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Khanna NN, Singh M, Maindarkar M, Kumar A, Johri AM, Mentella L, Laird JR, Paraskevas KI, Ruzsa Z, Singh N, Kalra MK, Fernandes JFE, Chaturvedi S, Nicolaides A, Rathore V, Singh I, Teji JS, Al-Maini M, Isenovic ER, Viswanathan V, Khanna P, Fouda MM, Saba L, Suri JS. Polygenic Risk Score for Cardiovascular Diseases in Artificial Intelligence Paradigm: A Review. J Korean Med Sci 2023; 38:e395. [PMID: 38013648 PMCID: PMC10681845 DOI: 10.3346/jkms.2023.38.e395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/15/2023] [Indexed: 11/29/2023] Open
Abstract
Cardiovascular disease (CVD) related mortality and morbidity heavily strain society. The relationship between external risk factors and our genetics have not been well established. It is widely acknowledged that environmental influence and individual behaviours play a significant role in CVD vulnerability, leading to the development of polygenic risk scores (PRS). We employed the PRISMA search method to locate pertinent research and literature to extensively review artificial intelligence (AI)-based PRS models for CVD risk prediction. Furthermore, we analyzed and compared conventional vs. AI-based solutions for PRS. We summarized the recent advances in our understanding of the use of AI-based PRS for risk prediction of CVD. Our study proposes three hypotheses: i) Multiple genetic variations and risk factors can be incorporated into AI-based PRS to improve the accuracy of CVD risk predicting. ii) AI-based PRS for CVD circumvents the drawbacks of conventional PRS calculators by incorporating a larger variety of genetic and non-genetic components, allowing for more precise and individualised risk estimations. iii) Using AI approaches, it is possible to significantly reduce the dimensionality of huge genomic datasets, resulting in more accurate and effective disease risk prediction models. Our study highlighted that the AI-PRS model outperformed traditional PRS calculators in predicting CVD risk. Furthermore, using AI-based methods to calculate PRS may increase the precision of risk predictions for CVD and have significant ramifications for individualized prevention and treatment plans.
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Affiliation(s)
- Narendra N Khanna
- Department of Cardiology, Indraprastha APOLLO Hospitals, New Delhi, India
- Asia Pacific Vascular Society, New Delhi, India
| | - Manasvi Singh
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, USA
- Bennett University, Greater Noida, India
| | - Mahesh Maindarkar
- Asia Pacific Vascular Society, New Delhi, India
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, USA
- School of Bioengineering Sciences and Research, Maharashtra Institute of Technology's Art, Design and Technology University, Pune, India
| | | | - Amer M Johri
- Department of Medicine, Division of Cardiology, Queen's University, Kingston, Canada
| | - Laura Mentella
- Department of Medicine, Division of Cardiology, University of Toronto, Toronto, Canada
| | - John R Laird
- Heart and Vascular Institute, Adventist Health St. Helena, St. Helena, CA, USA
| | | | - Zoltan Ruzsa
- Invasive Cardiology Division, University of Szeged, Szeged, Hungary
| | - Narpinder Singh
- Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun, Uttarakhand, India
| | | | | | - Seemant Chaturvedi
- Department of Neurology & Stroke Program, University of Maryland, Baltimore, MD, USA
| | - Andrew Nicolaides
- Vascular Screening and Diagnostic Centre and University of Nicosia Medical School, Cyprus
| | - Vijay Rathore
- Nephrology Department, Kaiser Permanente, Sacramento, CA, USA
| | - Inder Singh
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, USA
| | - Jagjit S Teji
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Mostafa Al-Maini
- Allergy, Clinical Immunology and Rheumatology Institute, Toronto, ON, Canada
| | - Esma R Isenovic
- Department of Radiobiology and Molecular Genetics, National Institute of The Republic of Serbia, University of Belgrade, Beograd, Serbia
| | | | - Puneet Khanna
- Department of Anaesthesiology, AIIMS, New Delhi, India
| | - Mostafa M Fouda
- Department of Electrical and Computer Engineering, Idaho State University, Pocatello, ID, USA
| | - Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria, Cagliari, Italy
| | - Jasjit S Suri
- Asia Pacific Vascular Society, New Delhi, India
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, USA
- Department of Computer Engineering, Graphic Era Deemed to be University, Dehradun, India.
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152
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Mustafa R, Ghanbari M, Karhunen V, Evangelou M, Dehghan A. Phenome-wide association study on miRNA-related sequence variants: the UK Biobank. Hum Genomics 2023; 17:104. [PMID: 37996941 PMCID: PMC10668386 DOI: 10.1186/s40246-023-00553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Genetic variants in the coding region could directly affect the structure and expression levels of genes and proteins. However, the importance of variants in the non-coding region, such as microRNAs (miRNAs), remain to be elucidated. Genetic variants in miRNA-related sequences could affect their biogenesis or functionality and ultimately affect disease risk. Yet, their implications and pleiotropic effects on many clinical conditions remain unknown. METHODS Here, we utilised genotyping and hospital records data in the UK Biobank (N = 423,419) to investigate associations between 346 genetic variants in miRNA-related sequences and a wide range of clinical diagnoses through phenome-wide association studies. Further, we tested whether changes in blood miRNA expression levels could affect disease risk through colocalisation and Mendelian randomisation analysis. RESULTS We identified 122 associations for six variants in the seed region of miRNAs, nine variants in the mature region of miRNAs, and 27 variants in the precursor miRNAs. These included associations with hypertension, dyslipidaemia, immune-related disorders, and others. Nineteen miRNAs were associated with multiple diagnoses, with six of them associated with multiple disease categories. The strongest association was reported between rs4285314 in the precursor of miR-3135b and celiac disease risk (odds ratio (OR) per effect allele increase = 0.37, P = 1.8 × 10-162). Colocalisation and Mendelian randomisation analysis highlighted potential causal role of miR-6891-3p in dyslipidaemia. CONCLUSIONS Our study demonstrates the pleiotropic effect of miRNAs and offers insights to their possible clinical importance.
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Affiliation(s)
- Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ville Karhunen
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- UK Dementia Research Institute, Imperial College London, London, UK.
- MRC Centre for Environment and Health, Imperial College London, London, UK.
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153
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Jia H, Liu Y, Liu D. Role of leisure sedentary behavior on type 2 diabetes and glycemic homeostasis: a Mendelian randomization analysis. Front Endocrinol (Lausanne) 2023; 14:1221228. [PMID: 38075044 PMCID: PMC10702218 DOI: 10.3389/fendo.2023.1221228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Purpose Utilize Mendelian randomization (MR) to examine the impact of leisure sedentary behavior (LSB) on the prevalence of type 2 diabetes mellitus (T2D) and glycemic homeostasis impairment, as well as to identify potential mediating pathways involved in these associations. Methods We chose genetic variants linked to LSB from a large genome-wide association study (GWAS) to use as instrumental variables (IVs). Then, we used a two-sample MR study to investigate the link between LSB and T2D and glycemic homeostasis. Multivariate MR (MVMR) and mediation analysis were also used to look at possible mediating paths. Results MR analysis showed a genetical link between leisure TV watching and T2D (OR 1.64, 95% CI 1.39-1.93, P< 0.001) and impaired Glycemic Homeostasis, while leisure computer use seemed to protect against T2D prevalence (OR 0.65, 95% CI 0.50-0.84, P< 0.001). It was found that leisure TV watching increases the risk of T2D through higher BMI (mediation effect 0.23, 95% CI 0.11-0.35, P< 0.001), higher triglycerides (mediation effect 0.07, 95% CI 0.04-0.11, P< 0.001), and less education (mediation effect 0.16, 95% CI 0.08-0.24, P< 0.001). Sensitivity and heterogeneity analyses further substantiated the robustness of these findings. Reverse MR analysis did not yield significant results. Conclusion This study shows LSB is linked to a higher rate of T2D and impaired glycemic homeostasis through obesity, lipid metabolism disorders, and reduced educational attainment.
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Affiliation(s)
- Hui Jia
- Department of Endocrinology, The Eighth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yifan Liu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, China
| | - Dandan Liu
- Department of Endocrinology, The Eighth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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154
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Chen R, Xu S, Ding Y, Li L, Huang C, Bao M, Li S, Wang Q. Dissecting causal associations of type 2 diabetes with 111 types of ocular conditions: a Mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1307468. [PMID: 38075077 PMCID: PMC10703475 DOI: 10.3389/fendo.2023.1307468] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Background Despite the well-established findings of a higher incidence of retina-related eye diseases in patients with diabetes, there is less investigation into the causal relationship between diabetes and non-retinal eye conditions, such as age-related cataracts and glaucoma. Methods We performed Mendelian randomization (MR) analysis to examine the causal relationship between type 2 diabetes mellitus (T2DM) and 111 ocular diseases. We employed a set of 184 single nucleotide polymorphisms (SNPs) that reached genome-wide significance as instrumental variables (IVs). The primary analysis utilized the inverse variance-weighted (IVW) method, with MR-Egger and weighted median (WM) methods serving as supplementary analyses. Results The results revealed suggestive positive causal relationships between T2DM and various ocular conditions, including "Senile cataract" (OR= 1.07; 95% CI: 1.03, 1.11; P=7.77×10-4), "Glaucoma" (OR= 1.08; 95% CI: 1.02, 1.13; P=4.81×10-3), and "Disorders of optic nerve and visual pathways" (OR= 1.10; 95% CI: 0.99, 1.23; P=7.01×10-2). Conclusion Our evidence supports a causal relationship between T2DM and specific ocular disorders. This provides a basis for further research on the importance of T2DM management and prevention strategies in maintaining ocular health.
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Affiliation(s)
- Rumeng Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shuling Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yining Ding
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Leyang Li
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunxia Huang
- School of Stomatology, Changsha Medical University, Changsha, China
| | - Meihua Bao
- The Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha, China
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, School of Pharmaceutical Science, Changsha Medical University, Changsha, China
| | - Sen Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Qiuhong Wang
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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155
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Bassyouni M, Mysara M, Wohlers I, Busch H, Saber-Ayad M, El-Hadidi M. A comprehensive analysis of genetic risk for metabolic syndrome in the Egyptian population via allele frequency investigation and Missense3D predictions. Sci Rep 2023; 13:20517. [PMID: 37993469 PMCID: PMC10665412 DOI: 10.1038/s41598-023-46844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Diabetes mellitus (DM) represents a major health problem in Egypt and worldwide, with increasing numbers of patients with prediabetes every year. Numerous factors, such as obesity, hyperlipidemia, and hypertension, which have recently become serious concerns, affect the complex pathophysiology of diabetes. These metabolic syndrome diseases are highly linked to genetic variability that drives certain populations, such as Egypt, to be more susceptible to developing DM. Here we conduct a comprehensive analysis to pinpoint the similarities and uniqueness among the Egyptian genome reference and the 1000-genome subpopulations (Europeans, Ad-Mixed Americans, South Asians, East Asians, and Africans), aiming at defining the potential genetic risk of metabolic syndromes. Selected approaches incorporated the analysis of the allele frequency of the different populations' variations, supported by genotypes' principal component analysis. Results show that the Egyptian's reference metabolic genes were clustered together with the Europeans', Ad-Mixed Americans', and South-Asians'. Additionally, 8563 variants were uniquely identified in the Egyptian cohort, from those, two were predicted to cause structural damage, namely, CDKAL1: 6_21065070 (A > T) and PPARG: 3_12351660 (C > T) utilizing the Missense3D database. The former is a protein coding gene associated with Type 2 DM while the latter is a key regulator of adipocyte differentiation and glucose homeostasis. Both variants were detected heterozygous in two different Egyptian individuals from overall 110 sample. This analysis sheds light on the unique genetic traits of the Egyptian population that play a role in the DM high prevalence in Egypt. The proposed analysis pipeline -available through GitHub- could be used to conduct similar analysis for other diseases across populations.
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Affiliation(s)
- Mahmoud Bassyouni
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Bioscience Research Laboratories Department, MARC for Medical Services and Scientific Research, 6th of October, Jiza, Egypt
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Microbiology unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Biomolecular Data Science in Pneumology, Research Center Borstel, 23845, Borstel, Germany
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Maha Saber-Ayad
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, UAE.
- Pharmacology Department, College of Medicine, Cairo University, Cairo, 12613, Egypt.
| | - Mohamed El-Hadidi
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates.
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156
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Mou X, He B, Zhang M, Zhu Y, Ou Y, Chen X. Causal influence of muscle weakness on cardiometabolic diseases and osteoporosis. Sci Rep 2023; 13:19974. [PMID: 37968290 PMCID: PMC10651997 DOI: 10.1038/s41598-023-46837-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
The causal roles of muscle weakness in cardiometabolic diseases and osteoporosis remain elusive. This two-sample Mendelian randomization (MR) study aims to explore the causal roles of muscle weakness in the risk of cardiometabolic diseases and osteoporosis. 15 single nucleotide polymorphisms (SNPs, P < 5 × 10-8) associated with muscle weakness were used as instrumental variables. Genetic predisposition to muscle weakness led to increased risk of coronary artery disease (inverse variance weighted [IVW] analysis, beta-estimate: 0.095, 95% confidence interval [CI]: 0.023 to 0.166, standard error [SE]:0.036, P-value = 0.009) and reduced risk of heart failure (weight median analysis, beta-estimate: - 0.137, 95% CI - 0.264 to - 0.009, SE:0.065, P-value = 0.036). In addition, muscle weakness may reduce the estimated bone mineral density (eBMD, weight median analysis, beta-estimate: - 0.059, 95% CI - 0.110 to - 0.008, SE:0.026, P-value = 0.023). We found no MR associations between muscle weakness and atrial fibrillation, type 2 diabetes or fracture. This study provides robust evidence that muscle weakness is causally associated with the incidence of coronary artery disease and heart failure, which may provide new insight to prevent and treat these two cardiometabolic diseases.
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Affiliation(s)
- Xiaoqing Mou
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Bin He
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Muzi Zhang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yunsheng Ou
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojun Chen
- Department of Orthopedics, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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157
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Guo Y, Chung W, Shan Z, Zhu Z, Costenbader KH, Liang L. Genome-Wide Assessment of Shared Genetic Architecture Between Rheumatoid Arthritis and Cardiovascular Diseases. J Am Heart Assoc 2023; 12:e030211. [PMID: 37947095 PMCID: PMC10727280 DOI: 10.1161/jaha.123.030211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Background Patients with rheumatoid arthritis (RA) have a 2- to 10-fold increased risk of cardiovascular disease (CVD), but the biological mechanisms and existence of causality underlying such associations remain to be investigated. We aimed to investigate the genetic associations and underlying mechanisms between RA and CVD by leveraging large-scale genomic data and genetic cross-trait analytic approaches. Methods and Results Within UK Biobank data, we examined the genetic correlation, shared genetics, and potential causality between RA (Ncases=6754, Ncontrols=452 384) and cardiovascular diseases (CVD, Ncases=44 238, Ncontrols=414 900) using linkage disequilibrium score regression, cross-trait meta-analysis, and Mendelian randomization. We observed significant genetic correlations of RA with myocardial infarction (rg:0.40 [95% CI, 0.24-0.56), angina (rg:0.42 [95% CI, 0.28-0.56]), coronary heart diseases (rg:0.41 [95% CI, 0.27-0.55]), and CVD (rg:0.43 [95% CI, 0.29-0.57]) after correcting for multiple testing (P<0.05/5). When stratified by frequent use of analgesics, we found increased genetic correlation between RA and CVD among participants without aspirin usage (rg:0.54 [95% CI, 0.30-0.78] for angina; Pvalue=6.69×10-6) and among participants with paracetamol usage (rg:0.75 [95% CI, 0.20-1.29] for myocardial infarction; Pvalue=8.90×10-3), whereas others remained similar. Cross-trait meta-analysis identified 9 independent shared loci between RA and CVD, including PTPN22 at chr1p13.2, BCL2L11 at chr2q13, and CCR3 at chr3p21.31 (Psingle trait<1×10-3 and Pmeta<5×10-8), highlighting potential shared pathogenesis including accelerating atherosclerosis, upregulating oxidative stress, and vascular permeability. Finally, Mendelian randomization estimates showed limited evidence of causality between RA and CVD. Conclusions Our results supported shared genetic pathogenesis rather than causality in explaining the observed association between RA and CVD. The identified shared genetic factors provided insights into potential novel therapeutic target for RA-CVD comorbidities.
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Affiliation(s)
- Yanjun Guo
- Department of Occupational and Environmental Health, School of Public HealthTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Division of Preventive MedicineBrigham and Women’s HospitalBostonMA
- Harvard Medical SchoolBostonMA
| | - Wonil Chung
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Department of Statistics and Actuarial ScienceSoongsil UniversitySeoulKorea
| | - Zhilei Shan
- Department of NutritionHarvard T.H. Chan School of Public HealthBostonMA
| | - Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Karen H. Costenbader
- Division of Preventive MedicineBrigham and Women’s HospitalBostonMA
- Division of Rheumatology, Inflammation and Immunity, Department of MedicineBrigham and Women’s HospitalBostonMA
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMA
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158
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Reim PK, Engelbrechtsen L, Gybel-Brask D, Schnurr TM, Kelstrup L, Høgdall EV, Hansen T. The influence of insulin-related genetic variants on fetal growth, fetal blood flow, and placental weight in a prospective pregnancy cohort. Sci Rep 2023; 13:19638. [PMID: 37949941 PMCID: PMC10638310 DOI: 10.1038/s41598-023-46910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
The fetal insulin hypothesis proposes that low birthweight and type 2 diabetes (T2D) in adulthood may be two phenotypes of the same genotype. In this study we aimed to explore this theory further by testing the effects of GWAS-identified genetic variants related to insulin release and sensitivity on fetal growth and blood flow from week 20 of gestation to birth and on placental weight at birth. We calculated genetic risk scores (GRS) of first phase insulin release (FPIR), fasting insulin (FI), combined insulin resistance and dyslipidaemia (IR + DLD) and insulin sensitivity (IS) in a study population of 665 genotyped newborns. Two-dimensional ultrasound measurements with estimation of fetal weight and blood flow were carried out at week 20, 25, and 32 of gestation in all 665 pregnancies. Birthweight and placental weight were registered at birth. Associations between the GRSs and fetal growth, blood flow and placental weight were investigated using linear mixed models. The FPIR GRS was directly associated with fetal growth from week 20 to birth, and both the FI GRS, IR + DLD GRS, and IS GRS were associated with placental weight at birth. Our findings indicate that insulin-related genetic variants might primarily affect fetal growth via the placenta.
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Affiliation(s)
- Pauline K Reim
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 8th Floor, 2200, Copenhagen, Denmark
| | - Line Engelbrechtsen
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 8th Floor, 2200, Copenhagen, Denmark
- Department of Gynaecology and Obstetrics, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Dorte Gybel-Brask
- Psycotherapeutic Outpatient Clinic, Department of Psychiatry, Ballerup Hospital, Ballerup, Denmark
| | - Theresia M Schnurr
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 8th Floor, 2200, Copenhagen, Denmark
| | - Louise Kelstrup
- Department of Gynaecology and Obstetrics, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Estrid V Høgdall
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Torben Hansen
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 8th Floor, 2200, Copenhagen, Denmark.
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159
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Chen S, Zhang W, Zheng Z, Shao X, Yang P, Yang X, Nan K. Unraveling genetic causality between type 2 diabetes and pulmonary tuberculosis on the basis of Mendelian randomization. Diabetol Metab Syndr 2023; 15:228. [PMID: 37950319 PMCID: PMC10636918 DOI: 10.1186/s13098-023-01213-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The comorbidity rate between type 2 diabetes mellitus (T2DM) and pulmonary tuberculosis (PTB) is high and imposes enormous strains on healthcare systems. However, whether T2DM is causally associated with PTB is unknown owing to limited evidence from prospective studies. Consequently, the present study aimed to clarify the genetic causality between T2DM and PTB on the basis of Mendelian randomization (MR) analysis. METHODS Genetic variants for T2DM and PTB were obtained from the IEU OpenGWAS project. The inverse variance weighted method was used as the main statistical analysis method and was supplemented with MR-Egger, weighted median, simple mode, and weighted mode methods. Heterogeneity was analyzed using Cochran's Q statistic. Horizontal pleiotropy was assessed using the MR-PRESSO global test and MR-Egger regression. Robustness of the results was verified using the leave-one-out method. RESULTS A total of 152 independent single-nucleotide polymorphisms (SNPs) were selected as instrumental variables (IVs) to assess the genetic causality between T2DM and PTB. Patients with T2DM had a higher risk of PTB at the genetic level (odds ratio (OR) for MR-Egger was 1.550, OR for weighted median was 1.540, OR for inverse variance weighted was 1.191, OR for simple mode was 1.629, OR for weighted mode was 1.529). There was no horizontal pleiotropy or heterogeneity among IVs. The results were stable when removing the SNPs one by one. CONCLUSIONS This is the first comprehensive MR analysis that revealed the genetic causality between T2DM and PTB in the East Asian population. The study provides convincing evidence that individuals with T2DM have a higher risk of developing PTB at the genetic level. This offers a significant basis for joint management of concurrent T2DM and PTB in clinical practice.
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Affiliation(s)
- Shengnan Chen
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China
- Medical Department of Xi'an Jiaotong University, Xi'an, 710048, Shaanxi, China
| | - Weisong Zhang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Zhenquan Zheng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Xiaolong Shao
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Peng Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Xiaobin Yang
- Hongdong County Hospital of Traditional Chinese Medicine, Hongdong, 041600, Shaanxi, China
| | - Kai Nan
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, People's Republic of China.
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160
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Dai H, Hou T, Wang Q, Hou Y, Zhu Z, Zhu Y, Zhao Z, Li M, Lin H, Wang S, Zheng R, Xu Y, Lu J, Wang T, Ning G, Wang W, Zheng J, Bi Y, Xu M. Roles of gut microbiota in atrial fibrillation: insights from Mendelian randomization analysis and genetic data from over 430,000 cohort study participants. Cardiovasc Diabetol 2023; 22:306. [PMID: 37940997 PMCID: PMC10633980 DOI: 10.1186/s12933-023-02045-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Gut microbiota imbalances have been suggested as a contributing factor to atrial fibrillation (AF), but the causal relationship is not fully understood. OBJECTIVES To explore the causal relationships between the gut microbiota and AF using Mendelian randomization (MR) analysis. METHODS Summary statistics were from genome-wide association studies (GWAS) of 207 gut microbial taxa (5 phyla, 10 classes, 13 orders, 26 families, 48 genera, and 105 species) (the Dutch Microbiome Project) and two large meta-GWASs of AF. The significant results were validated in FinnGen cohort and over 430,000 UK Biobank participants. Mediation MR analyses were conducted for AF risk factors, including type 2 diabetes, coronary artery disease (CAD), body mass index (BMI), blood lipids, blood pressure, and obstructive sleep apnea, to explore the potential mediation effect of these risk factors in between the gut microbiota and AF. RESULTS Two microbial taxa causally associated with AF: species Eubacterium ramulus (odds ratio [OR] 1.08, 95% confidence interval [CI] 1.04-1.12, P = 0.0001, false discovery rate (FDR) adjusted p-value = 0.023) and genus Holdemania (OR 1.15, 95% CI 1.07-1.25, P = 0.0004, FDR adjusted p-value = 0.042). Genus Holdemania was associated with incident AF risk in the UK Biobank. The proportion of mediation effect of species Eubacterium ramulus via CAD was 8.05% (95% CI 1.73% - 14.95%, P = 0.008), while the proportion of genus Holdemania on AF via BMI was 12.01% (95% CI 5.17% - 19.39%, P = 0.0005). CONCLUSIONS This study provided genetic evidence to support a potential causal mechanism between gut microbiota and AF and suggested the mediation role of AF risk factors.
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Affiliation(s)
- Huajie Dai
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianzhichao Hou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Hou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Zhu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijie Zhu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuangyuan Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruizhi Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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161
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Zhao YK, Zhu XD, Liu R, Yang X, Liang YL, Wang Y. The Role of PPARγ Gene Polymorphisms, Gut Microbiota in Type 2 Diabetes: Current Progress and Future Prospects. Diabetes Metab Syndr Obes 2023; 16:3557-3566. [PMID: 37954888 PMCID: PMC10638901 DOI: 10.2147/dmso.s429825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
Over the past decade, there has been a significant increase in studies investigating the relationship between the polymorphisms of the Peroxisome Proliferator-Activated Receptor gamma (PPARγ) gene and Type 2 Diabetes (T2D). PPARγ, a critical transcription factor, plays a central role in lipid metabolism, insulin resistance, and inflammatory response. Concurrently, the influence of gut microbiota on the development of T2D has gained increasing attention, especially their role in affecting host metabolism, such as lipid metabolism and the PPARγ signaling pathway. This review provides a comprehensive analysis of recent studies on PPARγ gene polymorphisms and their association with T2D, with a specific emphasis on the implications of gut microbiota and their interaction with PPARγ pathways. We also discuss the potential of manipulating gut microbiota and targeting PPARγ gene polymorphisms in T2D management. By deepening our understanding of these relationships, we aim to pave the way for novel preventative and therapeutic strategies for T2D.
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Affiliation(s)
- Yi-Kun Zhao
- Department of Basic Medical College, Gansu University of Chinese Medicine, Lanzhou City, People’s Republic of China
| | - Xiang-Dong Zhu
- Department of Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan city, People’s Republic of China
| | - Rong Liu
- Department of Basic Medical College, Gansu University of Chinese Medicine, Lanzhou City, People’s Republic of China
| | - Xia Yang
- Department of Basic Medical College, Gansu University of Chinese Medicine, Lanzhou City, People’s Republic of China
| | - Yong-Lin Liang
- Department of Basic Medical College, Gansu University of Chinese Medicine, Lanzhou City, People’s Republic of China
| | - Yan Wang
- Department of Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan city, People’s Republic of China
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162
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Yang L, Zhang L, Du Q, Gong X, Tian J. Exploring the molecular mechanism underlying the psoriasis and T2D by using microarray data analysis. Sci Rep 2023; 13:19313. [PMID: 37935955 PMCID: PMC10630520 DOI: 10.1038/s41598-023-46795-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023] Open
Abstract
Although a large number of evidence has identified that psoriasis is significantly correlated with type 2 diabetes (T2D), the common molecular mechanism of its occurrence remains unclear. Our study aims to further elucidate the mechanism of the occurrence of this complication. We obtained the gene expression data of psoriasis (GSE30999) and T2D (GSE28829) from the Gene Expression Omnibus (GEO) dataset. Then the common differentially expressed genes (DEGs) of T2D and psoriasis were identified. After that, we performed three types of analyses about these DEGs, including functional enrichment analysis, protein-protein interaction (PPI) network and module manufacture, hub genes identification and co-expression analysis. 132 common DEGs (14 upregulated genes and 118 downregulated genes) were identified for subsequent a series of analyses. Function enrichment analysis demonstrated that Rap1 signaling pathway, PI3K-Akt signaling pathway, and cGMP-PKG signaling pathway may play a significant role in pathogenesis of psoriasis and T2D. Finally, 3 important hub genes were selected by utilizing cytoHubba, including SNRPN, GNAS, IGF2. Our work reveals the potential common signaling pathways of psoriasis and T2D. These Hub genes and common signaling pathways provide insights for further investigation of molecular mechanism about psoriasis and T2D.
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Affiliation(s)
- Li Yang
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Lei Zhang
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Qingfang Du
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xiaoyu Gong
- Department of Ophthalmology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Jun Tian
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an, China.
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163
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Xue D, Narisu N, Taylor DL, Zhang M, Grenko C, Taylor HJ, Yan T, Tang X, Sinha N, Zhu J, Vandana JJ, Nok Chong AC, Lee A, Mansell EC, Swift AJ, Erdos MR, Zhong A, Bonnycastle LL, Zhou T, Chen S, Collins FS. Functional interrogation of twenty type 2 diabetes-associated genes using isogenic human embryonic stem cell-derived β-like cells. Cell Metab 2023; 35:1897-1914.e11. [PMID: 37858332 PMCID: PMC10841752 DOI: 10.1016/j.cmet.2023.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional roles of many loci remain unexplored. Here, we engineered isogenic knockout human embryonic stem cell lines for 20 genes associated with T2D risk. We examined the impacts of each knockout on β cell differentiation, functions, and survival. We generated gene expression and chromatin accessibility profiles on β cells derived from each knockout line. Analyses of T2D-association signals overlapping HNF4A-dependent ATAC peaks identified a likely causal variant at the FAIM2 T2D-association signal. Additionally, the integrative association analyses identified four genes (CP, RNASE1, PCSK1N, and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with β cell sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental line and identified a single likely functional variant at each of 23 T2D-association signals.
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Affiliation(s)
- Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - D Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meili Zhang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Caleb Grenko
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry J Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN Cambridge, UK
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Neelam Sinha
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angie Chi Nok Chong
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin C Mansell
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy J Swift
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ting Zhou
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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164
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Brotman SM, Oravilahti A, Rosen JD, Alvarez M, Heinonen S, van der Kolk BW, Fernandes Silva L, Perrin HJ, Vadlamudi S, Pylant C, Deochand S, Basta PV, Valone JM, Narain MN, Stringham HM, Boehnke M, Kuusisto J, Love MI, Pietiläinen KH, Pajukanta P, Laakso M, Mohlke KL. Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits. Diabetes 2023; 72:1707-1718. [PMID: 37647564 PMCID: PMC10588284 DOI: 10.2337/db23-0365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Understanding differences in adipose gene expression between individuals with different levels of clinical traits may reveal the genes and mechanisms leading to cardiometabolic diseases. However, adipose is a heterogeneous tissue. To account for cell-type heterogeneity, we estimated cell-type proportions in 859 subcutaneous adipose tissue samples with bulk RNA sequencing (RNA-seq) using a reference single-nuclear RNA-seq data set. Cell-type proportions were associated with cardiometabolic traits; for example, higher macrophage and adipocyte proportions were associated with higher and lower BMI, respectively. We evaluated cell-type proportions and BMI as covariates in tests of association between >25,000 gene expression levels and 22 cardiometabolic traits. For >95% of genes, the optimal, or best-fit, models included BMI as a covariate, and for 79% of associations, the optimal models also included cell type. After adjusting for the optimal covariates, we identified 2,664 significant associations (P ≤ 2e-6) for 1,252 genes and 14 traits. Among genes proposed to affect cardiometabolic traits based on colocalized genome-wide association study and adipose expression quantitative trait locus signals, 25 showed a corresponding association between trait and gene expression levels. Overall, these results suggest the importance of modeling cell-type proportion when identifying gene expression associations with cardiometabolic traits. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Sarah M. Brotman
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
| | - Anniina Oravilahti
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jonathan D. Rosen
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA
| | - Sini Heinonen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Birgitta W. van der Kolk
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hannah J. Perrin
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
| | | | - Cortney Pylant
- Department of Epidemiology, The University of North Carolina, Chapel Hill, NC
| | - Sonia Deochand
- Department of Epidemiology, The University of North Carolina, Chapel Hill, NC
| | - Patricia V. Basta
- Department of Epidemiology, The University of North Carolina, Chapel Hill, NC
| | - Jordan M. Valone
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
- UNC Neuroscience Center, The University of North Carolina, Chapel Hill, NC
| | - Morgan N. Narain
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
- Curriculum of Toxicology and Environmental Medicine, The University of North Carolina, Chapel Hill, NC
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Michael I. Love
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
- Department of Biostatistics, The University of North Carolina, Chapel Hill, NC
| | - Kirsi H. Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HealthyWeightHub, Endocrinology, Abdominal Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA
- Institute for Precision Health, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Karen L. Mohlke
- Department of Genetics, The University of North Carolina, Chapel Hill, NC
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165
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Zhang Z, Cui Y, Su V, Wang D, Tol MJ, Cheng L, Wu X, Kim J, Rajbhandari P, Zhang S, Li W, Tontonoz P, Villanueva CJ, Sallam T. A PPARγ/long noncoding RNA axis regulates adipose thermoneutral remodeling in mice. J Clin Invest 2023; 133:e170072. [PMID: 37909330 PMCID: PMC10617768 DOI: 10.1172/jci170072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/06/2023] [Indexed: 11/03/2023] Open
Abstract
Interplay between energy-storing white adipose cells and thermogenic beige adipocytes contributes to obesity and insulin resistance. Irrespective of specialized niche, adipocytes require the activity of the nuclear receptor PPARγ for proper function. Exposure to cold or adrenergic signaling enriches thermogenic cells though multiple pathways that act synergistically with PPARγ; however, the molecular mechanisms by which PPARγ licenses white adipose tissue to preferentially adopt a thermogenic or white adipose fate in response to dietary cues or thermoneutral conditions are not fully elucidated. Here, we show that a PPARγ/long noncoding RNA (lncRNA) axis integrates canonical and noncanonical thermogenesis to restrain white adipose tissue heat dissipation during thermoneutrality and diet-induced obesity. Pharmacologic inhibition or genetic deletion of the lncRNA Lexis enhances uncoupling protein 1-dependent (UCP1-dependent) and -independent thermogenesis. Adipose-specific deletion of Lexis counteracted diet-induced obesity, improved insulin sensitivity, and enhanced energy expenditure. Single-nuclei transcriptomics revealed that Lexis regulates a distinct population of thermogenic adipocytes. We systematically map Lexis motif preferences and show that it regulates the thermogenic program through the activity of the metabolic GWAS gene and WNT modulator TCF7L2. Collectively, our studies uncover a new mode of crosstalk between PPARγ and WNT that preserves white adipose tissue plasticity.
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Affiliation(s)
- Zhengyi Zhang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Ya Cui
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Vivien Su
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Dan Wang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Marcus J. Tol
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
| | - Lijing Cheng
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Xiaohui Wu
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Jason Kim
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sicheng Zhang
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Wei Li
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Peter Tontonoz
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
- Department of Biological Chemistry and
| | - Claudio J. Villanueva
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, College of Life Sciences, UCLA, Los Angeles, California, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
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166
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Rødevand L, Rahman Z, Hindley GFL, Smeland OB, Frei O, Tekin TF, Kutrolli G, Bahrami S, Hoseth EZ, Shadrin A, Lin A, Djurovic S, Dale AM, Steen NE, Andreassen OA. Characterizing the Shared Genetic Underpinnings of Schizophrenia and Cardiovascular Disease Risk Factors. Am J Psychiatry 2023; 180:815-826. [PMID: 37752828 DOI: 10.1176/appi.ajp.20220660] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
OBJECTIVE Schizophrenia is associated with increased risk of cardiovascular disease (CVD), although there is variation in risk among individuals. There are indications of shared genetic etiology between schizophrenia and CVD, but the nature of the overlap remains unclear. The aim of this study was to fill this gap in knowledge. METHODS Overlapping genetic architectures between schizophrenia and CVD risk factors were assessed by analyzing recent genome-wide association study (GWAS) results. The bivariate causal mixture model (MiXeR) was applied to estimate the number of shared variants and the conjunctional false discovery rate (conjFDR) approach was used to pinpoint specific shared loci. RESULTS Extensive genetic overlap was found between schizophrenia and CVD risk factors, particularly smoking initiation (N=8.6K variants) and body mass index (BMI) (N=8.1K variants). Several specific shared loci were detected between schizophrenia and BMI (N=304), waist-to-hip ratio (N=193), smoking initiation (N=293), systolic (N=294) and diastolic (N=259) blood pressure, type 2 diabetes (N=147), lipids (N=471), and coronary artery disease (N=35). The schizophrenia risk loci shared with smoking initiation had mainly concordant effect directions, and the risk loci shared with BMI had mainly opposite effect directions. The overlapping loci with lipids, blood pressure, waist-to-hip ratio, type 2 diabetes, and coronary artery disease had mixed effect directions. Functional analyses implicated mapped genes that are expressed in brain tissue and immune cells. CONCLUSIONS These findings indicate a genetic propensity to smoking and a reduced genetic risk of obesity among individuals with schizophrenia. The bidirectional effects of the shared loci with the other CVD risk factors may imply differences in genetic liability to CVD across schizophrenia subgroups, possibly underlying the variation in CVD comorbidity.
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Affiliation(s)
- Linn Rødevand
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Zillur Rahman
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Guy F L Hindley
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Olav B Smeland
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Oleksandr Frei
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Tahir Filiz Tekin
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Gleda Kutrolli
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Shahram Bahrami
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Eva Z Hoseth
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Alexey Shadrin
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Aihua Lin
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Srdjan Djurovic
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Anders M Dale
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Nils Eiel Steen
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
| | - Ole A Andreassen
- Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo (Rødevand, Rahman, Hindley, Smeland, Frei, Tekin, Kutrolli, Bahrami, Hoseth, Shadrin, Lin, Steen, Andreassen); Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Hindley); Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo (Frei); Division of Mental Health, Helse Møre Romsdal HF, Kristiansund, Norway (Hoseth); Department of Medical Genetics, Oslo University Hospital, Oslo, and NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway (Djurovic); Multimodal Imaging Laboratory and Departments of Radiology, Psychiatry, and Neurosciences, University of California San Diego, La Jolla (Dale)
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167
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Huang X, Zhao JV. The Associations of Genetically Predicted Plasma Alanine with Coronary Artery Disease and its Risk Factors: A Mendelian Randomization Study. Am J Clin Nutr 2023; 118:1020-1028. [PMID: 37640107 DOI: 10.1016/j.ajcnut.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Alanine is an amino acid commonly used as a nutritional supplement and plays a key role in the glucose-alanine cycle. Plasma alanine has been associated in observational studies with a higher risk of coronary artery disease (CAD) and unhealthier lipid profiles. However, evidence from large randomized controlled trials is lacking. OBJECTIVES Using Mendelian randomization (MR), we assessed the unconfounded associations of plasma alanine with CAD and CAD risk factors. METHODS We applied single nucleotide polymorphisms that were strongly (P < 5 ×10-8) associated with plasma alanine as genetic instruments to large genome-wide association studies of CAD (63,108 cases; 296,901 controls), diabetes (90,612 cases; 583,493 controls), glucose (515,538 participants), lipids (low-density lipoprotein [LDL] cholesterol, high-density lipoprotein [HDL] cholesterol, triglycerides, total cholesterol, and apolipoprotein B) (>1.1 million participants), blood pressure (BP) (757,601 participants), and body mass index (682,137 participants). Given the potential sex disparity, we also conducted sex-specific analyses. MR estimates per standard deviation increase in alanine concentrations were obtained using inverse variance weighting followed by sensitivity analyses using weighted median, MR-Egger, MR-Pleiotropy RESidual Sum and Outlier, and MR-Robust Adjusted Profile Score. RESULTS Genetically predicted plasma alanine was not associated with CAD but with a higher risk of diabetes (odds ratio [OR]: 1.35; 95% confidence interval [CI]: 1.06, 1.72), higher glucose (β: 0.11; 95% CI: 0.02, 0.19), LDL cholesterol (β: 0.08; 95% CI: 0.04, 0.12), triglycerides (β: 0.25; 95% CI: 0.13, 0.38), total cholesterol (β: 0.14; 95% CI: 0.08, 0.20), apolipoprotein B (β: 0.12; 95% CI: 0.03, 0.21), and BP (β: 1.17; 95% CI: 0.31, 2.04 for systolic BP: β: 0.97; 95% CI: 0.49, 1.45 for diastolic BP) overall. The positive associations of serum alanine with LDL cholesterol and triglycerides were more notable in women than in men. CONCLUSIONS Alanine or factors affecting alanine may have causal effects on diabetes, blood glucose, lipid profiles, and BP but not on CAD. Further studies are needed to clarify possible mechanisms.
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Affiliation(s)
- Xin Huang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jie V Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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168
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Elgamal RM, Kudtarkar P, Melton RL, Mummey HM, Benaglio P, Okino ML, Gaulton KJ. An Integrated Map of Cell Type-Specific Gene Expression in Pancreatic Islets. Diabetes 2023; 72:1719-1728. [PMID: 37582230 PMCID: PMC10588282 DOI: 10.2337/db23-0130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023]
Abstract
Pancreatic islets consist of multiple cell types that produce hormones required for glucose homeostasis, and islet dysfunction is a major factor in type 1 and type 2 diabetes. Numerous studies have assessed transcription across individual cell types using single-cell assays; however, there is no canonical reference of gene expression in islet cell types that is also easily accessible for researchers to query and use in bioinformatics pipelines. Here we present an integrated map of islet cell type-specific gene expression from 192,203 cells from single-cell RNA sequencing of 65 donors without diabetes, donors who were type 1 diabetes autoantibody positive, donors with type 1 diabetes, and donors with type 2 diabetes from the Human Pancreas Analysis Program. We identified 10 distinct cell types, annotated subpopulations of several cell types, and defined cell type-specific marker genes. We tested differential expression within each cell type across disease states and identified 1,701 genes with significant changes in expression, with most changes observed in β-cells from donors with type 1 diabetes. To facilitate user interaction, we provide several single-cell visualization and reference mapping tools, as well as the open-access analytical pipelines used to create this reference. The results will serve as a valuable resource to investigators studying islet biology. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Rebecca L. Melton
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA
| | - Hannah M. Mummey
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA
| | - Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Mei-Lin Okino
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
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169
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Zhang W, Zhang L, Zhu J, Xiao C, Cui H, Yang C, Yan P, Tang M, Wang Y, Chen L, Liu Y, Zou Y, Wu X, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Additional Evidence for the Relationship Between Type 2 Diabetes and Stroke Through Observational and Genetic Analyses. Diabetes 2023; 72:1671-1681. [PMID: 37552871 DOI: 10.2337/db22-0954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
While type 2 diabetes mellitus (T2DM) is commonly considered a putative causal risk factor for stroke, the effect of stroke on T2DM remains unclear. The intrinsic link underlying T2DM and stroke has not been thoroughly examined. We aimed to evaluate the phenotypic and genetic relationships underlying T2DM and stroke. We evaluated phenotypic associations using data from the UK Biobank (N = 472,050). We then investigated genetic relationships by leveraging genomic data in European ancestry for T2DM, with and without adjusting (adj) for BMI (T2DM: n = 74,124 case subjects/824,006 control subjects; T2DMadjBMI: n = 50,409 case subjects/523,897 control subjects), and for stroke (n = 73,652 case subjects/1,234,808 control subjects). We performed additional analyses using genomic data in East Asian ancestry for T2DM (n = 77,418 case subjects/356,122 control subjects) and for stroke (n = 27,413 case subjects/237,242 control subjects). Observational analyses suggested a significantly increased hazard of stroke among individuals with T2DM (hazard ratio 2.28 [95% CI 1.97-2.64]), but a slightly increased hazard of T2DM among individuals with stroke (1.22 [1.03-1.45]) which attenuated to 1.14 (0.96-1.36) in sensitivity analysis. A positive global T2DM-stroke genetic correlation was observed (rg = 0.35; P = 1.46 × 10-27), largely independent of BMI (T2DMadjBMI-stroke: rg = 0.27; P = 3.59 × 10-13). This was further corroborated by 38 shared independent loci and 161 shared expression-trait associations. Mendelian randomization analyses suggested a putative causal effect of T2DM on stroke in Europeans (odds ratio 1.07 [95% CI 1.06-1.09]), which remained significant in East Asians (1.03 [1.01-1.06]). Conversely, despite a putative causal effect of stroke on T2DM also observed in Europeans (1.21 [1.07-1.37]), it attenuated to 1.04 (0.91-1.19) in East Asians. Our study provides additional evidence to underscore the significant relationship between T2DM and stroke. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Jiang X, Zhang MJ, Zhang Y, Durvasula A, Inouye M, Holmes C, Price AL, McVean G. Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk. Nat Genet 2023; 55:1854-1865. [PMID: 37814053 PMCID: PMC10632146 DOI: 10.1038/s41588-023-01522-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 10/11/2023]
Abstract
The analysis of longitudinal data from electronic health records (EHRs) has the potential to improve clinical diagnoses and enable personalized medicine, motivating efforts to identify disease subtypes from patient comorbidity information. Here we introduce an age-dependent topic modeling (ATM) method that provides a low-rank representation of longitudinal records of hundreds of distinct diseases in large EHR datasets. We applied ATM to 282,957 UK Biobank samples, identifying 52 diseases with heterogeneous comorbidity profiles; analyses of 211,908 All of Us samples produced concordant results. We defined subtypes of the 52 heterogeneous diseases based on their comorbidity profiles and compared genetic risk across disease subtypes using polygenic risk scores (PRSs), identifying 18 disease subtypes whose PRS differed significantly from other subtypes of the same disease. We further identified specific genetic variants with subtype-dependent effects on disease risk. In conclusion, ATM identifies disease subtypes with differential genome-wide and locus-specific genetic risk profiles.
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Affiliation(s)
- Xilin Jiang
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Department of Statistics, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
| | - Martin Jinye Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yidong Zhang
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Radiation Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Arun Durvasula
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Cambridge, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Michael Inouye
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- The Alan Turing Institute, London, UK
| | - Chris Holmes
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
- The Alan Turing Institute, London, UK
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
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171
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Tang H, Wang J, Deng P, Li Y, Cao Y, Yi B, Zhu L, Zhu S, Lu Y. Transcriptome-wide association study-derived genes as potential visceral adipose tissue-specific targets for type 2 diabetes. Diabetologia 2023; 66:2087-2100. [PMID: 37540242 PMCID: PMC10542736 DOI: 10.1007/s00125-023-05978-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
AIMS/HYPOTHESIS This study aimed to assess the causal relationship between visceral obesity and type 2 diabetes and subsequently to screen visceral adipose tissue (VAT)-specific targets for type 2 diabetes. METHODS We examined the causal relationship between VAT and type 2 diabetes using bidirectional Mendelian randomisation (MR) followed by multivariable MR. We conducted a transcriptome-wide association study (TWAS) leveraging prediction models and a large-scale type 2 diabetes genome-wide association study (74,124 cases and 824,006 controls) to identify candidate genes in VAT and used summary-data-based MR (SMR) and co-localisation analysis to map causal genes. We performed enrichment and single-cell RNA-seq analyses to determine the cell-specific localisation of the TWAS-identified genes. We also conducted knockdown experiments in 3T3-L1 pre-adipocytes. RESULTS MR analyses showed a causal relationship between genetically increased VAT mass and type 2 diabetes (inverse-variance weighted OR 2.48 [95% CI 2.21, 2.79]). Ten VAT-specific candidate genes were associated with type 2 diabetes after Bonferroni correction, including five causal genes supported by SMR and co-localisation: PABPC4 (1p34.3); CCNE2 (8q22.1); HAUS6 (9p22.1); CWF19L1 (10q24.31); and CCDC92 (12q24.31). Combined with enrichment analyses, clarifying cell-type specificity with single-cell RNA-seq data indicated that most TWAS-identified candidate genes appear more likely to be associated with adipocytes in VAT. Knockdown experiments suggested that Pabpc4 likely contributes to regulating differentiation and energy metabolism in 3T3-L1 adipocytes. CONCLUSIONS/INTERPRETATION Our findings provide new insights into the genetic basis and biological processes of the association between VAT accumulation and type 2 diabetes and warrant investigation through further functional studies to validate these VAT-specific candidate genes.
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Affiliation(s)
- Haibo Tang
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jie Wang
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Peizhi Deng
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yalan Li
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yaoquan Cao
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Bo Yi
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Liyong Zhu
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Shaihong Zhu
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Yao Lu
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, China.
- School of Life Course Sciences, King's College London, London, UK.
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172
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Nobrega M, Farris K, Andersen E, Donkin I, Versteyhe S, Kristiansen VB, Simpson S, Barres R. Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype. RESEARCH SQUARE 2023:rs.3.rs-3487148. [PMID: 37961160 PMCID: PMC10635361 DOI: 10.21203/rs.3.rs-3487148/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.
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Affiliation(s)
| | | | | | | | | | | | | | - Romain Barres
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
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173
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Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR, Matsui H, Kim JH, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nat Commun 2023; 14:6928. [PMID: 37903777 PMCID: PMC10616100 DOI: 10.1038/s41467-023-42560-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The impact of genetic regulatory variation active in early pancreatic development on adult pancreatic disease and traits is not well understood. Here, we generate a panel of 107 fetal-like iPSC-derived pancreatic progenitor cells (iPSC-PPCs) from whole genome-sequenced individuals and identify 4065 genes and 4016 isoforms whose expression and/or alternative splicing are affected by regulatory variation. We integrate eQTLs identified in adult islets and whole pancreas samples, which reveal 1805 eQTL associations that are unique to the fetal-like iPSC-PPCs and 1043 eQTLs that exhibit regulatory plasticity across the fetal-like and adult pancreas tissues. Colocalization with GWAS risk loci for pancreatic diseases and traits show that some putative causal regulatory variants are active only in the fetal-like iPSC-PPCs and likely influence disease by modulating expression of disease-associated genes in early development, while others with regulatory plasticity likely exert their effects in both the fetal and adult pancreas by modulating expression of different disease genes in the two developmental stages.
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Affiliation(s)
- Jennifer P Nguyen
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kyohei Fujita
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bianca M Salgado
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Ji Hyun Kim
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, South Korea
| | | | - Matteo D'Antonio
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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174
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Brotman SM, El-Sayed Moustafa JS, Guan L, Broadaway KA, Wang D, Jackson AU, Welch R, Currin KW, Tomlinson M, Vadlamudi S, Stringham HM, Roberts AL, Lakka TA, Oravilahti A, Silva LF, Narisu N, Erdos MR, Yan T, Bonnycastle LL, Raulerson CK, Raza Y, Yan X, Parker SCJ, Kuusisto J, Pajukanta P, Tuomilehto J, Collins FS, Boehnke M, Love MI, Koistinen HA, Laakso M, Mohlke KL, Small KS, Scott LJ. Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563798. [PMID: 37961277 PMCID: PMC10634839 DOI: 10.1101/2023.10.26.563798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Complete characterization of the genetic effects on gene expression is needed to elucidate tissue biology and the etiology of complex traits. Here, we analyzed 2,344 subcutaneous adipose tissue samples and identified 34K conditionally distinct expression quantitative trait locus (eQTL) signals in 18K genes. Over half of eQTL genes exhibited at least two eQTL signals. Compared to primary signals, non-primary signals had lower effect sizes, lower minor allele frequencies, and less promoter enrichment; they corresponded to genes with higher heritability and higher tolerance for loss of function. Colocalization of eQTL with conditionally distinct genome-wide association study signals for 28 cardiometabolic traits identified 3,605 eQTL signals for 1,861 genes. Inclusion of non-primary eQTL signals increased colocalized signals by 46%. Among 30 genes with ≥2 pairs of colocalized signals, 21 showed a mediating gene dosage effect on the trait. Thus, expanded eQTL identification reveals more mechanisms underlying complex traits and improves understanding of the complexity of gene expression regulation.
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Affiliation(s)
- Sarah M Brotman
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Dongmeng Wang
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kevin W Currin
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Max Tomlinson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Anniina Oravilahti
- Institute of Clinical Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yasrab Raza
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Xinyu Yan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Johanna Kuusisto
- Department of Medicine and Clinical Research, Kuopio University Hospital, Kuopio, Finland
| | - Päivi Pajukanta
- Department of Human Genetics and Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
- Department of Medicine and Clinical Research, Kuopio University Hospital, Kuopio, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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175
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Kovac L, Speckmann T, Jähnert M, Gottmann P, Fritsche L, Häring HU, Birkenfeld AL, Fritsche A, Schürmann A, Ouni M. Identification of MicroRNAs Associated with Prediabetic Status in Obese Women. Int J Mol Sci 2023; 24:15673. [PMID: 37958657 PMCID: PMC10648886 DOI: 10.3390/ijms242115673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
MicroRNAs (miRNAs) recently emerged as means of communication between insulin-sensitive tissues to mediate diabetes development and progression, and as such they present a valuable proxy for epigenetic alterations associated with type 2 diabetes. In order to identify miRNA markers for the precursor of diabetes called prediabetes, we applied a translational approach encompassing analysis of human plasma samples, mouse tissues and an in vitro validation system. MiR-652-3p, miR-877-5p, miR-93-5p, miR-130a-3p, miR-152-3p and let-7i-5p were increased in plasma of women with impaired fasting glucose levels (IFG) compared to those with normal fasting glucose and normal glucose tolerance (NGT). Among these, let-7i-5p and miR-93-5p correlated with fasting blood glucose levels. Human data were then compared to miRNome data obtained from islets of Langerhans and adipose tissue of 10-week-old female New Zealand Obese mice, which differ in their degree of hyperglycemia and liver fat content. Similar to human plasma, let-7i-5p was increased in adipose tissue and islets of Langerhans of diabetes-prone mice. As predicted by the in silico analysis, overexpression of let-7i-5p in the rat β-cell line INS-1 832/12 resulted in downregulation of insulin signaling pathway components (Insr, Rictor, Prkcb, Clock, Sos1 and Kcnma1). Taken together, our integrated approach highlighted let-7i-5p as a potential regulator of whole-body insulin sensitivity and a novel marker of prediabetes in women.
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Affiliation(s)
- Leona Kovac
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
| | - Thilo Speckmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
| | - Louise Fritsche
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
- Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, University of Tübingen, 72074 Tübingen, Germany
| | - Hans-Ulrich Häring
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
- Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, University of Tübingen, 72074 Tübingen, Germany
- Department of Internal Medicine IV, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Andreas L. Birkenfeld
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
- Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, University of Tübingen, 72074 Tübingen, Germany
- Department of Internal Medicine IV, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Andreas Fritsche
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
- Institute of Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Center Munich, University of Tübingen, 72074 Tübingen, Germany
- Department of Internal Medicine IV, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
- Institute of Nutritional Sciences, University of Potsdam, 14558 Nuthetal, Germany
| | - Meriem Ouni
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; (L.K.); (M.J.); (P.G.); (M.O.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (L.F.); (H.-U.H.); (A.L.B.); (A.F.)
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176
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Zhao Z, D’Oliveira Albanus R, Taylor H, Tang X, Han Y, Orchard P, Varshney A, Zhang T, Manickam N, Erdos M, Narisu N, Taylor L, Saavedra X, Zhong A, Li B, Zhou T, Naji A, Liu C, Collins F, Parker SCJ, Chen S. An integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D associated genes and regulatory signals. RESEARCH SQUARE 2023:rs.3.rs-3343318. [PMID: 37886586 PMCID: PMC10602166 DOI: 10.21203/rs.3.rs-3343318/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Genome wide association studies (GWAS) have identified over 100 signals associated with type 1 diabetes (T1D). However, translating any given T1D GWAS signal into mechanistic insights, including putative causal variants and the context (cell type and cell state) in which they function, has been limited. Here, we present a comprehensive multi-omic integrative analysis of single-cell/nucleus resolution profiles of gene expression and chromatin accessibility in healthy and autoantibody+ (AAB+) human islets, as well as islets under multiple T1D stimulatory conditions. We broadly nominate effector cell types for all T1D GWAS signals. We further nominated higher-resolution contexts, including effector cell types, regulatory elements, and genes for three independent T1D risk variants acting through islet cells within the pancreas at the DLK1/MEG3, RASGRP1, and TOX loci. Subsequently, we created isogenic gene knockouts DLK1-/-, RASGRP1-/-, and TOX-/-, and the corresponding regulatory region knockout, RASGRP1Δ, and DLK1Δ hESCs. Loss of RASGRP1 or DLK1, as well as knockout of the regulatory region of RASGRP1 or DLK1, increased β cell apoptosis. Additionally, pancreatic β cells derived from isogenic hESCs carrying the risk allele of rs3783355A/A exhibited increased β cell death. Finally, RNA-seq and ATAC-seq identified five genes upregulated in both RASGRP1-/- and DLK1-/- β-like cells, four of which are associated with T1D. Together, this work reports an integrative approach for combining single cell multi-omics, GWAS, and isogenic hESC-derived β-like cells to prioritize the T1D associated signals and their underlying context-specific cell types, genes, SNPs, and regulatory elements, to illuminate biological functions and molecular mechanisms.
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Affiliation(s)
- Zeping Zhao
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | | | - Henry Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | - Yuling Han
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tuo Zhang
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Nandini Manickam
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mike Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaxia Saavedra
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Aaron Zhong
- Genomic Resource Core Facility, Weill Cornell Medical College, NY 10065, USA
| | - Bo Li
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Ting Zhou
- Genomic Resource Core Facility, Weill Cornell Medical College, NY 10065, USA
| | - Ali Naji
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA19104, USA
| | - Chengyang Liu
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA19104, USA
| | - Francis Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen CJ Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
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177
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Gómez-Sánchez G, Alonso L, Pérez MÁ, Morán I, Torrents D, Berral JL. Exhaustive Variant Interaction Analysis using Multifactor Dimensionality Reduction. RESEARCH SQUARE 2023:rs.3.rs-3401025. [PMID: 37886566 PMCID: PMC10602162 DOI: 10.21203/rs.3.rs-3401025/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
One of the main goals of human genetics is to understand the connections between genomic variation and the predisposition to develop a complex disorder. These disease-variant associations are usually studied in a single independent manner, disregarding the possible effect derived from the interaction between genomic variants. In particular, in a background of complex diseases, these interactions can be directly linked to the disorder and may play an important role in disease development. Although their study has been suggested to help to complete the understanding of the genetic bases of complex diseases, this still represents a big challenge due to large computing demands. Here, we have taken advantage of High-Performance Computing technologies to tackle this problem using a combination of machine learning methods and statistical approaches. As a result, we have created a containerized framework that uses Multifactor Dimensionality Reduction to detect pairs of variants associated with Type 2 Diabetes (T2D). This methodology has been tested in the Northwestern University NUgene project cohort using a dataset of 1,883,192 variant pairs with a certain degree of association with T2D. Out of the pairs studied, we have identified 104 significant pairs, two of which exhibit a potential functional relationship with T2D.
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Affiliation(s)
- Gonzalo Gómez-Sánchez
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Universitat Politècnica de Catalunya - BarcelonaTECH, Barcelona, Spain
| | - Lorena Alonso
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Ignasi Morán
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
| | - Josep Ll. Berral
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Universitat Politècnica de Catalunya - BarcelonaTECH, Barcelona, Spain
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178
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Benberin V, Karabaeva R, Kulmyrzaeva N, Bigarinova R, Vochshenkova T. Evolution of the search for a common mechanism of congenital risk of coronary heart disease and type 2 diabetes mellitus in the chromosomal locus 9p21.3. Medicine (Baltimore) 2023; 102:e35074. [PMID: 37832109 PMCID: PMC10578751 DOI: 10.1097/md.0000000000035074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/14/2023] [Indexed: 10/15/2023] Open
Abstract
9.21.3 chromosomal locus predisposes to coronary heart disease (CHD) and type 2 diabetes mellitus (DM2), but their overall pathological mechanism and clinical applicability remain unclear. The review uses publications of the study results of 9.21.3 chromosomal locus in association with CHD and DM2, which are important for changing the focus of clinical practice. The eligibility criteria are full-text articles published in the PubMed database (MEDLINE) up to December 31, 2022. A total of 56 publications were found that met the inclusion criteria. Using the examples of the progressive stages in understanding the role of the chromosomal locus 9p.21.3, scientific ideas were grouped, from a fragmentary study of independent pathological processes to a systematic study of the overall development of CHD and DM2. The presented review can become a source of new scientific hypotheses for further studies, the results of which can determine the general mechanism of the congenital risk of CHD and DM2 and change the focus of clinical practice.
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Affiliation(s)
- Valeriy Benberin
- Centre of Gerontology, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Raushan Karabaeva
- Centre of Gerontology, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Nazgul Kulmyrzaeva
- Centre of Gerontology, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Rauza Bigarinova
- Centre of Gerontology, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Tamara Vochshenkova
- Centre of Gerontology, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
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179
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Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023; 382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.
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Affiliation(s)
- Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Qiurui Zeng
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rosa G. Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jiaying Xu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas D. Johnson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia K. Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nora Emerson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jon Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jasper Lee
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Li
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Michelle Liem
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Caz O’Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | | | | | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Boaz P. Levi
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Ed Lein
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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180
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Hu M, Kim I, Morán I, Peng W, Sun O, Bonnefond A, Khamis A, Bonas-Guarch S, Froguel P, Rutter GA. Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548906. [PMID: 37502937 PMCID: PMC10369998 DOI: 10.1101/2023.07.13.548906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of T2D risk at this locus, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, combined allele-specific expression (cASE) analysis in human islets revealed multiple variants that influence SLC30A8 expression. Epigenomic mapping identified an islet-selective enhancer cluster at the SLC30A8 locus, hosting multiple T2D risk and cASE associations, which is spatially associated with the SLC30A8 promoter and additional neighbouring genes. Deletions of variant-bearing enhancer regions using CRISPR-Cas9 in human-derived EndoC-βH3 cells lowered the expression of SLC30A8 and several neighbouring genes, and improved insulin secretion. Whilst down-regulation of SLC30A8 had no effect on beta cell survival, loss of UTP23, RAD21 or MED30 markedly reduced cell viability. Although eQTL or cASE analyses in human islets did not support the association between these additional genes and diabetes risk, the transcriptional regulator JQ1 lowered the expression of multiple genes at the SLC30A8 locus and enhanced stimulated insulin secretion.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Innah Kim
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Ignasi Morán
- Life Sciences Department, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Weicong Peng
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Orien Sun
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Amélie Bonnefond
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Amna Khamis
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Silvia Bonas-Guarch
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Center for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Philippe Froguel
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, F-59000, France
- University of Lille, Lille University Hospital, Lille, F-59000, France.France
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
- Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore
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181
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Bagheri M, Bombin A, Shi M, Murthy VL, Shah R, Mosley JD, Ferguson JF. Genotype-based "virtual" metabolomics in a clinical biobank identifies novel metabolite-disease associations. RESEARCH SQUARE 2023:rs.3.rs-3222588. [PMID: 37790512 PMCID: PMC10543429 DOI: 10.21203/rs.3.rs-3222588/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Circulating metabolites act as biomarkers of dysregulated metabolism, and may inform disease pathophysiology. A portion of the inter-individual variability in circulating metabolites is influenced by common genetic variation. We evaluated whether a genetics-based "virtual" metabolomics approach can identify novel metabolite-disease associations. We examined the association between polygenic scores for 726 metabolites (derived from OMICSPRED) with 1,247 clinical phenotypes in 57,735 European ancestry and 15,754 African ancestry participants from the BioVU DNA Biobank. We probed significant relationships through Mendelian randomization (MR) using genetic instruments constructed from the METSIM Study, and validated significant MR associations using independent GWAS of candidate phenotypes. We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes among African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolite-phenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p<0.05). Validated findings included the metabolites bilirubin and X-21796 with cholelithiasis, phosphatidylcholine(16:0/22:5n3,18:1/20:4) and arachidonate(20:4n6) with inflammatory bowel disease and Crohn's disease, and campesterol with coronary artery disease and myocardial infarction. These associations may represent biomarkers or potentially targetable mediators of disease risk.
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Affiliation(s)
| | | | | | | | - Ravi Shah
- Vanderbilt University Medical Center
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182
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Bagheri M, Bombin A, Shi M, Murthy VL, Shah R, Mosley JD, Ferguson JF. Genotype-based "virtual" metabolomics in a clinical biobank identifies novel metabolite-disease associations. RESEARCH SQUARE 2023:rs.3.rs-3222588. [PMID: 37790512 PMCID: PMC10543429 DOI: 10.21203/rs.3.rs-3222588/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Circulating metabolites act as biomarkers of dysregulated metabolism, and may inform disease pathophysiology. A portion of the inter-individual variability in circulating metabolites is influenced by common genetic variation. We evaluated whether a genetics-based "virtual" metabolomics approach can identify novel metabolite-disease associations. We examined the association between polygenic scores for 726 metabolites (derived from OMICSPRED) with 1,247 clinical phenotypes in 57,735 European ancestry and 15,754 African ancestry participants from the BioVU DNA Biobank. We probed significant relationships through Mendelian randomization (MR) using genetic instruments constructed from the METSIM Study, and validated significant MR associations using independent GWAS of candidate phenotypes. We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes among African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolite-phenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p<0.05). Validated findings included the metabolites bilirubin and X-21796 with cholelithiasis, phosphatidylcholine(16:0/22:5n3,18:1/20:4) and arachidonate(20:4n6) with inflammatory bowel disease and Crohn's disease, and campesterol with coronary artery disease and myocardial infarction. These associations may represent biomarkers or potentially targetable mediators of disease risk.
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Affiliation(s)
| | | | | | | | - Ravi Shah
- Vanderbilt University Medical Center
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183
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Tovar A, Kyono Y, Nishino K, Bose M, Varshney A, Parker SCJ, Kitzman JO. Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561391. [PMID: 37873175 PMCID: PMC10592691 DOI: 10.1101/2023.10.08.561391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Recent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked to context-specific regulatory activity. We screened enhancer activity across a panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants in the 832/13 rat insulinoma cell line, a relevant model of pancreatic beta cells. We explored these fragments' context sensitivity by comparing their activities when placed up-or downstream of a reporter gene, and in combination with either a synthetic housekeeping promoter (SCP1) or a more biologically relevant promoter corresponding to the human insulin gene ( INS ). We identified clear effects of MPRA construct design on measured fragment enhancer activity. Specifically, a subset of fragments (n = 702/11,656) displayed positional bias, evenly distributed across up- and downstream preference. A separate set of fragments exhibited promoter bias (n = 698/11,656), mostly towards the cell-specific INS promoter (73.4%). To identify sequence features associated with promoter preference, we used Lasso regression with 562 genomic annotations and discovered that fragments with INS promoter-biased activity are enriched for HNF1 motifs. HNF1 family transcription factors are key regulators of glucose metabolism disrupted in maturity onset diabetes of the young (MODY), suggesting genetic convergence between rare coding variants that cause MODY and common T2D-associated regulatory variants. We designed a follow-up MPRA containing HNF1 motif-enriched fragments and observed several instances where deletion or mutation of HNF1 motifs disrupted the INS promoter-biased enhancer activity, specifically in the beta cell model but not in a skeletal muscle cell line, another diabetes-relevant cell type. Together, our study suggests that cell-specific regulatory activity is partially influenced by enhancer-promoter compatibility and indicates that careful attention should be paid when designing MPRA libraries to capture context-specific regulatory processes at disease-associated genetic signals.
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184
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Srinivasan S, Wu P, Mercader JM, Udler MS, Porneala BC, Bartz TM, Floyd JS, Sitlani C, Guo X, Haessler J, Kooperberg C, Liu J, Ahmad S, van Duijn C, Liu CT, Goodarzi MO, Florez JC, Meigs JB, Rotter JI, Rich SS, Dupuis J, Leong A. A Type 1 Diabetes Polygenic Score Is Not Associated With Prevalent Type 2 Diabetes in Large Population Studies. J Endocr Soc 2023; 7:bvad123. [PMID: 37841955 PMCID: PMC10576255 DOI: 10.1210/jendso/bvad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 10/17/2023] Open
Abstract
Context Both type 1 diabetes (T1D) and type 2 diabetes (T2D) have significant genetic contributions to risk and understanding their overlap can offer clinical insight. Objective We examined whether a T1D polygenic score (PS) was associated with a diagnosis of T2D in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Methods We constructed a T1D PS using 79 known single nucleotide polymorphisms associated with T1D risk. We analyzed 13 792 T2D cases and 14 169 controls from CHARGE cohorts to determine the association between the T1D PS and T2D prevalence. We validated findings in an independent sample of 2256 T2D cases and 27 052 controls from the Mass General Brigham Biobank (MGB Biobank). As secondary analyses in 5228 T2D cases from CHARGE, we used multivariable regression models to assess the association of the T1D PS with clinical outcomes associated with T1D. Results The T1D PS was not associated with T2D both in CHARGE (P = .15) and in the MGB Biobank (P = .87). The partitioned human leukocyte antigens only PS was associated with T2D in CHARGE (OR 1.02 per 1 SD increase in PS, 95% CI 1.01-1.03, P = .006) but not in the MGB Biobank. The T1D PS was weakly associated with insulin use (OR 1.007, 95% CI 1.001-1.012, P = .03) in CHARGE T2D cases but not with other outcomes. Conclusion In large biobank samples, a common variant PS for T1D was not consistently associated with prevalent T2D. However, possible heterogeneity in T2D cannot be ruled out and future studies are needed do subphenotyping.
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Affiliation(s)
- Shylaja Srinivasan
- Division of Pediatric Endocrinology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Josep M Mercader
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Miriam S Udler
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bianca C Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Xiquing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jun Liu
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford OX1 2JD, UK
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford OX1 2JD, UK
| | - Ching-Ti Liu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Aaron Leong
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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185
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Mullin BH, Zhu K, Brown SJ, Mullin S, Dudbridge F, Pavlos NJ, Richards JB, Grundberg E, Bell JT, Zeggini E, Walsh JP, Xu J, Wilson SG. Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis. Genetics 2023; 225:iyad150. [PMID: 37579195 PMCID: PMC10550309 DOI: 10.1093/genetics/iyad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - J Brent Richards
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Department of Medicine, Human Genetics, Epidemiology, and Biostatistics, Jewish General Hospital, McGill University, Montreal H3A 0G4, Canada
| | - Elin Grundberg
- Genomic Medicine Center, Children’s Mercy Kansas City, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Eleftheria Zeggini
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Translational Genomics, Neuherberg 85764, Germany
- TUM School of Medicine, Technical University of Munich (TUM) and Klinikum Rechts der Isar, Munich 81675, Germany
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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186
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Xu H, Sun Y, Francis M, Cheng CF, Modulla NT, Brenna JT, Chiang CWK, Ye K. Shared genetic basis informs the roles of polyunsaturated fatty acids in brain disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296500. [PMID: 37873425 PMCID: PMC10593041 DOI: 10.1101/2023.10.03.23296500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The neural tissue is rich in polyunsaturated fatty acids (PUFAs), components that are indispensable for the proper functioning of neurons, such as neurotransmission. PUFA nutritional deficiency and imbalance have been linked to a variety of chronic brain disorders, including major depressive disorder (MDD), anxiety, and anorexia. However, the effects of PUFAs on brain disorders remain inconclusive, and the extent of their shared genetic determinants is largely unknown. Here, we used genome-wide association summary statistics to systematically examine the shared genetic basis between six phenotypes of circulating PUFAs (N = 114,999) and 20 brain disorders (N = 9,725-762,917), infer their potential causal relationships, identify colocalized regions, and pinpoint shared genetic variants. Genetic correlation and polygenic overlap analyses revealed a widespread shared genetic basis for 77 trait pairs between six PUFA phenotypes and 16 brain disorders. Two-sample Mendelian randomization analysis indicated potential causal relationships for 16 pairs of PUFAs and brain disorders, including alcohol consumption, bipolar disorder (BIP), and MDD. Colocalization analysis identified 40 shared loci (13 unique) among six PUFAs and ten brain disorders. Twenty-two unique variants were statistically inferred as candidate shared causal variants, including rs1260326 (GCKR), rs174564 (FADS2) and rs4818766 (ADARB1). These findings reveal a widespread shared genetic basis between PUFAs and brain disorders, pinpoint specific shared variants, and provide support for the potential effects of PUFAs on certain brain disorders, especially MDD, BIP, and alcohol consumption.
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Affiliation(s)
- Huifang Xu
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Claire F. Cheng
- Department of Genetics, University of Georgia, Athens, Georgia
| | | | - J. Thomas Brenna
- Dell Pediatric Research Institute and Department of Pediatrics, The University of Texas at Austin, Texas
- Dell Pediatric Research Institute and Department of Chemistry, The University of Texas at Austin, Texas
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Texas
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, Georgia
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
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187
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Yew YW, Mina T, Ng HK, Lam BCC, Riboli E, Lee ES, Lee J, Ngeow J, Elliott P, Thng STG, Chambers JC, Loh M. Investigating causal relationships between obesity and skin barrier function in a multi-ethnic Asian general population cohort. Int J Obes (Lond) 2023; 47:963-969. [PMID: 37479793 PMCID: PMC10511308 DOI: 10.1038/s41366-023-01343-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Skin diseases impact significantly on the quality of life and psychology of patients. Obesity has been observed as a risk factor for skin diseases. Skin epidermal barrier dysfunctions are typical manifestations across several dermatological disturbances. OBJECTIVES We aim to establish the association between obesity and skin physiology measurements and investigate whether obesity may play a possible causal role on skin barrier dysfunction. METHODS We investigated the relationship of obesity with skin physiology measurements, namely transepidermal water loss (TEWL), skin surface moisture and skin pH in an Asian population cohort (n = 9990). To assess for a possible causal association between body mass index (BMI) and skin physiology measurements, we performed Mendelian Randomization (MR), along with subsequent additional analyses to assess the potential causal impact of known socioeconomic and comorbidities of obesity on TEWL. RESULTS Every 1 kg/m2 increase in BMI was associated with a 0.221% (95%CI: 0.144-0.298) increase in TEWL (P = 2.82E-08), a 0.336% (95%CI: 0.148-0.524) decrease in skin moisture (P = 4.66E-04) and a 0.184% (95%CI: 0.144-0.224) decrease in pH (P = 1.36E-19), adjusting for age, gender, and ethnicity. Relationships for both TEWL and pH with BMI remained strong (Beta 0.354; 95%CI: 0.189-0.520 and Beta -0.170; 95%CI: -0.253 to -0.087, respectively) even after adjusting for known confounders, with MR experiments further supporting BMI's possible causal relationship with TEWL. Based on additional MR performed, none of the socioeconomic and comorbidities of obesity investigated are likely to have possible causal relationships with TEWL. CONCLUSION We establish strong association of BMI with TEWL and skin pH, with MR results suggestive of a possible causal relationship of obesity with TEWL. It emphasizes the potential impact of obesity on skin barrier function and therefore opportunity for primary prevention.
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Affiliation(s)
- Yik Weng Yew
- National Skin Centre, Singapore, 308205, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Theresia Mina
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Benjamin Chih Chiang Lam
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Khoo Teck Puat Hospital, Integrated Care for Obesity & Diabetes, Singapore, 768828, Singapore
| | - Elio Riboli
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1NY, United Kingdom
| | - Eng Sing Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Clinical Research Unit, National Healthcare Group Polyclinic, Nexus@one-north, Singapore, 138543, Singapore
| | - Jimmy Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Research Division, Institute of Mental Health, Singapore, 539747, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Division of Medical Oncology, National Cancer Centre, Singapore, 169610, Singapore
| | - Paul Elliott
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1NY, United Kingdom
| | | | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1NY, United Kingdom
| | - Marie Loh
- National Skin Centre, Singapore, 308205, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore, 308232, Singapore.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1NY, United Kingdom.
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
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188
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Thorkildsen MS, Gustad LT, Mohus RM, Burgess S, Nilsen TIL, Damås JK, Rogne T. Association of Genetically Predicted Insomnia With Risk of Sepsis: A Mendelian Randomization Study. JAMA Psychiatry 2023; 80:1061-1065. [PMID: 37556136 PMCID: PMC10413214 DOI: 10.1001/jamapsychiatry.2023.2717] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 08/10/2023]
Abstract
Importance Insomnia has been associated with altered inflammatory response as well as increased risk of infections and sepsis in observational studies. However, these studies are prone to bias, such as residual confounding. To further understand the potential causal association between insomnia and sepsis risk, a 2-sample Mendelian randomization (MR) approach should be explored. Objective To evaluate whether genetically predicted insomnia is associated with risk of sepsis. Design, Setting, and Participants Two-sample MR was performed to estimate the association between genetically predicted insomnia and sepsis risk. Data were obtained from a genome-wide association study identifying 555 independent genetic variants (R2 < 0.01) strongly associated with insomnia (P < 5 × 10-8). Sensitivity analyses were conducted to address bias due to pleiotropy and sample overlap, along with mediation analyses and sex-stratified analyses. The insomnia data set included 2.4 million individuals of European ancestry from the UK Biobank and 23andMe. For sepsis, 462 918 individuals of European ancestry from the UK Biobank were included. Data were extracted between February and December 2022 and analyzed between March 2022 and March 2023. Exposure Genetically predicted insomnia. Main Outcome and Measure Sepsis. Results There were 593 724 individuals with insomnia and 10 154 cases of sepsis. A doubling in the population prevalence of genetically predicted insomnia was associated with an odds ratio of 1.37 (95% CI, 1.19-1.57; P = 7.6 × 10-6) for sepsis. Sensitivity analyses supported this observation. One-third of the association between genetically predicted insomnia and risk of sepsis was mediated through a combination of cardiometabolic risk factors for sepsis (body mass index, type 2 diabetes, smoking, or cardiovascular disease; overall proportion, 35.2%; 95% CI, 5.1-76.9). The association between insomnia and sepsis was more pronounced among women compared with men (women: odds ratio, 1.44; 95% CI, 1.24-1.68; men: OR, 1.10; 95% CI, 0.86-1.40). Conclusions and Relevance The concordance between these findings and previous observational studies supports that insomnia is potentially causally associated with the risk of sepsis. Thus, insomnia is a potential preventable risk factor of sepsis that should be further investigated, also in non-European populations.
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Affiliation(s)
- Marianne S. Thorkildsen
- Gemini Center for Sepsis Research at Institute of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lise T. Gustad
- Gemini Center for Sepsis Research at Institute of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Faculty of Nursing and Health Sciences, Nord University, Levanger, Norway
- Department of Medicine and Rehabilitation, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Randi M. Mohus
- Gemini Center for Sepsis Research at Institute of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Anesthesia and Intensive Care, St Olavs Hospital, Trondheim, Norway
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Tom I. L. Nilsen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan K. Damås
- Gemini Center for Sepsis Research at Institute of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Infectious Diseases, Clinic of Medicine, St Olavs Hospital, Trondheim, Norway
| | - Tormod Rogne
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, Connecticut
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189
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Sacks DB, Arnold M, Bakris GL, Bruns DE, Horvath AR, Lernmark Å, Metzger BE, Nathan DM, Kirkman MS. Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus. Diabetes Care 2023; 46:e151-e199. [PMID: 37471273 PMCID: PMC10516260 DOI: 10.2337/dci23-0036] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/11/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Numerous laboratory tests are used in the diagnosis and management of diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially. APPROACH An expert committee compiled evidence-based recommendations for laboratory analysis in screening, diagnosis, or monitoring of diabetes. The overall quality of the evidence and the strength of the recommendations were evaluated. The draft consensus recommendations were evaluated by invited reviewers and presented for public comment. Suggestions were incorporated as deemed appropriate by the authors (see Acknowledgments). The guidelines were reviewed by the Evidence Based Laboratory Medicine Committee and the Board of Directors of the American Association for Clinical Chemistry and by the Professional Practice Committee of the American Diabetes Association. CONTENT Diabetes can be diagnosed by demonstrating increased concentrations of glucose in venous plasma or increased hemoglobin A1c (HbA1c) in the blood. Glycemic control is monitored by the people with diabetes measuring their own blood glucose with meters and/or with continuous interstitial glucose monitoring (CGM) devices and also by laboratory analysis of HbA1c. The potential roles of noninvasive glucose monitoring, genetic testing, and measurement of ketones, autoantibodies, urine albumin, insulin, proinsulin, and C-peptide are addressed. SUMMARY The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
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Affiliation(s)
- David B. Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD
| | - Mark Arnold
- Department of Chemistry, University of Iowa, Iowa City, IA
| | - George L. Bakris
- Department of Medicine, American Heart Association Comprehensive Hypertension Center, Section of Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, Chicago, IL
| | - David E. Bruns
- Department of Pathology, University of Virginia Medical School, Charlottesville, VA
| | - Andrea R. Horvath
- New South Wales Health Pathology Department of Chemical Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital Malmö, Malmö, Sweden
| | - Boyd E. Metzger
- Division of Endocrinology, Northwestern University, The Feinberg School of Medicine, Chicago, IL
| | - David M. Nathan
- Massachusetts General Hospital Diabetes Center and Harvard Medical School, Boston, MA
| | - M. Sue Kirkman
- Department of Medicine, University of North Carolina, Chapel Hill, NC
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190
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Mehlig K, Foraita R, Nagrani R, Wright MN, De Henauw S, Molnár D, Moreno LA, Russo P, Tornaritis M, Veidebaum T, Lissner L, Kaprio J, Pigeot I. Genetic associations vary across the spectrum of fasting serum insulin: results from the European IDEFICS/I.Family children's cohort. Diabetologia 2023; 66:1914-1924. [PMID: 37420130 PMCID: PMC10473990 DOI: 10.1007/s00125-023-05957-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/27/2023] [Indexed: 07/09/2023]
Abstract
AIMS/HYPOTHESIS There is increasing evidence for the existence of shared genetic predictors of metabolic traits and neurodegenerative disease. We previously observed a U-shaped association between fasting insulin in middle-aged women and dementia up to 34 years later. In the present study, we performed genome-wide association (GWA) analyses for fasting serum insulin in European children with a focus on variants associated with the tails of the insulin distribution. METHODS Genotyping was successful in 2825 children aged 2-14 years at the time of insulin measurement. Because insulin levels vary during childhood, GWA analyses were based on age- and sex-specific z scores. Five percentile ranks of z-insulin were selected and modelled using logistic regression, i.e. the 15th, 25th, 50th, 75th and 85th percentile ranks (P15-P85). Additive genetic models were adjusted for age, sex, BMI, survey year, survey country and principal components derived from genetic data to account for ethnic heterogeneity. Quantile regression was used to determine whether associations with variants identified by GWA analyses differed across quantiles of log-insulin. RESULTS A variant in the SLC28A1 gene (rs2122859) was associated with the 85th percentile rank of the insulin z score (P85, p value=3×10-8). Two variants associated with low z-insulin (P15, p value <5×10-6) were located on the RBFOX1 and SH3RF3 genes. These genes have previously been associated with both metabolic traits and dementia phenotypes. While variants associated with P50 showed stable associations across the insulin spectrum, we found that associations with variants identified through GWA analyses of P15 and P85 varied across quantiles of log-insulin. CONCLUSIONS/INTERPRETATION The above results support the notion of a shared genetic architecture for dementia and metabolic traits. Our approach identified genetic variants that were associated with the tails of the insulin spectrum only. Because traditional heritability estimates assume that genetic effects are constant throughout the phenotype distribution, the new findings may have implications for understanding the discrepancy in heritability estimates from GWA and family studies and for the study of U-shaped biomarker-disease associations.
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Affiliation(s)
- Kirsten Mehlig
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Ronja Foraita
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
| | - Rajini Nagrani
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
| | - Marvin N Wright
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
- Department of Mathematics and Computer Science, University of Bremen, Bremen, Germany
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Stefaan De Henauw
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Dénes Molnár
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
| | - Luis A Moreno
- GENUD (Growth, Exercise, Nutrition and Development) Research Group, University of Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III, Madrid, Spain
| | - Paola Russo
- Institute of Food Sciences, National Research Council, Avellino, Italy
| | | | | | - Lauren Lissner
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Iris Pigeot
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
- Department of Mathematics and Computer Science, University of Bremen, Bremen, Germany
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191
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Eldjarn GH, Ferkingstad E, Lund SH, Helgason H, Magnusson OT, Gunnarsdottir K, Olafsdottir TA, Halldorsson BV, Olason PI, Zink F, Gudjonsson SA, Sveinbjornsson G, Magnusson MI, Helgason A, Oddsson A, Halldorsson GH, Magnusson MK, Saevarsdottir S, Eiriksdottir T, Masson G, Stefansson H, Jonsdottir I, Holm H, Rafnar T, Melsted P, Saemundsdottir J, Norddahl GL, Thorleifsson G, Ulfarsson MO, Gudbjartsson DF, Thorsteinsdottir U, Sulem P, Stefansson K. Large-scale plasma proteomics comparisons through genetics and disease associations. Nature 2023; 622:348-358. [PMID: 37794188 PMCID: PMC10567571 DOI: 10.1038/s41586-023-06563-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/22/2023] [Indexed: 10/06/2023]
Abstract
High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 data generated by the UK Biobank Pharma Proteomics Project1 on plasma samples from more than 50,000 UK Biobank participants with phenotypic and genotypic data, stratifying on British or Irish, African and South Asian ancestries. We compared the results with those of a SomaScan v4 study on plasma from 36,000 Icelandic people2, for 1,514 of whom Olink data were also available. We found modest correlation between the two platforms. Although cis protein quantitative trait loci were detected for a similar absolute number of assays on the two platforms (2,101 on Olink versus 2,120 on SomaScan), the proportion of assays with such supporting evidence for assay performance was higher on the Olink platform (72% versus 43%). A considerable number of proteins had genomic associations that differed between the platforms. We provide examples where differences between platforms may influence conclusions drawn from the integration of protein levels with the study of diseases. We demonstrate how leveraging the diverse ancestries of participants in the UK Biobank helps to detect novel associations and refine genomic location. Our results show the value of the information provided by the two most commonly used high-throughput proteomics platforms and demonstrate the differences between them that at times provides useful complementarity.
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Affiliation(s)
| | | | - Sigrun H Lund
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | - Agnar Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Magnus O Ulfarsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Electrical and Computer Engineering, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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192
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Zheng J, Wheeler E, Pietzner M, Andlauer TFM, Yau MS, Hartley AE, Brumpton BM, Rasheed H, Kemp JP, Frysz M, Robinson J, Reppe S, Prijatelj V, Gautvik KM, Falk L, Maerz W, Gergei I, Peyser PA, Kavousi M, de Vries PS, Miller CL, Bos M, van der Laan SW, Malhotra R, Herrmann M, Scharnagl H, Kleber M, Dedoussis G, Zeggini E, Nethander M, Ohlsson C, Lorentzon M, Wareham N, Langenberg C, Holmes MV, Davey Smith G, Tobias JH. Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and Its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization. Arthritis Rheumatol 2023; 75:1781-1792. [PMID: 37096546 PMCID: PMC10586470 DOI: 10.1002/art.42538] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/22/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE In this study, we aimed to establish the causal effects of lowering sclerostin, target of the antiosteoporosis drug romosozumab, on atherosclerosis and its risk factors. METHODS A genome-wide association study meta-analysis was performed of circulating sclerostin levels in 33,961 European individuals. Mendelian randomization (MR) was used to predict the causal effects of sclerostin lowering on 15 atherosclerosis-related diseases and risk factors. RESULTS We found that 18 conditionally independent variants were associated with circulating sclerostin. Of these, 1 cis signal in SOST and 3 trans signals in B4GALNT3, RIN3, and SERPINA1 regions showed directionally opposite signals for sclerostin levels and estimated bone mineral density. Variants with these 4 regions were selected as genetic instruments. MR using 5 correlated cis-SNPs suggested that lower sclerostin increased the risk of type 2 diabetes mellitus (DM) (odds ratio [OR] 1.32 [95% confidence interval (95% CI) 1.03-1.69]) and myocardial infarction (MI) (OR 1.35 [95% CI 1.01-1.79]); sclerostin lowering was also suggested to increase the extent of coronary artery calcification (CAC) (β = 0.24 [95% CI 0.02-0.45]). MR using both cis and trans instruments suggested that lower sclerostin increased hypertension risk (OR 1.09 [95% CI 1.04-1.15]), but otherwise had attenuated effects. CONCLUSION This study provides genetic evidence to suggest that lower levels of sclerostin may increase the risk of hypertension, type 2 DM, MI, and the extent of CAC. Taken together, these findings underscore the requirement for strategies to mitigate potential adverse effects of romosozumab treatment on atherosclerosis and its related risk factors.
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Affiliation(s)
- Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the People's Republic of China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of BristolBristolUK
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
| | - Michelle S. Yau
- Marcus Institute for Aging Research, Hebrew SeniorLifeHarvard Medical SchoolBostonMassachusetts
| | | | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, and HUNT Research Centre, Department of Public Health and Nursing, NTNUNorwegian University of Science and TechnologyLevangerNorway
| | - Humaira Rasheed
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway, and Division of Medicine and Laboratory Sciences, Faculty of MedicineUniversity of OsloOsloNorway
| | - John P. Kemp
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia, and The University of Queensland Diamantina InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Monika Frysz
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
| | - Jamie Robinson
- MRC IEU, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sjur Reppe
- Unger‐Vetlesen Institute, Lovisenberg Diaconal Hospital and Department of Plastic and Reconstructive Surgery, Oslo University Hospital and Department of Medical BiochemistryOslo University HospitalOsloNorway
| | - Vid Prijatelj
- Department of Internal MedicineErasmus MC University Medical CenterRotterdamThe Netherlands
| | | | - Louise Falk
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Winfried Maerz
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria, and SYNLAB Academy, SYNLAB Holding Deutschland GmbH and Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | - Ingrid Gergei
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, and Therapeutic Area Cardiovascular MedicineBoehringer Ingelheim International GmbHIngelheimGermany
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn Arbor
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public HealthThe University of Texas Health Science Center at Houston
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health SciencesUniversity of VirginiaCharlottesville
| | - Maxime Bos
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division of Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center UtrechtUtrecht UniversityUtrechtthe Netherlands
| | - Rajeev Malhotra
- Cardiology Division, Department of MedicineMassachusetts General HospitalBoston
| | - Markus Herrmann
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Marcus Kleber
- SYNLAB Academy, SYNLAB Holding Deutschland GmbHMannheimGermany
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and EducationHarokopio UniversityAthensGreece
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, and Technical University of Munich (TUM) and Klinikum Rechts der IsarTUM School of MedicineMunichGermany
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg and Bioinformatics and Data Centre, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of MedicineUniversity of GothenburgGothenburgSweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, and Region Västra Götaland, Geriatric Medicine, Sahlgrenska University Hospital, Mölndal, Sweden, and Mary McKillop Institute for Health ResearchAustralian Catholic UniversityMelbourneVictoriaAustralia
| | - Nick Wareham
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Michael V. Holmes
- MRC IEU, Bristol Medical School, University of Bristol, and Medical Research Council Population Health Research Unit, University of Oxford, and Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population HealthUniversity of Oxford, and National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University HospitalOxfordUK
| | | | - Jonathan H. Tobias
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
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193
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Zheng J, Xu M, Yang Q, Hu C, Walker V, Lu J, Wang J, Liu R, Xu Y, Wang T, Zhao Z, Yuan J, Burgess S, Au Yeung SL, Luo S, Anderson EL, Holmes MV, Smith GD, Ning G, Wang W, Gaunt TR, Bi Y. Efficacy of metformin targets on cardiometabolic health in the general population and non-diabetic individuals: a Mendelian randomization study. EBioMedicine 2023; 96:104803. [PMID: 37734206 PMCID: PMC10514430 DOI: 10.1016/j.ebiom.2023.104803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Metformin shows beneficial effects on cardiometabolic health in diabetic individuals. However, the beneficial effects in the general population, especially in non-diabetic individuals are unclear. We aim to estimate the effects of perturbation of seven metformin targets on cardiometabolic health using Mendelian randomization (MR). METHODS Genetic variants close to metformin-targeted genes associated with expression of the corresponding genes and glycated haemoglobin (HbA1c) level were used to proxy therapeutic effects of seven metformin-related drug targets. Eight cardiometabolic phenotypes under metformin trials were selected as outcomes (average N = 466,947). MR estimates representing the weighted average effects of the seven effects of metformin targets on the eight outcomes were generated. One-sample MR was applied to estimate the averaged and target-specific effects in 338,425 non-diabetic individuals in UK Biobank. FINDINGS Genetically proxied averaged effects of five metformin targets, equivalent to a 0.62% reduction of HbA1c level, was associated with 37.8% lower risk of coronary artery disease (CAD) (odds ratio [OR] = 0.62, 95% confidence interval [CI] = 0.46-0.84), lower levels of body mass index (BMI) (β = -0.22, 95% CI = -0.35 to -0.09), systolic blood pressure (SBP) (β = -0.19, 95% CI = -0.28 to -0.09) and diastolic blood pressure (DBP) levels (β = -0.29, 95% CI = -0.39 to -0.19). One-sample MR suggested that the seven metformin targets showed averaged and target-specific beneficial effects on BMI, SBP and DBP in non-diabetic individuals. INTERPRETATION This study showed that perturbation of seven metformin targets has beneficial effects on BMI and blood pressure in non-diabetic individuals. Clinical trials are needed to investigate whether similar effects can be achieved with metformin medications. FUNDING Funding information is provided in the Acknowledgements.
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Affiliation(s)
- Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom.
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qian Yang
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Chunyan Hu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Venexia Walker
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiqiu Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruixin Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinqiu Yuan
- Clinical Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China; Center for Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China; Guangzhou Women and Children Medical Center, Guangzhou, Guangdong, 510623, China; Division of Epidemiology, The JC School of Public Health & Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Stephen Burgess
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, CB2 0SR, United Kingdom; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Shiu Lun Au Yeung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shan Luo
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Emma L Anderson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom; Division of Psychiatry, Faculty of Brain Sciences, University College London, London, United Kingdom
| | - Michael V Holmes
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom; NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom; NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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194
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Zhu Y, Li M, Wang H, Yang F, Pang X, Du R, Zhang J, Huang X. Genetically proxied antidiabetic drugs targets and stroke risk. J Transl Med 2023; 21:681. [PMID: 37777789 PMCID: PMC10544120 DOI: 10.1186/s12967-023-04565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/22/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Previous studies have assessed the association between antidiabetic drugs and stroke risk, but the results are inconsistent. Mendelian randomization (MR) was used to assess effects of antidiabetic drugs on stroke risk. METHODS We selected blood glucose-lowering variants in genes encoding antidiabetic drugs targets from genome-wide association studies (GWAS). A two-sample MR and Colocalization analyses were applied to examine associations between antidiabetic drugs and the risk of stroke. For antidiabetic agents that had effect on stroke risk, an independent blood glucose GWAS summary data was used for further verification. RESULTS Genetic proxies for sulfonylureas targets were associated with reduced risk of any stroke (OR=0.062, 95% CI 0.013-0.295, P=4.65×10-4) and any ischemic stroke (OR=0.055, 95% CI 0.010-0.289, P=6.25×10-4), but not with intracranial hemorrhage. Colocalization supported shared casual variants for blood glucose with any stroke and any ischemic stroke within the encoding genes for sulfonylureas targets (KCNJ11 and ABCC8) (posterior probability>0.7). Furthermore, genetic variants in the targets of insulin/insulin analogues, glucagon-like peptide-1 analogues, thiazolidinediones, and metformin were not associated with the risk of any stroke, any ischemic stroke and intracranial hemorrhage. The association was consistent in the analysis of sulfonylureas with stroke risk using an independent blood glucose GWAS summary data. CONCLUSIONS Our findings showed that genetic proxies for sulfonylureas targets by lowering blood glucose were associated with a lower risk of any stroke and any ischemic stroke. The study might be of great significance to guide the selection of glucose-lowering drugs in individuals at high risk of stroke.
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Affiliation(s)
- Yahui Zhu
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Mao Li
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Hongfen Wang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Fei Yang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Xinyuan Pang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
- College of Medicine, Nankai University, Tianjin, China
| | - Rongrong Du
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
- College of Medicine, Nankai University, Tianjin, China
| | - Jinghong Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Xusheng Huang
- Medical School of Chinese PLA, Beijing, China.
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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195
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Lin D, Yu J, Lin L, Ou Q, Quan H. MRPS6 modulates glucose-stimulated insulin secretion in mouse islet cells through mitochondrial unfolded protein response. Sci Rep 2023; 13:16173. [PMID: 37758822 PMCID: PMC10533529 DOI: 10.1038/s41598-023-43438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023] Open
Abstract
Lack of efficient insulin secretion from the pancreas can lead to impaired glucose tolerance (IGT), prediabetes, and diabetes. We have previously identified two IGT-associated single nucleotide polymorphisms (SNPs) rs62212118 and rs13052524 located at two overlapping genes: MRPS6 and SLC5A3. In this study, we show that MRPS6 but not SLC5A3 regulates glucose-stimulated insulin secretion (GSIS) in primary human β-cell and a mouse pancreatic insulinoma β-cell line. Data mining and biochemical studies reveal that MRPS6 is positively regulated by the mitochondrial unfolded protein response (UPRmt), but feedback inhibits UPRmt. Disruption of such feedback by MRPS6 knockdown causes UPRmt hyperactivation in high glucose conditions, hence elevated ROS levels, increased apoptosis, and impaired GSIS. Conversely, MRPS6 overexpression reduces UPRmt, mitigates high glucose-induced ROS levels and apoptosis, and enhances GSIS in an ATF5-dependent manner. Consistently, UPRmt up-regulation or down-regulation by modulating ATF5 expression is sufficient to decrease or increase GSIS. The negative role of UPRmt in GSIS is further supported by analysis of public transcriptomic data from murine islets. In all, our studies identify MRPS6 and UPRmt as novel modulators of GSIS and apoptosis in β-cells, contributing to our understanding of the molecular and cellular mechanisms of IGT, prediabetes, and diabetes.
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Affiliation(s)
- Danhong Lin
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No.19 Xiuhua Road, Haikou, 570311, Hainan, China
| | - Jingwen Yu
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No.19 Xiuhua Road, Haikou, 570311, Hainan, China
| | - Leweihua Lin
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No.19 Xiuhua Road, Haikou, 570311, Hainan, China
| | - Qianying Ou
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No.19 Xiuhua Road, Haikou, 570311, Hainan, China
| | - Huibiao Quan
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No.19 Xiuhua Road, Haikou, 570311, Hainan, China.
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196
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Chen T, Zhang H, Mazumder R, Lin X. Ensembled best subset selection using summary statistics for polygenic risk prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559307. [PMID: 37886515 PMCID: PMC10602024 DOI: 10.1101/2023.09.25.559307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Polygenic risk scores (PRS) enhance population risk stratification and advance personalized medicine, yet existing methods face a tradeoff between predictive power and computational efficiency. We introduce ALL-Sum, a fast and scalable PRS method that combines an efficient summary statistic-based L 0 L 2 penalized regression algorithm with an ensembling step that aggregates estimates from different tuning parameters for improved prediction performance. In extensive large-scale simulations across a wide range of polygenicity and genome-wide association studies (GWAS) sample sizes, ALL-Sum consistently outperforms popular alternative methods in terms of prediction accuracy, runtime, and memory usage. We analyze 27 published GWAS summary statistics for 11 complex traits from 9 reputable data sources, including the Global Lipids Genetics Consortium, Breast Cancer Association Consortium, and FinnGen, evaluated using individual-level UKBB data. ALL-Sum achieves the highest accuracy for most traits, particularly for GWAS with large sample sizes. We provide ALL-Sum as a user-friendly command-line software with pre-computed reference data for streamlined user-end analysis.
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197
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Wang Y, Zhang L, Zhang W, Tang M, Cui H, Wu X, Zhao X, Chen L, Yan P, Yang C, Xiao C, Zou Y, Liu Y, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Understanding the relationship between circulating lipids and risk of chronic kidney disease: a prospective cohort study and large-scale genetic analyses. J Transl Med 2023; 21:671. [PMID: 37759214 PMCID: PMC10537816 DOI: 10.1186/s12967-023-04509-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND This study aims to comprehensively investigate the phenotypic and genetic relationships between four common lipids (high-density lipoprotein cholesterol, HDL-C; low-density lipoprotein cholesterol, LDL-C; total cholesterol, TC; and triglycerides, TG), chronic kidney disease (CKD), and estimated glomerular filtration rate (eGFR). METHODS We first investigated the observational association of lipids (exposures) with CKD (primary outcome) and eGFR (secondary outcome) using data from UK Biobank. We then explored the genetic relationship using summary statistics from the largest genome-wide association study of four lipids (N = 1,320,016), CKD (Ncase = 41,395, Ncontrol = 439,303), and eGFR(N = 567,460). RESULTS There were significant phenotypic associations (HDL-C: hazard ratio (HR) = 0.76, 95%CI = 0.60-0.95; TG: HR = 1.08, 95%CI = 1.02-1.13) and global genetic correlations (HDL-C: [Formula: see text] = - 0.132, P = 1.00 × 10-4; TG: [Formula: see text] = 0.176; P = 2.66 × 10-5) between HDL-C, TG, and CKD risk. Partitioning the whole genome into 2353 LD-independent regions, twelve significant regions were observed for four lipids and CKD. The shared genetic basis was largely explained by 29 pleiotropic loci and 36 shared gene-tissue pairs. Mendelian randomization revealed an independent causal relationship of genetically predicted HDL-C (odds ratio = 0.91, 95%CI = 0.85-0.98), but not for LDL-C, TC, or TG, with the risk of CKD. Regarding eGFR, a similar pattern of correlation and pleiotropy was observed. CONCLUSIONS Our work demonstrates a putative causal role of HDL-C in CKD and a significant biological pleiotropy underlying lipids and CKD in populations of European ancestry. Management of low HDL-C levels could potentially benefit in reducing the long-term risk of CKD.
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Affiliation(s)
- Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China.
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Jones AG, Shields BM, Oram RA, Dabelea DM, Hagopian WA, Lustigova E, Shah AS, Knupp J, Mottl AK, DÀgostino RB, Williams A, Marcovina SM, Pihoker C, Divers J, Redondo MJ. Clinical prediction models combining routine clinical measures identify participants with youth-onset diabetes who maintain insulin secretion in the range associated with type 2 diabetes: The SEARCH for Diabetes in Youth Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.27.23296128. [PMID: 37808789 PMCID: PMC10557841 DOI: 10.1101/2023.09.27.23296128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Objective With the high prevalence of pediatric obesity and overlapping features between diabetes subtypes, accurately classifying youth-onset diabetes can be challenging. We aimed to develop prediction models that, using characteristics available at diabetes diagnosis, can identify youth who will retain endogenous insulin secretion at levels consistent with type 2 diabetes (T2D). Methods We studied 2,966 youth with diabetes in the prospective SEARCH study (diagnosis age ≤19 years) to develop prediction models to identify participants with fasting c-peptide ≥250 pmol/L (≥0.75ng/ml) after >3 years (median 74 months) of diabetes duration. Models included clinical measures at baseline visit, at a mean diabetes duration of 11 months (age, BMI, sex, waist circumference, HDL-C), with and without islet autoantibodies (GADA, IA-2A) and a Type 1 Diabetes Genetic Risk Score (T1DGRS). Results Models using routine clinical measures with or without autoantibodies and T1DGRS were highly accurate in identifying participants with c-peptide ≥0.75 ng/ml (17% of participants; 2.3% and 53% of those with and without positive autoantibodies) (area under receiver operator curve [AUCROC] 0.95-0.98). In internal validation, optimism was very low, with excellent calibration (slope=0.995-0.999). Models retained high performance for predicting retained c-peptide in older youth with obesity (AUCROC 0.88-0.96), and in subgroups defined by self-reported race/ethnicity (AUCROC 0.88-0.97), autoantibody status (AUCROC 0.87-0.96), and clinically diagnosed diabetes types (AUCROC 0.81-0.92). Conclusion Prediction models combining routine clinical measures at diabetes diagnosis, with or without islet autoantibodies or T1DGRS, can accurately identify youth with diabetes who maintain endogenous insulin secretion in the range associated with type 2 diabetes.
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Affiliation(s)
| | | | | | | | | | | | - Amy S Shah
- University of Cincinnati & Cincinnati Children's Hospital Medical Center
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199
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Smeland OB, Kutrolli G, Bahrami S, Fominykh V, Parker N, Hindley GFL, Rødevand L, Jaholkowski P, Tesfaye M, Parekh P, Elvsåshagen T, Grotzinger AD, Steen NE, van der Meer D, O’Connell KS, Djurovic S, Dale AM, Shadrin AA, Frei O, Andreassen OA. The shared genetic risk architecture of neurological and psychiatric disorders: a genome-wide analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.21.23292993. [PMID: 37503175 PMCID: PMC10371109 DOI: 10.1101/2023.07.21.23292993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
While neurological and psychiatric disorders have historically been considered to reflect distinct pathogenic entities, recent findings suggest shared pathobiological mechanisms. However, the extent to which these heritable disorders share genetic influences remains unclear. Here, we performed a comprehensive analysis of GWAS data, involving nearly 1 million cases across ten neurological diseases and ten psychiatric disorders, to compare their common genetic risk and biological underpinnings. Using complementary statistical tools, we demonstrate widespread genetic overlap across the disorders, even in the absence of genetic correlations. This indicates that a large set of common variants impact risk of multiple neurological and psychiatric disorders, but with divergent effect sizes. Furthermore, biological interrogation revealed a range of biological processes associated with neurological diseases, while psychiatric disorders consistently implicated neuronal biology. Altogether, the study indicates that neurological and psychiatric disorders share key etiological aspects, which has important implications for disease classification, precision medicine, and clinical practice.
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Affiliation(s)
- Olav B. Smeland
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gleda Kutrolli
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Shahram Bahrami
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vera Fominykh
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nadine Parker
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guy F. L. Hindley
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Psychosis Studies, Institute of Psychiatry, Psychology and Neurosciences, King’s College London, London, United Kingdom
| | - Linn Rødevand
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Piotr Jaholkowski
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Markos Tesfaye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatry, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Pravesh Parekh
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Elvsåshagen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
| | - Andrew D. Grotzinger
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | | | | | - Nils Eiel Steen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dennis van der Meer
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands
| | - Kevin S. O’Connell
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anders M. Dale
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, USA
- Department of Neurosciences, University of California San Diego, La Jolla, USA
- Department of Radiology, University of California, San Diego, La Jolla, USA
| | - Alexey A. Shadrin
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
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200
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Stanzick KJ, Stark KJ, Gorski M, Schödel J, Krüger R, Kronenberg F, Warth R, Heid IM, Winkler TW. KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies. BMC Bioinformatics 2023; 24:355. [PMID: 37735349 PMCID: PMC10512588 DOI: 10.1186/s12859-023-05472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with kidney function. By combining these findings with post-GWAS information (e.g., statistical fine-mapping to identify independent association signals and to narrow down signals to causal variants; or different sources of annotation data), new hypotheses regarding physiology and disease aetiology can be obtained. These hypotheses need to be tested in laboratory experiments, for example, to identify new therapeutic targets. For this purpose, the evidence obtained from GWAS and post-GWAS analyses must be processed and presented in a way that they are easily accessible to kidney researchers without specific GWAS expertise. MAIN: Here we present KidneyGPS, a user-friendly web-application that combines genetic variant association for estimated glomerular filtration rate (eGFR) from the Chronic Kidney Disease Genetics consortium with annotation of (i) genetic variants with functional or regulatory effects ("SNP-to-gene" mapping), (ii) genes with kidney phenotypes in mice or human ("gene-to-phenotype"), and (iii) drugability of genes (to support re-purposing). KidneyGPS adopts a comprehensive approach summarizing evidence for all 5906 genes in the 424 GWAS loci for eGFR identified previously and the 35,885 variants in the 99% credible sets of 594 independent signals. KidneyGPS enables user-friendly access to the abundance of information by search functions for genes, variants, and regions. KidneyGPS also provides a function ("GPS tab") to generate lists of genes with specific characteristics thus enabling customizable Gene Prioritisation (GPS). These specific characteristics can be as broad as any gene in the 424 loci with a known kidney phenotype in mice or human; or they can be highly focussed on genes mapping to genetic variants or signals with particularly with high statistical support. KidneyGPS is implemented with RShiny in a modularized fashion to facilitate update of input data ( https://kidneygps.ur.de/gps/ ). CONCLUSION With the focus on kidney function related evidence, KidneyGPS fills a gap between large general platforms for accessing GWAS and post-GWAS results and the specific needs of the kidney research community. This makes KidneyGPS an important platform for kidney researchers to help translate in silico research results into in vitro or in vivo research.
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Affiliation(s)
- Kira J Stanzick
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, and Uniklinikum Erlangen, Erlangen, Germany
| | - René Krüger
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, and Uniklinikum Erlangen, Erlangen, Germany
| | - Florian Kronenberg
- Department of Genetics, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Warth
- Medical Cell Biology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
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