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Joseph A, Baslet G, O'Neal MA, Polich G, Gonsalvez I, Christoforou AN, Dworetzky BA, Spagnolo PA. Prevalence of autoimmune diseases in functional neurological disorder: influence of psychiatric comorbidities and biological sex. J Neurol Neurosurg Psychiatry 2024; 95:865-869. [PMID: 38514177 DOI: 10.1136/jnnp-2023-332825] [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: 10/18/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Functional neurological disorder (FND) is a common and disabling neuropsychiatric condition, which disproportionally affects women compared with men. While the etiopathogenesis of this disorder remains elusive, immune dysregulation is emerging as one potential mechanism. To begin to understand the role of immune dysfunctions in FND, we assessed the prevalence of several common autoimmune diseases (ADs) in a large cohort of patients with FND and examined the influence of psychiatric comorbidities and biological sex. METHODS Using a large biorepository database (Mass General Brigham Biobank), we obtained demographic and clinical data of a cohort of 643 patients diagnosed with FND between January 2015 and December 2021. The proportion of ADs was calculated overall, by sex and by the presence of psychiatric comorbidities. RESULTS The overall prevalence of ADs in our sample was 41.9%, with connective tissue and autoimmune endocrine diseases being the most commonly observed ADs. Among patients with FND and ADs, 27.7% had ≥2 ADs and 8% met criteria for multiple autoimmune syndrome. Rates of ADs were significantly higher in subjects with comorbid major depressive disorder and post-traumatic stress disorder (p= 0.02). Women represented the largest proportion of patients with concurrent ADs, both in the overall sample and in the subgroups of interest (p's < 0.05). CONCLUSIONS This study is unique in providing evidence of an association between FND and ADs. Future studies are needed to investigate the mechanisms underlying this association and to understand whether FND is characterised by distinct dysregulations in immune response.
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Affiliation(s)
- Anna Joseph
- Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Gaston Baslet
- Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mary A O'Neal
- Harvard Medical School, Boston, Massachusetts, USA
- Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ginger Polich
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Boston, Boston, Massachusetts, USA
| | - Irene Gonsalvez
- Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea N Christoforou
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital Boston, Boston, Massachusetts, USA
| | - Barbara A Dworetzky
- Harvard Medical School, Boston, Massachusetts, USA
- Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Primavera A Spagnolo
- Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Nopsopon T, Chen Y, Chen Q, Wheelock CE, Weiss ST, McGeachie M, Lasky-Su J, Akenroye A. Untargeted metabolomic analysis reveals different metabolites associated with response to mepolizumab and omalizumab in asthma. ERJ Open Res 2024; 10:00931-2023. [PMID: 39104961 PMCID: PMC11298997 DOI: 10.1183/23120541.00931-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/31/2024] [Indexed: 08/07/2024] Open
Abstract
Background There is limited evidence on biomarkers associated with response to the monoclonal antibodies currently approved for asthma treatment. We sought to identify circulatory metabolites associated with response to treatment with mepolizumab or omalizumab. Methods We conducted global metabolomic profiling of pre-treatment plasma samples from 100 patients with moderate-to-severe asthma who initiated mepolizumab (n=31) or omalizumab (n=69). The primary outcome was the change in exacerbations within 12 months of therapy. Negative binomial models were used to assess the association between each metabolite and exacerbations, adjusting for age, sex, body mass index, baseline exacerbations and inhaled corticosteroid use. Chemical similarity enrichment analysis (ChemRICH) was conducted to identify chemical subclasses associated with treatment response. Results The mean age of the mepolizumab group was 58.7 years with on average 2.9 exacerbations over the year prior to initiation of biologic therapy. The mean age in the omalizumab group was 48.8 years with 1.5 exacerbations in the preceding year. Patients with higher levels of two tocopherol metabolites were associated with more exacerbations on mepolizumab (δ-carboxyethyl hydroxychroman (CEHC) (p=2.65E-05, false discovery rate (FDR=0.01) and δ-CEHC glucuronide (p=2.47E-06, FDR=0.003)). Higher levels of six androgenic steroids, three carnitine metabolites and two bile acid metabolites were associated with decreased exacerbations in the omalizumab group. In enrichment analyses, xanthine metabolites (cluster FDR=0.0006) and tocopherol metabolites (cluster FDR=0.02) were associated with worse mepolizumab response, while androgenic steroids (cluster FDR=1.9E-18), pregnenolone steroids (cluster p=3.2E-07, FDR=1.4E-05) and secondary bile acid metabolites (cluster p=0.0003, FDR=0.006) were the top subclasses associated with better omalizumab response. Conclusion This study identifies distinct metabolites associated with response to mepolizumab and omalizumab, with androgenic steroids associated with response to both mepolizumab and omalizumab.
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Affiliation(s)
- Tanawin Nopsopon
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig E. Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Scott. T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Ayobami Akenroye
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- These authors contributed equally
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3
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Campion TR, Craven CK, Dorr DA, Bernstam EV, Knosp BM. Understanding enterprise data warehouses to support clinical and translational research: impact, sustainability, demand management, and accessibility. J Am Med Inform Assoc 2024; 31:1522-1528. [PMID: 38777803 PMCID: PMC11187432 DOI: 10.1093/jamia/ocae111] [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: 02/16/2024] [Revised: 04/10/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
OBJECTIVES Healthcare organizations, including Clinical and Translational Science Awards (CTSA) hubs funded by the National Institutes of Health, seek to enable secondary use of electronic health record (EHR) data through an enterprise data warehouse for research (EDW4R), but optimal approaches are unknown. In this qualitative study, our goal was to understand EDW4R impact, sustainability, demand management, and accessibility. MATERIALS AND METHODS We engaged a convenience sample of informatics leaders from CTSA hubs (n = 21) for semi-structured interviews and completed a directed content analysis of interview transcripts. RESULTS EDW4R have created institutional capacity for single- and multi-center studies, democratized access to EHR data for investigators from multiple disciplines, and enabled the learning health system. Bibliometrics have been challenging due to investigator non-compliance, but one hub's requirement to link all study protocols with funding records enabled quantifying an EDW4R's multi-million dollar impact. Sustainability of EDW4R has relied on multiple funding sources with a general shift away from the CTSA grant toward institutional and industry support. To address EDW4R demand, institutions have expanded staff, used different governance approaches, and provided investigator self-service tools. EDW4R accessibility can benefit from improved tools incorporating user-centered design, increased data literacy among scientists, expansion of informaticians in the workforce, and growth of team science. DISCUSSION As investigator demand for EDW4R has increased, approaches to tracking impact, ensuring sustainability, and improving accessibility of EDW4R resources have varied. CONCLUSION This study adds to understanding of how informatics leaders seek to support investigators using EDW4R across the CTSA consortium and potentially elsewhere.
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Affiliation(s)
- Thomas R Campion
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY 10022, United States
| | - Catherine K Craven
- Division of Clinical Research Informatics, Department of Population Health Sciences, The University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - David A Dorr
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, United States
- Department of Medicine, Oregon Health & Science University, Portland, OR 97239, United States
| | - Elmer V Bernstam
- D. Bradley McWilliams School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX 77030, United States
- Division of General Internal Medicine, McGovern Medical School and Center for Clinical and Translational Sciences, The University of Texas Health Science Center, Houston, TX 77030, United States
| | - Boyd M Knosp
- Roy J. and Lucille A. Carver College of Medicine and the Institute for Clinical & Translational Science, University of Iowa, Iowa City, IA 52242, United States
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Hahn G, Prokopenko D, Hecker J, Lutz SM, Mullin K, Sejour L, Hide W, Vlachos I, DeSantis S, Tanzi RE, Lange C. Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data. Brief Bioinform 2024; 25:bbae267. [PMID: 38836403 PMCID: PMC11151121 DOI: 10.1093/bib/bbae267] [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: 10/17/2023] [Revised: 04/17/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In precision medicine, both predicting the disease susceptibility of an individual and forecasting its disease-free survival are areas of key research. Besides the classical epidemiological predictor variables, data from multiple (omic) platforms are increasingly available. To integrate this wealth of information, we propose new methodology to combine both cooperative learning, a recent approach to leverage the predictive power of several datasets, and polygenic hazard score models. Polygenic hazard score models provide a practitioner with a more differentiated view of the predicted disease-free survival than the one given by merely a point estimate, for instance computed with a polygenic risk score. Our aim is to leverage the advantages of cooperative learning for the computation of polygenic hazard score models via Cox's proportional hazard model, thereby improving the prediction of the disease-free survival. In our experimental study, we apply our methodology to forecast the disease-free survival for Alzheimer's disease (AD) using three layers of data. One layer contains epidemiological variables such as sex, APOE (apolipoprotein E, a genetic risk factor for AD) status and 10 leading principal components. Another layer contains selected genomic loci, and the last layer contains methylation data for selected CpG sites. We demonstrate that the survival curves computed via cooperative learning yield an AUC of around $0.7$, above the state-of-the-art performance of its competitors. Importantly, the proposed methodology returns (1) a linear score that can be easily interpreted (in contrast to machine learning approaches), and (2) a weighting of the predictive power of the involved data layers, allowing for an assessment of the importance of each omic (or other) platform. Similarly to polygenic hazard score models, our methodology also allows one to compute individual survival curves for each patient.
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Affiliation(s)
- Georg Hahn
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
| | - Dmitry Prokopenko
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Julian Hecker
- Channing Divsion of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, 02115, Boston, MA, USA
| | - Sharon M Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
| | - Kristina Mullin
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Leinal Sejour
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Winston Hide
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Ioannis Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Stacia DeSantis
- Houston Campus, The University of Texas Health Science Center, 1200 Pressler Street, 77030, Houston, TX, USA
| | - Rudolph E Tanzi
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
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Akenroye A, Nopsopon T, Hacker JJ, Laidlaw TM. Ratio of plasma IL-13/TNF- ∝ and CXCL10/CCL17 predicts mepolizumab and omalizumab response in asthma better than eosinophil count or immunoglobulin E level. Sci Rep 2024; 14:10404. [PMID: 38710930 PMCID: PMC11074109 DOI: 10.1038/s41598-024-60864-3] [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: 11/04/2023] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
To date, most studies to identify biomarkers associated with response to the anti-interleukin 5 agent, mepolizumab, and to the anti-immunoglobulin E agent, omalizumab have focused on clinically available biomarkers, such as the peripheral blood eosinophil counts (BEC) and total immunoglobulin E (IgE). However, these biomarkers often have low predictive accuracy, with many patients with eosinophilic or allergic asthma failing to demonstrate clinical response to mepolizumab or omalizumab respectively. In this study, we evaluated the association of baseline pre-biologic plasma levels of 26 cytokines and chemokines, including T-helper 1 (Th1)-, Th2-, Th17-related cytokines, and their ratios with subsequent clinical response to mepolizumab or omalizumab. We defined clinical response as a reduction in the baseline annual exacerbation rate by half or more over the one-year period following initiation of the biologic. Baseline levels of plasma IL-13 were differentially elevated in responders versus non-responders to mepolizumab and plasma CXCL10 levels were differentially elevated in responders to omalizumab. The ratio of IL-13/TNF-α had the best sensitivity and specificity in predicting response to mepolizumab and CXCL10/CCL17 to omalizumab, and these performed better as predictive biomarkers of response than BEC and IgE. Cytokines and chemokines associated with airway eosinophilia, allergic inflammation, or Th2 inflammation, such as IL-13 and CXCL10, may be better predictors of clinical response to mepolizumab and omalizumab, than IL-5 or IgE, the targets of mepolizumab and omalizumab.
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Affiliation(s)
- Ayobami Akenroye
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, MA, 02115, USA.
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Tanawin Nopsopon
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Jonathan J Hacker
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Tanya M Laidlaw
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, MA, 02115, USA
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6
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Huerta-Chagoya A, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Zaitlen N, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry polygenic mechanisms of type 2 diabetes. Nat Med 2024; 30:1065-1074. [PMID: 38443691 PMCID: PMC11175990 DOI: 10.1038/s41591-024-02865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Type 2 diabetes (T2D) is a multifactorial disease with substantial genetic risk, for which the underlying biological mechanisms are not fully understood. In this study, we identified multi-ancestry T2D genetic clusters by analyzing genetic data from diverse populations in 37 published T2D genome-wide association studies representing more than 1.4 million individuals. We implemented soft clustering with 650 T2D-associated genetic variants and 110 T2D-related traits, capturing known and novel T2D clusters with distinct cardiometabolic trait associations across two independent biobanks representing diverse genetic ancestral populations (African, n = 21,906; Admixed American, n = 14,410; East Asian, n =2,422; European, n = 90,093; and South Asian, n = 1,262). The 12 genetic clusters were enriched for specific single-cell regulatory regions. Several of the polygenic scores derived from the clusters differed in distribution among ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a body mass index (BMI) of 30 kg m-2 in the European subpopulation and 24.2 (22.9-25.5) kg m-2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg m-2 in the East Asian group. Thus, these multi-ancestry T2D genetic clusters encompass a broader range of biological mechanisms and provide preliminary insights to explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J Deutsch
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia Huerta-Chagoya
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H Schroeder
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melina Claussnitzer
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C Florez
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M Mercader
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Miriam S Udler
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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7
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Cho SMJ, Lee H, Koyama S, Zou RS, Schuermans A, Ganesh S, Hornsby W, Honigberg MC, Natarajan P. Cumulative Diastolic Blood Pressure Burden in Normal Systolic Blood Pressure and Cardiovascular Disease. Hypertension 2024; 81:273-281. [PMID: 38084606 PMCID: PMC10841692 DOI: 10.1161/hypertensionaha.123.22160] [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: 10/02/2023] [Accepted: 11/16/2023] [Indexed: 12/22/2023]
Abstract
BACKGROUND The clinical significance of isolated diastolic hypertension defined by the 2017 American College of Cardiology/American Heart Association blood pressure (BP) guidelines remains inconsistent. We examined whether long-term diastolic burden predicts the first major adverse cardiovascular event in participants with sustained and untreated normal systolic BP. METHODS The Mass General Brigham Biobank is a New England health care-based cohort recruited between 2010 and 2021. A total of 15 979 participants aged 18 to 64 years and without prior cardiovascular disease, antihypertensives, or high systolic BP were studied. The cumulative diastolic burden was determined as the area under the curve for diastolic BP (DBP) ≥80 mm Hg over 5 years before enrollment. Major adverse cardiovascular event was defined as a composite of first incident ischemic heart disease, stroke, heart failure, or all-cause death. RESULTS Of the 15 979 participants, mean (SD) age at enrollment was 47.6 (14.3) years, 11 950 (74.8%) were women, and the mean (SD) systolic BP and DBP were 118.0 (12.9) and 72.2 (9.3) mm Hg, respectively. Over a median (interquartile range) follow-up of 3.5 (1.8-5.4) years, 2467 (15.4%) major adverse cardiovascular events occurred. Using Cox proportional hazards regression, each SD increase in cumulative DBP was independently associated with a hazard ratio (95% CI) of 1.06 (1.02-1.10) without effect modification by sex (P=0.65), age (P=0.46), or race/ethnicity (P=0.24). In addition to traditional risk factors, cumulative DBP modestly improved the discrimination C index (95% CI) from 0.74 (0.72-0.75) to 0.75 (0.74-0.76; likelihood ratio test, P=0.037). CONCLUSIONS Among individuals with normal systolic BP, cumulative DBP may augment cardiovascular disease risk stratification beyond a single DBP measure and traditional risk factors.
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Affiliation(s)
- So Mi Jemma Cho
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hokyou Lee
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Satoshi Koyama
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Roger S. Zou
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Art Schuermans
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Flanders, Belgium
| | - Shriienidhie Ganesh
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Whitney Hornsby
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael C. Honigberg
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
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Akenroye A, Nopsopon T, Cho L, Moll M, Weiss ST. Lower myostatin and higher MUC1 levels are associated with better response to mepolizumab and omalizumab in asthma: a protein-protein interaction analyses. Respir Res 2023; 24:305. [PMID: 38057814 PMCID: PMC10698971 DOI: 10.1186/s12931-023-02620-1] [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: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023] Open
Abstract
INTRODUCTION Biomarkers are needed to inform the choice of biologic therapy in patients with asthma given the increasing number of biologics. We aimed to identify proteins associated with response to omalizumab and mepolizumab. METHODS Aptamer-based proteomic profiling (SomaScan) was used to assess 1437 proteins from 51 patients with moderate to severe asthma who received omalizumab (n = 29) or mepolizumab (n = 22). Response was defined as the change in asthma-related exacerbations in the 12 months following therapy initiation. All models were adjusted for age, sex, and pre-treatment exacerbation rate. Additionally, body mass index was included in the omalizumab model and eosinophil count in the mepolizumab model. We evaluated the association between molecular signatures and response using negative binomial regression correcting for the false discovery rate (FDR) and gene set enrichment analyses (GSEA) to identify associated pathways. RESULTS Over two-thirds of patients were female. The average age for omalizumab patients was 42 years and 57 years for mepolizumab. At baseline, the average exacerbation rate was 1.5/year for omalizumab and 2.4/year for mepolizumab. Lower levels of LOXL2 (unadjusted p: 1.93 × 10E-05, FDR-corrected: 0.028) and myostatin (unadjusted: 3.87 × 10E-05, FDR-corrected: 0.028) were associated with better response to mepolizumab. Higher levels of CD9 antigen (unadjusted: 5.30 × 10E-07, FDR-corrected: 0.0006) and MUC1 (unadjusted: 1.15 × 10E-06, FDR-corrected: 0.0006) were associated with better response to omalizumab, and LTB4R (unadjusted: 1.12 × 10E-06, FDR-corrected: 0.0006) with worse response. Protein-protein interaction network modeling showed an enrichment of the TNF- and NF-kB signaling pathways for patients treated with mepolizumab and multiple pathways involving MAPK, including the FcER1 pathway, for patients treated with omalizumab. CONCLUSIONS This study provides novel fundamental data on proteins associated with response to mepolizumab or omalizumab in severe asthma and warrants further validation as potential biomarkers for therapy selection.
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Affiliation(s)
- Ayobami Akenroye
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, 60 Fenwood Road, BostonBoston, MA, 02115, USA.
| | - Tanawin Nopsopon
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Laura Cho
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, 60 Fenwood Road, BostonBoston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, 60 Fenwood Road, BostonBoston, MA, 02115, USA
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Lee YH, Thaweethai T, Sheu YH, Feng YCA, Karlson EW, Ge T, Kraft P, Smoller JW. Impact of selection bias on polygenic risk score estimates in healthcare settings. Psychol Med 2023; 53:7435-7445. [PMID: 37226828 DOI: 10.1017/s0033291723001186] [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] [Indexed: 05/26/2023]
Abstract
BACKGROUND Hospital-based biobanks are being increasingly considered as a resource for translating polygenic risk scores (PRS) into clinical practice. However, since these biobanks originate from patient populations, there is a possibility of bias in polygenic risk estimation due to overrepresentation of patients with higher frequency of healthcare interactions. METHODS PRS for schizophrenia, bipolar disorder, and depression were calculated using summary statistics from the largest available genomic studies for a sample of 24 153 European ancestry participants in the Mass General Brigham (MGB) Biobank. To correct for selection bias, we fitted logistic regression models with inverse probability (IP) weights, which were estimated using 1839 sociodemographic, clinical, and healthcare utilization features extracted from electronic health records of 1 546 440 non-Hispanic White patients eligible to participate in the Biobank study at their first visit to the MGB-affiliated hospitals. RESULTS Case prevalence of bipolar disorder among participants in the top decile of bipolar disorder PRS was 10.0% (95% CI 8.8-11.2%) in the unweighted analysis but only 6.2% (5.0-7.5%) when selection bias was accounted for using IP weights. Similarly, case prevalence of depression among those in the top decile of depression PRS was reduced from 33.5% (31.7-35.4%) to 28.9% (25.8-31.9%) after IP weighting. CONCLUSIONS Non-random selection of participants into volunteer biobanks may induce clinically relevant selection bias that could impact implementation of PRS in research and clinical settings. As efforts to integrate PRS in medical practice expand, recognition and mitigation of these biases should be considered and may need to be optimized in a context-specific manner.
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Affiliation(s)
- Younga Heather Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tanayott Thaweethai
- Harvard Medical School, Boston, Massachusetts, USA
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yi-Han Sheu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Yen-Chen Anne Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Elizabeth W Karlson
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Immunity, and Inflammation, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
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10
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Chen Q, Dwaraka VB, Carreras-Gallo N, Mendez K, Chen Y, Begum S, Kachroo P, Prince N, Went H, Mendez T, Lin A, Turner L, Moqri M, Chu SH, Kelly RS, Weiss ST, Rattray NJ, Gladyshev VN, Karlson E, Wheelock C, Mathé EA, Dahlin A, McGeachie MJ, Smith R, Lasky-Su JA. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562114. [PMID: 37904959 PMCID: PMC10614756 DOI: 10.1101/2023.10.16.562114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that is reflected in omic profiles. Using common clinical laboratory measures in ~30,000 individuals from the MGB-Biobank, we developed a robust, predictive biological aging phenotype, EMRAge, that balances clinical biomarkers with overall mortality risk and can be broadly recapitulated across EMRs. We then applied elastic-net regression to model EMRAge with DNA-methylation (DNAm) and multiple omics, generating DNAmEMRAge and OMICmAge, respectively. Both biomarkers demonstrated strong associations with chronic diseases and mortality that outperform current biomarkers across our discovery (MGB-ABC, n=3,451) and validation (TruDiagnostic, n=12,666) cohorts. Through the use of epigenetic biomarker proxies, OMICmAge has the unique advantage of expanding the predictive search space to include epigenomic, proteomic, metabolomic, and clinical data while distilling this in a measure with DNAm alone, providing opportunities to identify clinically-relevant interconnections central to the aging process.
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Affiliation(s)
- Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aaron Lin
- TruDiagnostic, Inc., Lexington, KY USA
| | | | - Mahdi Moqri
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Su H. Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas J.W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde, Glasgow, UK
| | - Vadim N. Gladyshev
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Department of Personalized Medicine, Mass General Brigham and Harvard Medical School, Boston, MA, USA
| | - Craig Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michae J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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11
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. RESEARCH SQUARE 2023:rs.3.rs-3399145. [PMID: 37886436 PMCID: PMC10602111 DOI: 10.21203/rs.3.rs-3399145/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
We identified genetic subtypes of type 2 diabetes (T2D) by analyzing genetic data from diverse groups, including non-European populations. We implemented soft clustering with 650 T2D-associated genetic variants, capturing known and novel T2D subtypes with distinct cardiometabolic trait associations. The twelve genetic clusters were distinctively enriched for single-cell regulatory regions. Polygenic scores derived from the clusters differed in distribution between ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a BMI of 30 kg/m2 in the European subpopulation and 24.2 (22.9-25.5) kg/m2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg/m2 in the East Asian group, explaining about 75% of the difference in BMI thresholds. Thus, these multi-ancestry T2D genetic subtypes encompass a broader range of biological mechanisms and help explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J. Deutsch
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H. Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E. Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Melina Claussnitzer
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C. Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Miriam S. Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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12
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Chen Y, Mendez K, Begum S, Dean E, Chatelaine H, Braisted J, Fangal VD, Cote M, Huang M, Chu SH, Stav M, Chen Q, Prince N, Kelly R, Christopher KB, Diray-Arce J, Mathé EA, Lasky-Su J. The value of prospective metabolomic susceptibility endotypes: broad applicability for infectious diseases. EBioMedicine 2023; 96:104791. [PMID: 37734204 PMCID: PMC10518609 DOI: 10.1016/j.ebiom.2023.104791] [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: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND As new infectious diseases (ID) emerge and others continue to mutate, there remains an imminent threat, especially for vulnerable individuals. Yet no generalizable framework exists to identify the at-risk group prior to infection. Metabolomics has the advantage of capturing the existing physiologic state, unobserved via current clinical measures. Furthermore, metabolomics profiling during acute disease can be influenced by confounding factors such as indications, medical treatments, and lifestyles. METHODS We employed metabolomic profiling to cluster infection-free individuals and assessed their relationship with COVID severity and influenza incidence/recurrence. FINDINGS We identified a metabolomic susceptibility endotype that was strongly associated with both severe COVID (ORICUadmission = 6.7, p-value = 1.2 × 10-08, ORmortality = 4.7, p-value = 1.6 × 10-04) and influenza (ORincidence = 2.9; p-values = 2.2 × 10-4, βrecurrence = 1.03; p-value = 5.1 × 10-3). We observed similar severity associations when recapitulating this susceptibility endotype using metabolomics from individuals during and after acute COVID infection. We demonstrate the value of using metabolomic endotyping to identify a metabolically susceptible group for two-and potentially more-IDs that are driven by increases in specific amino acids, including microbial-related metabolites such as tryptophan, bile acids, histidine, polyamine, phenylalanine, and tyrosine metabolism, as well as carbohydrates involved in glycolysis. INTERPRETATIONS These metabolites may be identified prior to infection to enable protective measures for these individuals. FUNDING The Longitudinal EMR and Omics COVID-19 Cohort (LEOCC) and metabolomic profiling were supported by the National Heart, Lung, and Blood Institute and the Intramural Research Program of the National Center for Advancing Translational Sciences, National Institutes of Health.
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Affiliation(s)
- Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Emily Dean
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Haley Chatelaine
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - John Braisted
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Vrushali D Fangal
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Margaret Cote
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mengna Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Su H Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meryl Stav
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kenneth B Christopher
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Renal Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ewy A Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA.
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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13
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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296294. [PMID: 37808749 PMCID: PMC10557820 DOI: 10.1101/2023.09.28.23296294] [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
We identified genetic subtypes of type 2 diabetes (T2D) by analyzing genetic data from diverse groups, including non-European populations. We implemented soft clustering with 650 T2D-associated genetic variants, capturing known and novel T2D subtypes with distinct cardiometabolic trait associations. The twelve genetic clusters were distinctively enriched for single-cell regulatory regions. Polygenic scores derived from the clusters differed in distribution between ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a BMI of 30 kg/m2 in the European subpopulation and 24.2 (22.9-25.5) kg/m2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg/m2 in the East Asian group, explaining about 75% of the difference in BMI thresholds. Thus, these multi-ancestry T2D genetic subtypes encompass a broader range of biological mechanisms and help explain ancestry-associated differences in T2D risk profiles.
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Affiliation(s)
- Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron J. Deutsch
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carolyn McGrail
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah Hsu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip H. Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth E. Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lukasz Szczerbinski
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Williamson
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Melina Claussnitzer
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose C. Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Miriam S. Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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14
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Rodriguez Llorian E, Kopac N, Waliji LA, Borle K, Dragojlovic N, Elliott AM, Lynd LD. A Rapid Review on the Value of Biobanks Containing Genetic Information. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:1286-1295. [PMID: 36921900 DOI: 10.1016/j.jval.2023.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVES Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access. METHODS Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity). RESULTS Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients. CONCLUSIONS Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.
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Affiliation(s)
- Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Nicola Kopac
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Louloua Ashikhusein Waliji
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kennedy Borle
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada; Centre for Health Evaluation and Outcome Sciences (CHÉOS), St. Paul's Hospital, Vancouver, BC, Canada
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15
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Luo Q, Dwaraka VB, Chen Q, Tong H, Zhu T, Seale K, Raffaele JM, Zheng SC, Mendez TL, Chen Y, Carreras N, Begum S, Mendez K, Voisin S, Eynon N, Lasky-Su JA, Smith R, Teschendorff AE. A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes. Genome Med 2023; 15:59. [PMID: 37525279 PMCID: PMC10388560 DOI: 10.1186/s13073-023-01211-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition. METHODS Here we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes. RESULTS Our meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67-0.72), which increased to 0.83 (0.80-0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity. CONCLUSIONS This work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes.
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Affiliation(s)
- Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Varun B Dwaraka
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Joseph M Raffaele
- PhysioAge LLC, 30 Central Park South / Suite 8A, New York, NY, 10019, USA
| | - Shijie C Zheng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Tavis L Mendez
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ryan Smith
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA.
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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16
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Wolfien M, Ahmadi N, Fitzer K, Grummt S, Heine KL, Jung IC, Krefting D, Kühn A, Peng Y, Reinecke I, Scheel J, Schmidt T, Schmücker P, Schüttler C, Waltemath D, Zoch M, Sedlmayr M. Ten Topics to Get Started in Medical Informatics Research. J Med Internet Res 2023; 25:e45948. [PMID: 37486754 PMCID: PMC10407648 DOI: 10.2196/45948] [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: 01/23/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 07/25/2023] Open
Abstract
The vast and heterogeneous data being constantly generated in clinics can provide great wealth for patients and research alike. The quickly evolving field of medical informatics research has contributed numerous concepts, algorithms, and standards to facilitate this development. However, these difficult relationships, complex terminologies, and multiple implementations can present obstacles for people who want to get active in the field. With a particular focus on medical informatics research conducted in Germany, we present in our Viewpoint a set of 10 important topics to improve the overall interdisciplinary communication between different stakeholders (eg, physicians, computational experts, experimentalists, students, patient representatives). This may lower the barriers to entry and offer a starting point for collaborations at different levels. The suggested topics are briefly introduced, then general best practice guidance is given, and further resources for in-depth reading or hands-on tutorials are recommended. In addition, the topics are set to cover current aspects and open research gaps of the medical informatics domain, including data regulations and concepts; data harmonization and processing; and data evaluation, visualization, and dissemination. In addition, we give an example on how these topics can be integrated in a medical informatics curriculum for higher education. By recognizing these topics, readers will be able to (1) set clinical and research data into the context of medical informatics, understanding what is possible to achieve with data or how data should be handled in terms of data privacy and storage; (2) distinguish current interoperability standards and obtain first insights into the processes leading to effective data transfer and analysis; and (3) value the use of newly developed technical approaches to utilize the full potential of clinical data.
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Affiliation(s)
- Markus Wolfien
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Dresden, Germany
| | - Najia Ahmadi
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kai Fitzer
- Core Unit Data Integration Center, University Medicine Greifswald, Greifswald, Germany
| | - Sophia Grummt
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Kilian-Ludwig Heine
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ian-C Jung
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Dagmar Krefting
- Department of Medical Informatics, University Medical Center, Goettingen, Germany
| | - Andreas Kühn
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Yuan Peng
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ines Reinecke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Julia Scheel
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Tobias Schmidt
- Institute for Medical Informatics, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Paul Schmücker
- Institute for Medical Informatics, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Christina Schüttler
- Central Biobank Erlangen, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dagmar Waltemath
- Core Unit Data Integration Center, University Medicine Greifswald, Greifswald, Germany
- Department of Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Michele Zoch
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin Sedlmayr
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Dresden, Germany
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17
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Mezue K, Osborne MT, Abohashem S, Zureigat H, Gharios C, Grewal SS, Radfar A, Cardeiro A, Abbasi T, Choi KW, Fayad ZA, Smoller JW, Rosovsky R, Shin L, Pitman R, Tawakol A. Reduced Stress-Related Neural Network Activity Mediates the Effect of Alcohol on Cardiovascular Risk. J Am Coll Cardiol 2023; 81:2315-2325. [PMID: 37316112 PMCID: PMC10333800 DOI: 10.1016/j.jacc.2023.04.015] [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: 01/27/2023] [Revised: 03/28/2023] [Accepted: 04/10/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Chronic stress associates with major adverse cardiovascular events (MACE) via increased stress-related neural network activity (SNA). Light/moderate alcohol consumption (ACl/m) has been linked to lower MACE risk, but the mechanisms are unclear. OBJECTIVES The purpose of this study was to evaluate whether the association between ACl/m and MACE is mediated by decreased SNA. METHODS Individuals enrolled in the Mass General Brigham Biobank who completed a health behavior survey were studied. A subset underwent 18F-fluorodeoxyglucose positron emission tomography, enabling assessment of SNA. Alcohol consumption was classified as none/minimal, light/moderate, or high (<1, 1-14, or >14 drinks/week, respectively). RESULTS Of 53,064 participants (median age 60 years, 60% women), 23,920 had no/minimal alcohol consumption and 27,053 ACl/m. Over a median follow-up of 3.4 years, 1,914 experienced MACE. ACl/m (vs none/minimal) associated with lower MACE risk (HR: 0.786; 95% CI: 0.717-0.862; P < 0.0001) after adjusting for cardiovascular risk factors. In 713 participants with brain imaging, ACl/m (vs none/minimal) associated with decreased SNA (standardized beta -0.192; 95% CI: -0.338 to -0.046; P = 0.01). Lower SNA partially mediated the beneficial effect of ACl/m on MACE (log OR: -0.040; 95% CI: -0.097 to -0.003; P < 0.05). Further, ACl/m associated with larger decreases in MACE risk among individuals with (vs without) prior anxiety (HR: 0.60 [95% CI: 0.50-0.72] vs 0.78 [95% CI: 0.73-0.80]; P interaction = 0.003). CONCLUSIONS ACl/m associates with reduced MACE risk, in part, by lowering activity of a stress-related brain network known for its association with cardiovascular disease. Given alcohol's potential health detriments, new interventions with similar effects on SNA are needed.
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Affiliation(s)
- Kenechukwu Mezue
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael T Osborne
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shady Abohashem
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Hadil Zureigat
- Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charbel Gharios
- Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Simran S Grewal
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Azar Radfar
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander Cardeiro
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Taimur Abbasi
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Karmel W Choi
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA; Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Zahi A Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jordan W Smoller
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rachel Rosovsky
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lisa Shin
- Department of Psychology, Tufts University, Medford, Massachusetts, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Roger Pitman
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Ahmed Tawakol
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Cardiovascular Imaging Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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18
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Cohen RY, Kovacheva VP. A Methodology for a Scalable, Collaborative, and Resource-Efficient Platform, MERLIN, to Facilitate Healthcare AI Research. IEEE J Biomed Health Inform 2023; 27:3014-3025. [PMID: 37030761 PMCID: PMC10275625 DOI: 10.1109/jbhi.2023.3259395] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Healthcare artificial intelligence (AI) holds the potential to increase patient safety, augment efficiency and improve patient outcomes, yet research is often limited by data access, cohort curation, and tools for analysis. Collection and translation of electronic health record data, live data, and real-time high-resolution device data can be challenging and time-consuming. The development of clinically relevant AI tools requires overcoming challenges in data acquisition, scarce hospital resources, and requirements for data governance. These bottlenecks may result in resource-heavy needs and long delays in research and development of AI systems. We present a system and methodology to accelerate data acquisition, dataset development and analysis, and AI model development. We created an interactive platform that relies on a scalable microservice architecture. This system can ingest 15,000 patient records per hour, where each record represents thousands of multimodal measurements, text notes, and high-resolution data. Collectively, these records can approach a terabyte of data. The platform can further perform cohort generation and preliminary dataset analysis in 2-5 minutes. As a result, multiple users can collaborate simultaneously to iterate on datasets and models in real time. We anticipate that this approach will accelerate clinical AI model development, and, in the long run, meaningfully improve healthcare delivery.
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19
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Vannier AGL, Przybyszewski EM, Shay J, Patel SJ, Schaefer E, Goodman RP, Luther J. Psychotherapy for Alcohol Use Disorder Is Associated With Reduced Risk of Incident Alcohol-Associated Liver Disease. Clin Gastroenterol Hepatol 2023; 21:1571-1580.e7. [PMID: 35964893 PMCID: PMC9918606 DOI: 10.1016/j.cgh.2022.08.001] [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: 04/13/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Alcohol-associated liver disease (ALD) is a devastating complication of alcohol use disorder (AUD). Once it develops, ALD is exceedingly difficult to treat; it therefore is critical to identify ways to prevent ALD. By treating the causes of increased alcohol consumption, psychotherapy may offer prophylactic benefit against the development of ALD for patients with AUD. METHODS In this retrospective cohort study, we used International Classification of Diseases, 9th and 10th revision, codes to identify 9635 patients with AUD in the Mass General Brigham Biobank. The mean follow-up period from AUD diagnosis was 9.2 years. We used Cox regression models to generate hazard ratios (HR) for the development of ALD given the receipt or nonreceipt of psychotherapy, adjusting for a range of other contributors including the receipt of medication-assisted treatment. RESULTS In our cohort, 60.4% of patients were men, 83.5% of patients were white, the median age was 57.0 years, and 3544 patients (36.8%) received psychotherapy. ALD developed in 1135 patients (11.8%). In multivariable analysis, psychotherapy was associated with a reduced rate of ALD (HR, 0.59; 95% CI, 0.50-0.71; P < .001). This association held for both individual psychotherapy (HR, 0.70; 95% CI, 0.56-0.86; P < .001) and group psychotherapy (HR, 0.76; 95% CI, 0.61-0.94; P = .01). Among patients with cirrhosis, psychotherapy was associated with a lower rate of hepatic decompensation (HR, 0.68; 95% CI, 0.48-0.95; P = .03). CONCLUSIONS The receipt of psychotherapy in the setting of AUD is associated with reduced incidence and progression of ALD. Given the safety and potential benefit of psychotherapy, clinicians should consider using it to prevent the development of ALD.
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Affiliation(s)
- Augustin G L Vannier
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jessica Shay
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Suraj J Patel
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Esperance Schaefer
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Russell P Goodman
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Jay Luther
- Massachusetts General Hospital Alcohol Liver Center, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts.
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20
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Chen CY, Tian R, Ge T, Lam M, Sanchez-Andrade G, Singh T, Urpa L, Liu JZ, Sanderson M, Rowley C, Ironfield H, Fang T, Daly M, Palotie A, Tsai EA, Huang H, Hurles ME, Gerety SS, Lencz T, Runz H. The impact of rare protein coding genetic variation on adult cognitive function. Nat Genet 2023:10.1038/s41588-023-01398-8. [PMID: 37231097 DOI: 10.1038/s41588-023-01398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Compelling evidence suggests that human cognitive function is strongly influenced by genetics. Here, we conduct a large-scale exome study to examine whether rare protein-coding variants impact cognitive function in the adult population (n = 485,930). We identify eight genes (ADGRB2, KDM5B, GIGYF1, ANKRD12, SLC8A1, RC3H2, CACNA1A and BCAS3) that are associated with adult cognitive function through rare coding variants with large effects. Rare genetic architecture for cognitive function partially overlaps with that of neurodevelopmental disorders. In the case of KDM5B we show how the genetic dosage of one of these genes may determine the variability of cognitive, behavioral and molecular traits in mice and humans. We further provide evidence that rare and common variants overlap in association signals and contribute additively to cognitive function. Our study introduces the relevance of rare coding variants for cognitive function and unveils high-impact monogenic contributions to how cognitive function is distributed in the normal adult population.
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Affiliation(s)
- Chia-Yen Chen
- Research and Development, Biogen Inc, Cambridge, MA, USA.
| | - Ruoyu Tian
- Research and Development, Biogen Inc, Cambridge, MA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lea Urpa
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jimmy Z Liu
- Research and Development, Biogen Inc, Cambridge, MA, USA
- GlaxoSmithKline, Philadelphia, PA, USA
| | | | | | | | - Terry Fang
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen A Tsai
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Heiko Runz
- Research and Development, Biogen Inc, Cambridge, MA, USA.
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Cromer SJ, Lakhani CM, Mercader JM, Majarian TD, Schroeder P, Cole JB, Florez JC, Patel CJ, Manning AK, Burnett-Bowie SAM, Merino J, Udler MS. Association and Interaction of Genetics and Area-Level Socioeconomic Factors on the Prevalence of Type 2 Diabetes and Obesity. Diabetes Care 2023; 46:944-952. [PMID: 36787958 PMCID: PMC10154653 DOI: 10.2337/dc22-1954] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/17/2022] [Indexed: 02/16/2023]
Abstract
OBJECTIVE Quantify the impact of genetic and socioeconomic factors on risk of type 2 diabetes (T2D) and obesity. RESEARCH DESIGN AND METHODS Among participants in the Mass General Brigham Biobank (MGBB) and UK Biobank (UKB), we used logistic regression models to calculate cross-sectional odds of T2D and obesity using 1) polygenic risk scores for T2D and BMI and 2) area-level socioeconomic risk (educational attainment) measures. The primary analysis included 26,737 participants of European genetic ancestry in MGBB with replication in UKB (N = 223,843), as well as in participants of non-European ancestry (MGBB N = 3,468; UKB N = 7,459). RESULTS The area-level socioeconomic measure most strongly associated with both T2D and obesity was percent without a college degree, and associations with disease prevalence were independent of genetic risk (P < 0.001 for each). Moving from lowest to highest quintiles of combined genetic and socioeconomic burden more than tripled T2D (3.1% to 22.2%) and obesity (20.9% to 69.0%) prevalence. Favorable socioeconomic risk was associated with lower disease prevalence, even in those with highest genetic risk (T2D 13.0% vs. 22.2%, obesity 53.6% vs. 69.0% in lowest vs. highest socioeconomic risk quintiles). Additive effects of genetic and socioeconomic factors accounted for 13.2% and 16.7% of T2D and obesity prevalence, respectively, explained by these models. Findings were replicated in independent European and non-European ancestral populations. CONCLUSIONS Genetic and socioeconomic factors significantly interact to increase risk of T2D and obesity. Favorable area-level socioeconomic status was associated with an almost 50% lower T2D prevalence in those with high genetic risk.
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Affiliation(s)
- Sara J. Cromer
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Chirag M. Lakhani
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Josep M. Mercader
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Philip Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Joanne B. Cole
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO
| | - Jose C. Florez
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Alisa K. Manning
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Sherri-Ann M. Burnett-Bowie
- Department of Medicine, Harvard Medical School, Boston, MA
- Endocrine Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
| | - Jordi Merino
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Miriam S. Udler
- Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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22
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Cho SMJ, Koyama S, Ruan Y, Lannery K, Wong M, Ajufo E, Lee H, Khera AV, Honigberg MC, Natarajan P. Measured Blood Pressure, Genetically Predicted Blood Pressure, and Cardiovascular Disease Risk in the UK Biobank. JAMA Cardiol 2022; 7:1129-1137. [PMID: 36169945 PMCID: PMC9520434 DOI: 10.1001/jamacardio.2022.3191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022]
Abstract
Importance Hypertension remains the major cardiovascular disease risk factor globally, but variability in measured blood pressure may result in suboptimal management. Whether genetic contributors to elevated blood pressure may complementarily inform cardiovascular disease risk assessment is unknown. Objective To examine incident cardiovascular disease by blood pressure polygenic risk score independent of measured blood pressures and antihypertensive medication prescriptions. Design, Setting, and Participants The cohort study (UK Biobank) recruited UK residents aged 40 to 69 years between March 2006 and August 2010. Participants without a prior physician diagnosis of cardiovascular disease, including myocardial infarction, stroke, or heart failure, were included. Excluded were individuals with mismatch between self-reported and genotypically inferred sex, sex aneuploidy, missing genotype rates of 1% or greater, and excess genotypic heterozygosity. Data analyses were performed from September 25, 2021, to July 21, 2022. Exposures Measured blood pressure and externally derived blood pressure polygenic risk score stratified by hypertension diagnosis and management, which included normal blood pressure (<130/80 mm Hg without antihypertensives), untreated hypertension (systolic blood pressure ≥130 mm Hg or diastolic blood pressure ≥80 mm Hg without antihypertensives), and treated hypertension (current antihypertensives prescriptions). Main Outcomes and Measures Composite of first incident myocardial infarction, stroke, heart failure, or cardiovascular-related death. Results Of the 331 078 study participants included (mean [SD] age at enrollment, 56.9 [8.1] years; 178 824 female [54.0%]), 83 094 (25.1%) had normal blood pressure, 197 597 (59.7%) had untreated hypertension, and 50 387 (15.2%) had treated hypertension. Over a median (IQR) follow-up of 11.1 (10.4-11.8) years, the primary outcome occurred in 15 293 participants. Among those with normal blood pressure, untreated hypertension, and treated hypertension, each SD increase in measured systolic blood pressure was associated with hazard ratios of 1.08 (95% CI, 0.93-1.25), 1.20 (95% CI, 1.16-1.23), and 1.16 (95% CI, 1.11-1.20), respectively, for the primary outcome. Among these same categories, each SD increase in genetically predicted systolic blood pressure was associated with increased hazard ratios of 1.13 (95% CI, 1.05-1.20), 1.04 (95% CI, 1.01-1.07), and 1.06 (95% CI, 1.02-1.10), respectively, for the primary outcome independent of measured blood pressures and other covariates. Findings were similar for measured and genetically predicted diastolic blood pressure. Conclusions and Relevance Blood pressure polygenic risk score may augment identification of individuals at heightened cardiovascular risk, including those with both normal blood pressure and hypertension. Whether it may also guide antihypertensive initiation or intensification requires further study.
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Affiliation(s)
- So Mi Jemma Cho
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Korea
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Seoul, Korea
| | - Satoshi Koyama
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Yunfeng Ruan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Kim Lannery
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Megan Wong
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Ezimamaka Ajufo
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Hokyou Lee
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Amit V. Khera
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Massachusetts General Hospital, Boston
- Verve Therapeutics, Cambridge, Massachusetts
| | - Michael C. Honigberg
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Massachusetts General Hospital, Boston
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Massachusetts General Hospital, Boston
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23
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Murphy SN, Visweswaran S, Becich MJ, Campion TR, Knosp BM, Melton-Meaux GB, Lenert LA. Research data warehouse best practices: catalyzing national data sharing through informatics innovation. J Am Med Inform Assoc 2022; 29:581-584. [PMID: 35289371 PMCID: PMC8922176 DOI: 10.1093/jamia/ocac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shawn N Murphy
- Research Information Science and Computing, Mass General Brigham, Somerville, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas R Campion
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, New York, USA
| | - Boyd M Knosp
- Roy J. and Lucille A. Carver College of Medicine and the Institute for Clinical & Translational Science, University of Iowa, Iowa City, Iowa, USA
| | - Genevieve B Melton-Meaux
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Health Informatics (IHI), University of Minnesota, Minneapolis, Minnesota, USA
| | - Leslie A Lenert
- Biomedical Informatics Center (BMIC), Medical University of South Carolina, Charleston, South Carolina, USA
- Health Sciences South Carolina, Columbia, South Carolina, USA
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