently achieved high accuracy (UKBB 87% and 87% and DARE 85% and 88%, respectively). For identifying T1D with minimal misclassification, models with high thresholds or young diagnosis age (<20 years) had highest performance. Findings were incorporated into an online tool identifying optimum approaches based on variable availability. CONCLUSION: Models combining continuous features with early insulin requirement are the most accurate methods for classifying insulin-treated diabetes in research datasets without measured classification biomarkers.


Subject(s)
Diabetes Mellitus, Type 1 , Diabetes Mellitus, Type 2 , Humans , Young Adult , Adult , Diabetes Mellitus, Type 1/drug therapy , Diabetes Mellitus, Type 1/genetics , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/drug therapy , Diabetes Mellitus, Type 2/genetics , Risk Factors , Insulin/therapeutic use , Biomarkers
6.
Diabetes Care ; 45(5): 1124-1131, 2022 05 01.
Article in English | MEDLINE | ID: mdl-35312757

ABSTRACT

OBJECTIVE: Genetic risk scores (GRS) aid classification of diabetes type in White European adult populations. We aimed to assess the utility of GRS in the classification of diabetes type among racially/ethnically diverse youth in the U.S. RESEARCH DESIGN AND METHODS: We generated type 1 diabetes (T1D)- and type 2 diabetes (T2D)-specific GRS in 2,045 individuals from the SEARCH for Diabetes in Youth study. We assessed the distribution of genetic risk stratified by diabetes autoantibody positive or negative (DAA+/-) and insulin sensitivity (IS) or insulin resistance (IR) and self-reported race/ethnicity (White, Black, Hispanic, and other). RESULTS: T1D and T2D GRS were strong independent predictors of etiologic type. The T1D GRS was highest in the DAA+/IS group and lowest in the DAA-/IR group, with the inverse relationship observed with the T2D GRS. Discrimination was similar across all racial/ethnic groups but showed differences in score distribution. Clustering by combined genetic risk showed DAA+/IR and DAA-/IS individuals had a greater probability of T1D than T2D. In DAA- individuals, genetic probability of T1D identified individuals most likely to progress to absolute insulin deficiency. CONCLUSIONS: Diabetes type-specific GRS are consistent predictors of diabetes type across racial/ethnic groups in a U.S. youth cohort, but future work needs to account for differences in GRS distribution by ancestry. T1D and T2D GRS may have particular utility for classification of DAA- children.


Subject(s)
Diabetes Mellitus, Type 1 , Diabetes Mellitus, Type 2 , Insulin Resistance , Adolescent , Adult , Child , Diabetes Mellitus, Type 1/drug therapy , Diabetes Mellitus, Type 2/drug therapy , Diabetes Mellitus, Type 2/genetics , Genetic Predisposition to Disease , Humans , Insulin/therapeutic use , Insulin Resistance/genetics , Risk Factors
9.
Nat Commun ; 12(1): 6441, 2021 11 08.
Article in English | MEDLINE | ID: mdl-34750397

ABSTRACT

Clinical classification is essential for estimating disease prevalence but is difficult, often requiring complex investigations. The widespread availability of population level genetic data makes novel genetic stratification techniques a highly attractive alternative. We propose a generalizable mathematical framework for determining disease prevalence within a cohort using genetic risk scores. We compare and evaluate methods based on the means of genetic risk scores' distributions; the Earth Mover's Distance between distributions; a linear combination of kernel density estimates of distributions; and an Excess method. We demonstrate the performance of genetic stratification to produce robust prevalence estimates. Specifically, we show that robust estimates of prevalence are still possible even with rarer diseases, smaller cohort sizes and less discriminative genetic risk scores, highlighting the general utility of these approaches. Genetic stratification techniques offer exciting new research tools, enabling unbiased insights into disease prevalence and clinical characteristics unhampered by clinical classification criteria.


Subject(s)
Algorithms , Diabetes Mellitus, Type 1/genetics , Diabetes Mellitus, Type 2/genetics , Genetic Predisposition to Disease/genetics , Models, Genetic , Cohort Studies , Computer Simulation , Diabetes Mellitus, Type 1/diagnosis , Diabetes Mellitus, Type 1/epidemiology , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/epidemiology , Humans , Multifactorial Inheritance/genetics , Polymorphism, Single Nucleotide , Prevalence , Reproducibility of Results , Risk Factors , Sensitivity and Specificity
10.
Diabetologia ; 64(10): 2258-2265, 2021 10.
Article in English | MEDLINE | ID: mdl-34272580

ABSTRACT

AIMS/HYPOTHESIS: Among white European children developing type 1 diabetes, the otherwise common HLA haplotype DR15-DQ6 is rare, and highly protective. Adult-onset type 1 diabetes is now known to represent more overall cases than childhood onset, but it is not known whether DR15-DQ6 is protective in older-adult-onset type 1 diabetes. We sought to quantify DR15-DQ6 protection against type 1 diabetes as age of onset increased. METHODS: In two independent cohorts we assessed the proportion of type 1 diabetes cases presenting through the first 50 years of life with DR15-DQ6, compared with population controls. In the After Diabetes Diagnosis Research Support System-2 (ADDRESS-2) cohort (n = 1458) clinician-diagnosed type 1 diabetes was confirmed by positivity for one or more islet-specific autoantibodies. In UK Biobank (n = 2502), we estimated type 1 diabetes incidence rates relative to baseline HLA risk for each HLA group using Poisson regression. Analyses were restricted to white Europeans and were performed in three groups according to age at type 1 diabetes onset: 0-18 years, 19-30 years and 31-50 years. RESULTS: DR15-DQ6 was protective against type 1 diabetes through to age 50 years (OR < 1 for each age group, all p < 0.001). The following ORs for type 1 diabetes, relative to a neutral HLA genotype, were observed in ADDRESS-2: age 5-18 years OR 0.16 (95% CI 0.08, 0.31); age 19-30 years OR 0.10 (0.04, 0.23); and age 31-50 years OR 0.37 (0.21, 0.68). DR15-DQ6 also remained highly protective at all ages in UK Biobank. Without DR15-DQ6, the presence of major type 1 diabetes high-risk haplotype (either DR3-DQ2 or DR4-DQ8) was associated with increased risk of type 1 diabetes. CONCLUSIONS/INTERPRETATION: HLA DR15-DQ6 confers dominant protection from type 1 diabetes across the first five decades of life.


Subject(s)
Diabetes Mellitus, Type 1/genetics , HLA-DQ Antigens/genetics , HLA-DR Serological Subtypes/genetics , Adolescent , Adult , Age of Onset , Autoantibodies/blood , Case-Control Studies , Child , Child, Preschool , Cohort Studies , Diabetes Mellitus, Type 1/epidemiology , Diabetes Mellitus, Type 1/immunology , Female , Genotype , HLA-DQ Antigens/immunology , HLA-DR Serological Subtypes/immunology , Humans , Infant , Infant, Newborn , Male , Middle Aged , Polymorphism, Genetic , Risk Factors , United Kingdom , Young Adult
11.
Kidney Int Rep ; 5(10): 1643-1650, 2020 Oct.
Article in English | MEDLINE | ID: mdl-33102956

ABSTRACT

BACKGROUND: IgA nephropathy (IgAN) is the commonest glomerulonephritis worldwide. Its prevalence is difficult to estimate, as people with mild disease do not commonly receive a biopsy diagnosis. We aimed to generate an IgA nephropathy genetic risk score (IgAN-GRS) and estimate the proportion of people with hematuria who had IgAN in the UK Biobank (UKBB). METHODS: We calculated an IgAN-GRS using 14 single-nucleotide polymorphisms (SNPs) drawn from the largest European Genome-Wide Association Study (GWAS) and validated the IgAN-GRS in 464 biopsy-proven IgAN European cases from the UK Glomerulonephritis DNA Bank (UKGDB) and in 379,767 Europeans in the UKBB. We used the mean of IgAN-GRS to calculate the proportion of potential IgAN in 14,181 with hematuria and other nonspecific renal phenotypes from 379,767 Europeans in the UKBB. RESULTS: The IgAN-GRS was higher in the IgAN cohort (4.30; 95% confidence interval [95% CI: 4.23-4.38) than in controls (3.98; 3.97-3.98; P < 0.0001). The mean GRS in UKBB participants with hematuria (n = 12,858) was higher (4.04; 4.02-4.06) than UKBB controls (3.98; 3.97-3.98; P < 0.0001) and higher in those with hematuria, hypertension, and microalbuminuria (n = 1323) (4.07; 4.02-4.13) versus (3.98; 3.97-3.98; P = 0.0003). Using the difference in these means, we estimated that IgAN accounted for 19% of noncancer hematuria and 28% with hematuria, hypertension, and microalbuminuria in UKBB. CONCLUSIONS: We used an IgAN-GRS to estimate the prevalence of IgAN contributing to common phenotypes that are not always biopsied. The noninvasive use of polygenic risk in this setting may have further utility to identify likely etiology of nonspecific renal phenotypes in large population cohorts.

12.
Nat Med ; 26(8): 1247-1255, 2020 08.
Article in English | MEDLINE | ID: mdl-32770166

ABSTRACT

Type 1 diabetes (T1D)-an autoimmune disease that destroys the pancreatic islets, resulting in insulin deficiency-often begins early in life when islet autoantibody appearance signals high risk1. However, clinical diabetes can follow in weeks or only after decades, and is very difficult to predict. Ketoacidosis at onset remains common2,3 and is most severe in the very young4,5, in whom it can be life threatening and difficult to treat6-9. Autoantibody surveillance programs effectively prevent most ketoacidosis10-12 but require frequent evaluations whose expense limits public health adoption13. Prevention therapies applied before onset, when greater islet mass remains, have rarely been feasible14 because individuals at greatest risk of impending T1D are difficult to identify. To remedy this, we sought accurate, cost-effective estimation of future T1D risk by developing a combined risk score incorporating both fixed and variable factors (genetic, clinical and immunological) in 7,798 high-risk children followed closely from birth for 9.3 years. Compared with autoantibodies alone, the combined model dramatically improves T1D prediction at ≥2 years of age over horizons up to 8 years of age (area under the receiver operating characteristic curve ≥ 0.9), doubles the estimated efficiency of population-based newborn screening to prevent ketoacidosis, and enables individualized risk estimates for better prevention trial selection.


Subject(s)
Autoantibodies/blood , Diabetes Mellitus, Type 1/epidemiology , Ketosis/blood , Risk Assessment , Autoantibodies/immunology , Autoimmunity/genetics , Child , Child, Preschool , Diabetes Mellitus, Type 1/blood , Diabetes Mellitus, Type 1/immunology , Female , Genetic Predisposition to Disease , Humans , Infant , Infant, Newborn , Insulin/deficiency , Insulin/immunology , Islets of Langerhans/immunology , Islets of Langerhans/pathology , Ketosis/immunology , Male , Neonatal Screening , Risk Factors
13.
Aliment Pharmacol Ther ; 52(7): 1165-1173, 2020 10.
Article in English | MEDLINE | ID: mdl-32790217

ABSTRACT

BACKGROUND: Single nucleotide polymorphism-based genetic risk scores (GRS) model genetic risk as a continuum and can discriminate coeliac disease but have not been validated in clinic. Human leukocyte antigen (HLA) DQ gene testing is available in clinic but does not include non-HLA attributed risk and is limited by discrete risk stratification. AIMS: To accurately characterise both HLA and non-HLA coeliac disease genetic risk as a single nucleotide polymorphism-based GRS and evaluate diagnostic utility. METHODS: We developed a 42 single nucleotide polymorphism coeliac disease GRS from a European case-control study (12 041 cases vs 12 228 controls) using HLA-DQ imputation and published genome-wide association studies. We validated the GRS in UK Biobank (1237 cases) and developed direct genotyping assays. We tested the coeliac disease GRS in a pilot clinical cohort of 128 children presenting with suspected coeliac disease. RESULTS: The GRS was more discriminative of coeliac disease than HLA-DQ stratification in UK Biobank (receiver operating characteristic area under the curve [ROC-AUC] = 0.88 [95% CIs: 0.87-0.89] vs 0.82 [95% CIs: 0.80-0.83]). We demonstrated similar discrimination in the pilot clinical cohort (114 cases vs 40 controls, ROC-AUC = 0.84 [95% CIs: 0.76-0.91]). As a rule-out test, no children with coeliac disease in the clinical cohort had a GRS below 38th population centile. CONCLUSIONS: A single nucleotide polymorphism-based GRS may offer more effective and cost-efficient testing of coeliac disease genetic risk in comparison to HLA-DQ stratification. As a comparatively inexpensive test it could facilitate non-invasive coeliac disease diagnosis but needs detailed assessment in the context of other diagnostic tests and against current diagnostic algorithms.


Subject(s)
Celiac Disease/genetics , Genetic Predisposition to Disease , Case-Control Studies , Celiac Disease/diagnosis , Celiac Disease/epidemiology , Genome-Wide Association Study , Humans , Pilot Projects , Polymorphism, Single Nucleotide , Risk Factors
14.
Sci Rep ; 10(1): 9450, 2020 06 11.
Article in English | MEDLINE | ID: mdl-32528078

ABSTRACT

Type 1 diabetes (T1D) is a significant problem in Indians and misclassification of T1D and type 2 diabetes (T2D) is a particular problem in young adults in this population due to the high prevalence of early onset T2D at lower BMI. We have previously shown a genetic risk score (GRS) can be used to discriminate T1D from T2D in Europeans. We aimed to test the ability of a T1D GRS to discriminate T1D from T2D and controls in Indians. We studied subjects from Pune, India of Indo-European ancestry; T1D (n = 262 clinically defined, 200 autoantibody positive), T2D (n = 345) and controls (n = 324). We used the 9 SNP T1D GRS generated in Europeans and assessed its ability to discriminate T1D from T2D and controls in Indians. We compared Indians with Europeans from the Wellcome Trust Case Control Consortium study; T1D (n = 1963), T2D (n = 1924) and controls (n = 2938). The T1D GRS was discriminative of T1D from T2D in Indians but slightly less than in Europeans (ROC AUC 0.84 v 0.87, p < 0.0001). HLA SNPs contributed the majority of the discriminative power in Indians. A T1D GRS using SNPs defined in Europeans is discriminative of T1D from T2D and controls in Indians. As with Europeans, the T1D GRS may be useful for classifying diabetes in Indians.


Subject(s)
Asian People/genetics , Diabetes Mellitus, Type 1/genetics , Genetic Predisposition to Disease/genetics , Polymorphism, Single Nucleotide/genetics , Adolescent , Adult , Alleles , Case-Control Studies , Child , Diabetes Mellitus, Type 2/genetics , Female , Humans , India , Male , Middle Aged , Risk Factors
15.
AANA J ; 87(3): 199-204, 2019 Jun.
Article in English | MEDLINE | ID: mdl-31584397

ABSTRACT

This retrospective cohort study aimed to explore the study institution's intraoperative ketamine use during kyphoplasty and compare narcotic requirements in patients who received intraoperative ketamine with those who did not. The authors hypothesized that a single dose of ketamine during kyphoplasty would reduce postoperative narcotic consumption. Included patients underwent kyphoplasty under monitored anesthesia care between 2012 and 2013. Excluded patients were younger than 18 years or had general anesthesia, endotracheal intubation, or major intraoperative complications. Narcotics were converted into morphine equivalents for comparison. Analysis included c2, correlation analyses, multivariate regression analysis, and analysis of variance. Overall, 279 patients were included. Men were a minority of the sample, 26.2% (73/279). More than 83% of patients were ASA class 3 (232/279), and more than 50% repaired a single vertebra (154/279). A single dose of ketamine was administered in 15.8% of kyphoplasties, with an average dose of 38.7 mg (range = 2-150 mg). Intraoperative ketamine administration was predictive of decreased intraoperative narcotic requirements (P < .001) but was not associated with decreased postoperative narcotic requirements (P = .442). Patients remained hemodynamically stable in the preoperative and postoperative period. Ketamine did not reduce postoperative narcotic consumption but reduced intraoperative narcotic consumption in this sample.


Subject(s)
Analgesics, Opioid/therapeutic use , Anesthesia, General , Anesthetics, Dissociative/therapeutic use , Ketamine/therapeutic use , Kyphoplasty , Pain, Postoperative/drug therapy , Aged , Analgesics, Opioid/administration & dosage , Anesthetics, Dissociative/administration & dosage , Cohort Studies , Female , Humans , Intraoperative Period , Ketamine/administration & dosage , Male , Nurse Anesthetists , Retrospective Studies , Treatment Outcome
16.
J Crohns Colitis ; 13(12): 1578-1582, 2019 Dec 10.
Article in English | MEDLINE | ID: mdl-31125052

ABSTRACT

BACKGROUND AND AIMS: The causes of microscopic colitis are currently poorly understood. Previous reports have found clinical associations with coeliac disease and genetic associations at the human leukocyte antigen [HLA] locus on the ancestral 8.1 haplotype. We investigated pharmacological and genetic factors associated with microscopic colitis in the UK Biobank. METHODS: In total, 483 European UK Biobank participants were identified by ICD10 coding, and a genome-wide association study was performed using BOLT-LMM, with a sensitivity analysis performed excluding potential confounders. The HLA*IMP:02 algorithm was used to estimate allele frequency at 11 classical HLA genes, and downstream analysis was performed using FUMA. Genetic overlap with inflammatory bowel disease [Crohn's disease and ulcerative colitis] was investigated using genetic risk scores. RESULTS: We found significant phenotypic associations with smoking status, coeliac disease and the use of proton-pump inhibitors but not with other commonly reported pharmacological risk factors. Using the largest sample size to date, we confirmed a recently reported association with the MHC Ancestral 8.1 Haplotype. Downstream analysis suggests association with digestive tract morphogenesis. By calculating genetic risk scores, we also report suggestive evidence of shared genetic risk with Crohn's disease, but not with ulcerative colitis. CONCLUSIONS: This report confirms the role of genetic determinants in the HLA in the pathogenesis of microscopic colitis. The genetic overlap with Crohn's disease suggests a common underlying mechanism of disease.


Subject(s)
Colitis, Microscopic , Proton Pump Inhibitors/therapeutic use , Biological Variation, Population , Colitis, Microscopic/drug therapy , Colitis, Microscopic/genetics , Colitis, Microscopic/immunology , Databases, Genetic/statistics & numerical data , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Middle Aged , Pharmacogenomic Variants , Polymorphism, Single Nucleotide , United Kingdom/epidemiology
17.
Nat Commun ; 10(1): 1585, 2019 04 05.
Article in English | MEDLINE | ID: mdl-30952852

ABSTRACT

Sleep is an essential human function but its regulation is poorly understood. Using accelerometer data from 85,670 UK Biobank participants, we perform a genome-wide association study of 8 derived sleep traits representing sleep quality, quantity and timing, and validate our findings in 5,819 individuals. We identify 47 genetic associations at P < 5 × 10-8, of which 20 reach a stricter threshold of P < 8 × 10-10. These include 26 novel associations with measures of sleep quality and 10 with nocturnal sleep duration. The majority of identified variants associate with a single sleep trait, except for variants previously associated with restless legs syndrome. For sleep duration we identify a missense variant (p.Tyr727Cys) in PDE11A as the likely causal variant. As a group, sleep quality loci are enriched for serotonin processing genes. Although accelerometer-derived measures of sleep are imperfect and may be affected by restless legs syndrome, these findings provide new biological insights into sleep compared to previous efforts based on self-report sleep measures.


Subject(s)
Polysomnography/methods , Sleep Wake Disorders/genetics , Sleep/genetics , Accelerometry/methods , Circadian Rhythm , Humans , Polymorphism, Single Nucleotide , Serotonin/genetics , Serotonin/metabolism , Sleep Wake Disorders/diagnosis , Waist-Hip Ratio
18.
Nat Commun ; 10(1): 343, 2019 01 29.
Article in English | MEDLINE | ID: mdl-30696823

ABSTRACT

Being a morning person is a behavioural indicator of a person's underlying circadian rhythm. Using genome-wide data from 697,828 UK Biobank and 23andMe participants we increase the number of genetic loci associated with being a morning person from 24 to 351. Using data from 85,760 individuals with activity-monitor derived measures of sleep timing we find that the chronotype loci associate with sleep timing: the mean sleep timing of the 5% of individuals carrying the most morningness alleles is 25 min earlier than the 5% carrying the fewest. The loci are enriched for genes involved in circadian regulation, cAMP, glutamate and insulin signalling pathways, and those expressed in the retina, hindbrain, hypothalamus, and pituitary. Using Mendelian Randomisation, we show that being a morning person is causally associated with better mental health but does not affect BMI or risk of Type 2 diabetes. This study offers insights into circadian biology and its links to disease in humans.


Subject(s)
Circadian Rhythm , Genome-Wide Association Study , White People/genetics , Adult , Aged , Cyclic AMP/metabolism , Female , Genetic Loci , Glutamic Acid/metabolism , Humans , Male , Middle Aged , Sleep , United Kingdom
19.
Diabetes Care ; 42(2): 200-207, 2019 02.
Article in English | MEDLINE | ID: mdl-30655379

ABSTRACT

OBJECTIVE: Previously generated genetic risk scores (GRSs) for type 1 diabetes (T1D) have not captured all known information at non-HLA loci or, particularly, at HLA risk loci. We aimed to more completely incorporate HLA alleles, their interactions, and recently discovered non-HLA loci into an improved T1D GRS (termed the "T1D GRS2") to better discriminate diabetes subtypes and to predict T1D in newborn screening studies. RESEARCH DESIGN AND METHODS: In 6,481 case and 9,247 control subjects from the Type 1 Diabetes Genetics Consortium, we analyzed variants associated with T1D both in the HLA region and across the genome. We modeled interactions between variants marking strongly associated HLA haplotypes and generated odds ratios to create the improved GRS, the T1D GRS2. We validated our findings in UK Biobank. We assessed the impact of the T1D GRS2 in newborn screening and diabetes classification and sought to provide a framework for comparison with previous scores. RESULTS: The T1D GRS2 used 67 single nucleotide polymorphisms (SNPs) and accounted for interactions between 18 HLA DR-DQ haplotype combinations. The T1D GRS2 was highly discriminative for all T1D (area under the curve [AUC] 0.92; P < 0.0001 vs. older scores) and even more discriminative for early-onset T1D (AUC 0.96). In simulated newborn screening, the T1D GRS2 was nearly twice as efficient as HLA genotyping alone and 50% better than current genetic scores in general population T1D prediction. CONCLUSIONS: An improved T1D GRS, the T1D GRS2, is highly useful for classifying adult incident diabetes type and improving newborn screening. Given the cost-effectiveness of SNP genotyping, this approach has great clinical and research potential in T1D.


Subject(s)
Diabetes Mellitus, Type 1/diagnosis , Diabetes Mellitus, Type 1/genetics , Genetic Testing , Neonatal Screening/methods , Neonatal Screening/standards , Alleles , Case-Control Studies , Diabetes Mellitus, Type 1/epidemiology , Female , Genetic Predisposition to Disease , Genetic Testing/methods , Genetic Testing/standards , HLA Antigens/genetics , Haplotypes , Humans , Incidence , Infant, Newborn , Male , Polymorphism, Single Nucleotide , Quality Improvement , Reference Standards , Research Design/standards , Risk Factors , United Kingdom
20.
Int J Epidemiol ; 48(3): 834-848, 2019 06 01.
Article in English | MEDLINE | ID: mdl-30423117

ABSTRACT

BACKGROUND: Depression is more common in obese than non-obese individuals, especially in women, but the causal relationship between obesity and depression is complex and uncertain. Previous studies have used genetic variants associated with BMI to provide evidence that higher body mass index (BMI) causes depression, but have not tested whether this relationship is driven by the metabolic consequences of BMI nor for differences between men and women. METHODS: We performed a Mendelian randomization study using 48 791 individuals with depression and 291 995 controls in the UK Biobank, to test for causal effects of higher BMI on depression (defined using self-report and Hospital Episode data). We used two genetic instruments, both representing higher BMI, but one with and one without its adverse metabolic consequences, in an attempt to 'uncouple' the psychological component of obesity from the metabolic consequences. We further tested causal relationships in men and women separately, and using subsets of BMI variants from known physiological pathways. RESULTS: Higher BMI was strongly associated with higher odds of depression, especially in women. Mendelian randomization provided evidence that higher BMI partly causes depression. Using a 73-variant BMI genetic risk score, a genetically determined one standard deviation (1 SD) higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals [odds ratio (OR): 1.18, 95% confidence interval (CI): 1.09, 1.28, P = 0.00007) and women only (OR: 1.24, 95% CI: 1.11, 1.39, P = 0.0001). Meta-analysis with 45 591 depression cases and 97 647 controls from the Psychiatric Genomics Consortium (PGC) strengthened the statistical confidence of the findings in all individuals. Similar effect size estimates were obtained using different Mendelian randomization methods, although not all reached P < 0.05. Using a metabolically favourable adiposity genetic risk score, and meta-analysing data from the UK biobank and PGC, a genetically determined 1 SD higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals (OR: 1.26, 95% CI: 1.06, 1.50], P = 0.010), but with weaker statistical confidence. CONCLUSIONS: Higher BMI, with and without its adverse metabolic consequences, is likely to have a causal role in determining the likelihood of an individual developing depression.


Subject(s)
Body Mass Index , Depressive Disorder/epidemiology , Obesity/epidemiology , Adult , Aged , Causality , Female , Humans , Male , Mendelian Randomization Analysis , Middle Aged , Obesity/genetics , Obesity, Metabolically Benign/epidemiology , Obesity, Metabolically Benign/genetics , United Kingdom/epidemiology
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