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Iman MN, Haslam DE, Liang L, Guo K, Joshipura K, Pérez CM, Clish C, Tucker KL, Manson JE, Bhupathiraju SN, Fukusaki E, Lasky-Su J, Putri SP. Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food. Food Chem 2024; 446:138744. [PMID: 38432131 DOI: 10.1016/j.foodchem.2024.138744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
This study introduces a multidisciplinary approach to investigate bioactive food metabolites often overlooked due to their low concentrations. We integrated an in-house food metabolite library (n = 494), a human metabolite library (n = 891) from epidemiological studies, and metabolite pharmacological databases to screen for food metabolites with potential bioactivity. We identified six potential metabolites, including meglutol (3-hydroxy-3-methylglutarate), an understudied low-density lipoprotein (LDL)-lowering compound. We further focused on meglutol as a case study to showcase the range of characterizations achievable with this approach. Green pea tempe was identified to contain the highest meglutol concentration (21.8 ± 4.6 mg/100 g). Furthermore, we identified a significant cross-sectional association between plasma meglutol (per 1-standard deviation) and lower LDL cholesterol in two Hispanic adult cohorts (n = 1,628) (β [standard error]: -5.5 (1.6) mg/dl, P = 0.0005). These findings highlight how multidisciplinary metabolomics can serve as a systematic tool for discovering and enhancing bioactive metabolites in food, such as meglutol, with potential applications in personalized dietary approaches for disease prevention.
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Affiliation(s)
- Marvin N Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - Danielle E Haslam
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kai Guo
- Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Kaumudi Joshipura
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Cynthia M Pérez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Clary Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, USA
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shilpa N Bhupathiraju
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan.
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2
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Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ. Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria. Cell 2024; 187:1834-1852.e19. [PMID: 38569543 DOI: 10.1016/j.cell.2024.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.
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Affiliation(s)
- Chenhao Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tina Lebar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Shijie Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Lockart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrea Dame
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qi Yan Ang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachele Invernizzi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Tinoco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Ramachandran S Vasan
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA; Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; University of Texas School of Public Health, San Antonio, TX, USA
| | - Emily Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stanley Y Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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3
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Perry AS, Piaggi P, Huang S, Nayor M, Freedman J, North K, Below J, Clish C, Murthy VL, Krakoff J, Shah RV. Human metabolic chambers reveal a coordinated metabolic-physiologic response to nutrition. medRxiv 2024:2024.04.08.24305087. [PMID: 38645000 PMCID: PMC11030300 DOI: 10.1101/2024.04.08.24305087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The emerging field of precision nutrition is based on the notion that inter-individual responses across diets of different calorie-macronutrient content may contribute to inter-individual differences in metabolism, adiposity, and weight gain. Free-living diet studies have been traditionally challenged by difficulties in controlling adherence to prescribed calories and macronutrient content and rarely allow a period of metabolic stability prior to metabolic measures (to minimize influences of weight changes). In this context, key physiologic measures central to precision nutrition responses may be most precisely quantified via whole room indirect calorimetry over 24-h, in which precise control of activity and nutrition can be achieved. In addition, these studies represent unique "N of 1" human crossover metabolic-physiologic experiments during which specific molecular pathways central to nutrient metabolism may be discerned. Here, we quantified 263 circulating metabolites during a ≈40-day inpatient admission in which up to 94 participants underwent seven monitored 24-h nutritional interventions of differing macronutrient composition in a whole-room indirect calorimeter to capture precision metabolic responses. Broadly, we observed heterogenous responses in metabolites across dietary chambers, with the exception of carnitines which tracked with 24-h respiratory quotient. We identified excursions in shared metabolic species (e.g., carnitines, glycerophospholipids, amino acids) that mapped onto gold-standard calorimetric measures of substrate oxidation preference and lipid availability. These findings support a coordinated metabolic-physiologic response to nutrition, highlighting the relevance of these controlled settings to uncover biological pathways of energy utilization during precision nutrition studies.
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Mendez KM, Begum S, Tiwari A, Sharma R, Chen Q, Kelly RS, Prince N, Huang M, Kachroo P, Chu SH, Chen Y, Lee-Sarwar K, Broadhurst DI, Reinke SN, Gerszten R, Clish C, Avila L, Celedón JC, Wheelock CE, Weiss ST, McGeachie M, Lasky-Su JA. Metabolite signatures associated with microRNA miR-143-3p serve as drivers of poor lung function trajectories in childhood asthma. EBioMedicine 2024; 102:105025. [PMID: 38458111 PMCID: PMC10937568 DOI: 10.1016/j.ebiom.2024.105025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Lung function trajectories (LFTs) have been shown to be an important measure of long-term health in asthma. While there is a growing body of metabolomic studies on asthma status and other phenotypes, there are no prospective studies of the relationship between metabolomics and LFTs or their genomic determinants. METHODS We utilized ordinal logistic regression to identify plasma metabolite principal components associated with four previously-published LFTs in children from the Childhood Asthma Management Program (CAMP) (n = 660). The top significant metabolite principal component (PCLF) was evaluated in an independent cross-sectional child cohort, the Genetic Epidemiology of Asthma in Costa Rica Study (GACRS) (n = 1151) and evaluated for association with spirometric measures. Using meta-analysis of CAMP and GACRS, we identified associations between PCLF and microRNA, and SNPs in their target genes. Statistical significance was determined using an false discovery rate-adjusted Q-value. FINDINGS The top metabolite principal component, PCLF, was significantly associated with better LFTs after multiple-testing correction (Q-value = 0.03). PCLF is composed of the urea cycle, caffeine, corticosteroid, carnitine, and potential microbial (secondary bile acid, tryptophan, linoleate, histidine metabolism) metabolites. Higher levels of PCLF were also associated with increases in lung function measures and decreased circulating neutrophil percentage in both CAMP and GACRS. PCLF was also significantly associated with microRNA miR-143-3p, and SNPs in three miR-143-3p target genes; CCZ1 (P-value = 2.6 × 10-5), SLC8A1 (P-value = 3.9 × 10-5); and TENM4 (P-value = 4.9 × 10-5). INTERPRETATION This study reveals associations between metabolites, miR-143-3p and LFTs in children with asthma, offering insights into asthma physiology and possible interventions to enhance lung function and long-term health. FUNDING Molecular data for CAMP and GACRS via the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung, and Blood Institute (NHLBI).
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Affiliation(s)
- Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Centre for Integrative Metabolomics & Computational Biology, School of Science, Edith Cowan University, Perth, Australia
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anshul Tiwari
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Rinku Sharma
- 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
| | - Rachel S Kelly
- 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
| | - Mengna Huang
- 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
| | - Su H Chu
- 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
| | - Kathleen Lee-Sarwar
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Allergy and Clinical Immunology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David I Broadhurst
- Centre for Integrative Metabolomics & Computational Biology, School of Science, Edith Cowan University, Perth, Australia
| | - Stacey N Reinke
- Centre for Integrative Metabolomics & Computational Biology, School of Science, Edith Cowan University, Perth, Australia
| | - Robert Gerszten
- Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Lydiana Avila
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, 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 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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5
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Shorer EF, Rubin LH, French AL, Weber KM, Daubert E, Yohannes T, Morack R, Clish C, Bullock K, Gustafson D, Sharma A, Rogando AC, Qi Q, Burgess HJ, Dastgheyb RM. Tryptophan-kynurenine metabolic pathway and daytime dysfunction in women with HIV. J Neurovirol 2024:10.1007/s13365-024-01195-x. [PMID: 38472641 DOI: 10.1007/s13365-024-01195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Sleep disturbances are prevalent in women with HIV (WWH). Tryptophan-kynurenine (T-K) pathway metabolites are associated with alterations in actigraphy derived sleep measures in WWH, although may not always correlate with functional impairment. We investigated the relationship between T-K pathway metabolites and self-reported daytime dysfunction in WWH and women without HIV (WWoH). 141 WWH on stable antiretroviral therapy and 140 demographically similar WWoH enrolled in the IDOze Study had targeted plasma T-K metabolites measured using liquid chromatography-tandem mass spectrometry. We utilized the daytime dysfunction component of the Pittsburgh Sleep Quality Index (PSQI) to assess functional impairment across HIV-serostatus. Lower levels of 5-hydroxytryptophan and serotonin were associated with greater daytime dysfunction in all women. In WWH, daytime dysfunction was associated with increased kynurenic acid (R = 0.26, p < 0.05), and kynurenic acid-tryptophan (KA-T) ratio (R = 0.28, p < 0.01). WWH with daytime dysfunction had a 0.7 log fold increase in kynurenic acid compared to WWH without daytime dysfunction. Kynurenic acid levels and the KA-T ratio were associated with daytime dysfunction in WWH but not in WWoH. Longitudinal studies are needed to establish a causal relationship and directionality between T-K metabolic changes and sleep impairment in WWH.
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Affiliation(s)
- Eran Frank Shorer
- Department of Neurology, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Room 490, Carnegie Building, 600 North Wolfe Street, Baltimore, MD, USA.
| | - Leah H Rubin
- Department of Neurology, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Room 490, Carnegie Building, 600 North Wolfe Street, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County, Chicago, IL, USA
| | | | | | | | | | - Clary Clish
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kevin Bullock
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrea C Rogando
- Hektoen Institute of Medicine, Chicago, IL, USA
- College of Science and Health at Charles R. Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Helen J Burgess
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Raha M Dastgheyb
- Department of Neurology, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Room 490, Carnegie Building, 600 North Wolfe Street, Baltimore, MD, USA
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6
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García-Gavilán JF, Atzeni A, Babio N, Liang L, Belzer C, Vioque J, Corella D, Fitó M, Vidal J, Moreno-Indias I, Torres-Collado L, Coltell O, Toledo E, Clish C, Hernando J, Yun H, Hernández-Cacho A, Jeanfavre S, Dennis C, Gómez-Pérez AM, Martínez MA, Ruiz-Canela M, Tinahones FJ, Hu FB, Salas-Salvadó J. Effect of 1-year lifestyle intervention with energy-reduced Mediterranean diet and physical activity promotion on the gut metabolome and microbiota: a randomized clinical trial. Am J Clin Nutr 2024:S0002-9165(24)00167-9. [PMID: 38428742 DOI: 10.1016/j.ajcnut.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The health benefits of the Mediterranean diet (MedDiet) have been linked to the presence of beneficial gut microbes and related metabolites. However, its impact on the fecal metabolome remains poorly understood. OBJECTIVES Our goal was to investigate the weight-loss effects of a 1-y lifestyle intervention based on an energy-reduced MedDiet coupled with physical activity (intervention group), compared with an ad libitum MedDiet (control group), on fecal metabolites, fecal microbiota, and their potential association with cardiovascular disease risk factors. METHODS A total of 400 participants (200 from each study group), aged 55-75 y, and at high cardiovascular disease risk, were included. Dietary and lifestyle information, anthropometric measurements, blood biochemical parameters, and stool samples were collected at baseline and after 1 y of follow-up. Liquid chromatography-tandem mass spectrometry was used to profile endogenous fecal metabolites, and 16S amplicon sequencing was employed to profile the fecal microbiota. RESULTS Compared with the control group, the intervention group exhibited greater weight loss and improvement in various cardiovascular disease risk factors. We identified intervention effects on 4 stool metabolites and subnetworks primarily composed of bile acids, ceramides, and sphingosines, fatty acids, carnitines, nucleotides, and metabolites of purine and the Krebs cycle. Some of these were associated with changes in several cardiovascular disease risk factors. In addition, we observed a reduction in the abundance of the genera Eubacterium hallii group and Dorea, and an increase in alpha diversity in the intervention group after 1 y of follow-up. Changes in the intervention-related microbiota profiles were also associated with alterations in different fecal metabolite subnetworks and some cardiovascular disease risk factors. CONCLUSIONS An intervention based on an energy-reduced MedDiet and physical activity promotion, compared with an ad libitum MedDiet, was associated with improvements in cardiometabolic risk factors, potentially through modulation of the fecal microbiota and metabolome. This trial was registered at https://www.isrctn.com/ as ISRCTN89898870 (https://doi.org/10.1186/ISRCTN89898870).
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Affiliation(s)
- Jesús F García-Gavilán
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Alessandro Atzeni
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.
| | - Nancy Babio
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Jesús Vioque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigación Sanitaria y Biomédica de Alicante, Universidad Miguel Hernández (ISABIAL-UMH), Alicante, Spain
| | - Dolores Corella
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Montserrat Fitó
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Josep Vidal
- CIBER Diabetes y Enfermedades Metabólicas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain; Department of Endocrinology, Institut d'Investigacions Biomédiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Isabel Moreno-Indias
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Laura Torres-Collado
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigación Sanitaria y Biomédica de Alicante, Universidad Miguel Hernández (ISABIAL-UMH), Alicante, Spain
| | - Oscar Coltell
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Computer Languages and Systems, Jaume I University, Castellón, Spain
| | - Estefanía Toledo
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; Epidemiología y Salud Pública, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Clary Clish
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Boston, MA, United States
| | - Javier Hernando
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Huan Yun
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Adrián Hernández-Cacho
- Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Sarah Jeanfavre
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Boston, MA, United States
| | - Courtney Dennis
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Boston, MA, United States
| | - Ana M Gómez-Pérez
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Maria Angeles Martínez
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Miguel Ruiz-Canela
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; Epidemiología y Salud Pública, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Francisco J Tinahones
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Frank B Hu
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States; Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Jordi Salas-Salvadó
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain; Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició, Desenvolupament i Salut Mental (ANUT-DSM), Universitat Rovira i Virgili, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.
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7
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Lee DH, Jin Q, Shi N, Wang F, Bever AM, Liang L, Hu FB, Song M, Zeleznik OA, Zhang X, Joshi A, Wu K, Jeon JY, Meyerhardt JA, Chan AT, Eliassen AH, Clish C, Clinton SK, Giovannucci EL, Li J, Tabung FK. The metabolic potential of inflammatory and insulinaemic dietary patterns and risk of type 2 diabetes. Diabetologia 2024; 67:88-101. [PMID: 37816982 DOI: 10.1007/s00125-023-06021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023]
Abstract
AIMS/HYPOTHESIS Diets with higher inflammatory and insulinaemic potential have been associated with an increased risk of type 2 diabetes. However, it remains unknown whether plasma metabolomic profiles related to proinflammatory/hyperinsulinaemic diets and to inflammatory/insulin biomarkers are associated with type 2 diabetes risk. METHODS We analysed 6840 participants from the Nurses' Health Study and Health Professionals Follow-up Study to identify the plasma metabolome related to empirical dietary inflammatory pattern (EDIP), empirical dietary index for hyperinsulinemia (EDIH), four circulating inflammatory biomarkers and C-peptide. Dietary intakes were assessed using validated food frequency questionnaires. Plasma metabolomic profiling was conducted by LC-MS/MS. Metabolomic signatures were derived using elastic net regression. Multivariable Cox regression was used to examine associations of the metabolomic profiles with type 2 diabetes risk. RESULTS We identified 27 metabolites commonly associated with both EDIP and inflammatory biomarker z score and 21 commonly associated with both EDIH and C-peptide. Higher metabolomic dietary inflammatory potential (MDIP), reflecting higher metabolic potential of both an inflammatory dietary pattern and circulating inflammatory biomarkers, was associated with higher type 2 diabetes risk. The HR comparing highest vs lowest quartiles of MDIP was 3.26 (95% CI 2.39, 4.44). We observed a strong positive association with type 2 diabetes risk for the metabolomic signature associated with EDIP-only (HR 3.75; 95% CI 2.71, 5.17) or inflammatory biomarkers-only (HR 4.07; 95% CI 2.91, 5.69). In addition, higher metabolomic dietary index for hyperinsulinaemia (MDIH), reflecting higher metabolic potential of both an insulinaemic dietary pattern and circulating C-peptide, was associated with greater type 2 diabetes risk (HR 3.00; 95% CI 2.22, 4.06); further associations with type 2 diabetes were HR 2.79 (95% CI 2.07, 3.76) for EDIH-only signature and HR 3.89 (95% CI 2.82, 5.35) for C-peptide-only signature. The diet scores were significantly associated with risk, although adjustment for the corresponding metabolomic signature scores attenuated the associations with type 2 diabetes, these remained significant. CONCLUSIONS/INTERPRETATION The metabolomic signatures reflecting proinflammatory or hyperinsulinaemic diets and related biomarkers were positively associated with type 2 diabetes risk, supporting that these dietary patterns may influence type 2 diabetes risk via the regulation of metabolism.
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Affiliation(s)
- Dong Hoon Lee
- Department of Sport Industry Studies, Yonsei University, Seoul, Republic of Korea
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qi Jin
- Department of Exercise and Nutrition Sciences, Moyes College of Education, Weber State University, Ogden, UT, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA
| | - Ni Shi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Fenglei Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alaina M Bever
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amit Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Justin Y Jeon
- Department of Sport Industry Studies, Yonsei University, Seoul, Republic of Korea
- Cancer Prevention Center, Yonsei Cancer Center, Seoul, Republic of Korea
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Andrew T Chan
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - A Heather Eliassen
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven K Clinton
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Edward L Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fred K Tabung
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA.
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, OH, USA.
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8
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García-Gavilán JF, Babio N, Toledo E, Semnani-Azad Z, Razquin C, Dennis C, Deik A, Corella D, Estruch R, Ros E, Fitó M, Arós F, Fiol M, Lapetra J, Lamuela-Raventos R, Clish C, Ruiz-Canela M, Martínez-González MÁ, Hu F, Salas-Salvadó J, Guasch-Ferré M. Olive oil consumption, plasma metabolites, and risk of type 2 diabetes and cardiovascular disease. Cardiovasc Diabetol 2023; 22:340. [PMID: 38093289 PMCID: PMC10720204 DOI: 10.1186/s12933-023-02066-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Olive oil consumption has been inversely associated with the risk of type 2 diabetes (T2D) and cardiovascular disease (CVD). However, the impact of olive oil consumption on plasma metabolites remains poorly understood. This study aims to identify plasma metabolites related to total and specific types of olive oil consumption, and to assess the prospective associations of the identified multi-metabolite profiles with the risk of T2D and CVD. METHODS The discovery population included 1837 participants at high cardiovascular risk from the PREvención con DIeta MEDiterránea (PREDIMED) trial with available metabolomics data at baseline. Olive oil consumption was determined through food-frequency questionnaires (FFQ) and adjusted for total energy. A total of 1522 participants also had available metabolomics data at year 1 and were used as the internal validation sample. Plasma metabolomics analyses were performed using LC-MS. Cross-sectional associations between 385 known candidate metabolites and olive oil consumption were assessed using elastic net regression analysis. A 10-cross-validation (CV) procedure was used, and Pearson correlation coefficients were assessed between metabolite-weighted models and FFQ-derived olive oil consumption in each pair of training-validation data sets within the discovery sample. We further estimated the prospective associations of the identified plasma multi-metabolite profile with incident T2D and CVD using multivariable Cox regression models. RESULTS We identified a metabolomic signature for the consumption of total olive oil (with 74 metabolites), VOO (with 78 metabolites), and COO (with 17 metabolites), including several lipids, acylcarnitines, and amino acids. 10-CV Pearson correlation coefficients between total olive oil consumption derived from FFQs and the multi-metabolite profile were 0.40 (95% CI 0.37, 0.44) and 0.27 (95% CI 0.22, 0.31) for the discovery and validation sample, respectively. We identified several overlapping and distinct metabolites according to the type of olive oil consumed. The baseline metabolite profiles of total and extra virgin olive oil were inversely associated with CVD incidence (HR per 1SD: 0.79; 95% CI 0.67, 0.92 for total olive oil and 0.70; 0.59, 0.83 for extra virgin olive oil) after adjustment for confounders. However, no significant associations were observed between these metabolite profiles and T2D incidence. CONCLUSIONS This study reveals a panel of plasma metabolites linked to the consumption of total and specific types of olive oil. The metabolite profiles of total olive oil consumption and extra virgin olive oil were associated with a decreased risk of incident CVD in a high cardiovascular-risk Mediterranean population, though no associations were observed with T2D incidence. TRIAL REGISTRATION The PREDIMED trial was registered at ISRCTN ( http://www.isrctn.com/ , ISRCTN35739639).
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Affiliation(s)
- Jesús F García-Gavilán
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain.
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain.
| | - Nancy Babio
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Estefanía Toledo
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of Navarra, IdiSNA, Pamplona, Spain
| | - Zhila Semnani-Azad
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Cristina Razquin
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of Navarra, IdiSNA, Pamplona, Spain
| | | | - Amy Deik
- The Broad Institute of Harvard and MIT, Boston, MA, USA
| | - Dolores Corella
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Ramón Estruch
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Internal Medicine, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
- Institut de Nutrició I Seguretat Alimentària (INSA-UB), Universitat de Barcelona, Barcelona, Spain
| | - Emilio Ros
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition, Lipid Clinic, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Montserrat Fitó
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular and Nutrition Research Group, Institut de Recerca Hospital del Mar, Barcelona, Spain
| | - Fernando Arós
- Bioaraba Health Research Institute, Osakidetza Basque Health Service, Araba University Hospital, University of the Basque Country UPV/EHU, 01009, Vitoria-Gasteiz, Spain
| | - Miquel Fiol
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Plataforma de Ensayos Clínicos, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120, Palma, Spain
| | - José Lapetra
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Family Medicine, Research Unit, Distrito Sanitario Atención Primaria Sevilla, Seville, Spain
| | - Rosa Lamuela-Raventos
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Institut de Nutrició I Seguretat Alimentària (INSA-UB), Universitat de Barcelona, Barcelona, Spain
- Polyphenol Research Group, Departament de Nutrició, Ciències de L'Alimentació I Gastronomia, Universitat de Barcelon (UB), Av. de Joan XXII, 27-31, 08028, Barcelona, Spain
| | - Clary Clish
- The Broad Institute of Harvard and MIT, Boston, MA, USA
| | - Miguel Ruiz-Canela
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of Navarra, IdiSNA, Pamplona, Spain
| | - Miguel Ángel Martínez-González
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of Navarra, IdiSNA, Pamplona, Spain
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Frank Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jordi Salas-Salvadó
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentaciò, Nutrició Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Øster Farimagsgade 5, 1014, Copenhagen, Denmark.
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9
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Yin Z, Rosenzweig N, Kleemann KL, Zhang X, Brandão W, Margeta MA, Schroeder C, Sivanathan KN, Silveira S, Gauthier C, Mallah D, Pitts KM, Durao A, Herron S, Shorey H, Cheng Y, Barry JL, Krishnan RK, Wakelin S, Rhee J, Yung A, Aronchik M, Wang C, Jain N, Bao X, Gerrits E, Brouwer N, Deik A, Tenen DG, Ikezu T, Santander NG, McKinsey GL, Baufeld C, Sheppard D, Krasemann S, Nowarski R, Eggen BJL, Clish C, Tanzi RE, Madore C, Arnold TD, Holtzman DM, Butovsky O. APOE4 impairs the microglial response in Alzheimer's disease by inducing TGFβ-mediated checkpoints. Nat Immunol 2023; 24:1839-1853. [PMID: 37749326 PMCID: PMC10863749 DOI: 10.1038/s41590-023-01627-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
The APOE4 allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD). The contribution of microglial APOE4 to AD pathogenesis is unknown, although APOE has the most enriched gene expression in neurodegenerative microglia (MGnD). Here, we show in mice and humans a negative role of microglial APOE4 in the induction of the MGnD response to neurodegeneration. Deletion of microglial APOE4 restores the MGnD phenotype associated with neuroprotection in P301S tau transgenic mice and decreases pathology in APP/PS1 mice. MGnD-astrocyte cross-talk associated with β-amyloid (Aβ) plaque encapsulation and clearance are mediated via LGALS3 signaling following microglial APOE4 deletion. In the brains of AD donors carrying the APOE4 allele, we found a sex-dependent reciprocal induction of AD risk factors associated with suppression of MGnD genes in females, including LGALS3, compared to individuals homozygous for the APOE3 allele. Mechanistically, APOE4-mediated induction of ITGB8-transforming growth factor-β (TGFβ) signaling impairs the MGnD response via upregulation of microglial homeostatic checkpoints, including Inpp5d, in mice. Deletion of Inpp5d in microglia restores MGnD-astrocyte cross-talk and facilitates plaque clearance in APP/PS1 mice. We identify the microglial APOE4-ITGB8-TGFβ pathway as a negative regulator of microglial response to AD pathology, and restoring the MGnD phenotype via blocking ITGB8-TGFβ signaling provides a promising therapeutic intervention for AD.
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Affiliation(s)
- Zhuoran Yin
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Neta Rosenzweig
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kilian L Kleemann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- School of Computing, University of Portsmouth, Portsmouth, UK
| | - Xiaoming Zhang
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wesley Brandão
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Milica A Margeta
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Caitlin Schroeder
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kisha N Sivanathan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sebastian Silveira
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian Gauthier
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dania Mallah
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristen M Pitts
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ana Durao
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shawn Herron
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Hannah Shorey
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yiran Cheng
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jen-Li Barry
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sam Wakelin
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jared Rhee
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anthony Yung
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Aronchik
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chao Wang
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing, China
| | - Nimansha Jain
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Bao
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Emma Gerrits
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nieske Brouwer
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Tsuneya Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nicolas G Santander
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Instituto de Ciencias de la Salud, Universidad de O´Higgins, Rancagua, Chile
| | - Gabriel L McKinsey
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Baufeld
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dean Sheppard
- Department of Medicine, Cardiovascular Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Susanne Krasemann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany
| | - Roni Nowarski
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Charlotte Madore
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratoire NutriNeuro, UMR1286, INRAE, Bordeaux INP, University of Bordeaux, Bordeaux, France
| | - Thomas D Arnold
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Oleg Butovsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Li T, Ferraro N, Strober BJ, Aguet F, Kasela S, Arvanitis M, Ni B, Wiel L, Hershberg E, Ardlie K, Arking DE, Beer RL, Brody J, Blackwell TW, Clish C, Gabriel S, Gerszten R, Guo X, Gupta N, Johnson WC, Lappalainen T, Lin HJ, Liu Y, Nickerson DA, Papanicolaou G, Pritchard JK, Qasba P, Shojaie A, Smith J, Sotoodehnia N, Taylor KD, Tracy RP, Van Den Berg D, Wheeler MT, Rich SS, Rotter JI, Battle A, Montgomery SB. The functional impact of rare variation across the regulatory cascade. Cell Genom 2023; 3:100401. [PMID: 37868038 PMCID: PMC10589633 DOI: 10.1016/j.xgen.2023.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/08/2023] [Accepted: 08/10/2023] [Indexed: 10/24/2023]
Abstract
Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.
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Affiliation(s)
- Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Ferraro
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | - Benjamin J. Strober
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Harvard School of Public Health, Epidemiology Department, Boston, MA, USA
| | | | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Marios Arvanitis
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Laurens Wiel
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca L. Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Robert Gerszten
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Henry J. Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - George Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA
| | - Josh Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P. Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew T. Wheeler
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Malone Center for Engineering of Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
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11
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Wang F, Tessier AJ, Liang L, Wittenbecher C, Haslam DE, Fernández-Duval G, Heather Eliassen A, Rexrode KM, Tobias DK, Li J, Zeleznik O, Grodstein F, Martínez-González MA, Salas-Salvadó J, Clish C, Lee KH, Sun Q, Stampfer MJ, Hu FB, Guasch-Ferré M. Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals. Nat Commun 2023; 14:5744. [PMID: 37717037 PMCID: PMC10505179 DOI: 10.1038/s41467-023-41515-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
Experimental studies reported biochemical actions underpinning aging processes and mortality, but the relevant metabolic alterations in humans are not well understood. Here we examine the associations of 243 plasma metabolites with mortality and longevity (attaining age 85 years) in 11,634 US (median follow-up of 22.6 years, with 4288 deaths) and 1878 Spanish participants (median follow-up of 14.5 years, with 525 deaths). We find that, higher levels of N2,N2-dimethylguanosine, pseudouridine, N4-acetylcytidine, 4-acetamidobutanoic acid, N1-acetylspermidine, and lipids with fewer double bonds are associated with increased risk of all-cause mortality and reduced odds of longevity; whereas L-serine and lipids with more double bonds are associated with lower mortality risk and a higher likelihood of longevity. We further develop a multi-metabolite profile score that is associated with higher mortality risk. Our findings suggest that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality. The underlying mechanisms remain to be determined.
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Affiliation(s)
- Fenglei Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne-Julie Tessier
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clemens Wittenbecher
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- SciLifeLab, Division of Food Science and Nutrition, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Danielle E Haslam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonzalo Fernández-Duval
- Department of Preventive Medicine and Public Health, Navarra Health Research Institute (IDISNA), University of Navarra, Pamplona, Spain
| | - A Heather Eliassen
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kathryn M Rexrode
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Women's Health, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Deirdre K Tobias
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Oana Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Miguel A Martínez-González
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Preventive Medicine and Public Health, Navarra Health Research Institute (IDISNA), University of Navarra, Pamplona, Spain
- Consorcio CIBER, Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Jordi Salas-Salvadó
- Consorcio CIBER, Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Clary Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyu Ha Lee
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qi Sun
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meir J Stampfer
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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12
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Yazdani A, Mendez-Giraldez R, Yazdani A, Schaid D, Won Kong S, Hadi M, Samiei A, Wittenbecher C, Lasky-Su J, Clish C, Marotta F, Kosorok M, Mora S, Muehlschlegel J, Chasman D, Larson M, Elsea S. Broadcasters, receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors. Res Sq 2023:rs.3.rs-3246406. [PMID: 37645766 PMCID: PMC10462252 DOI: 10.21203/rs.3.rs-3246406/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
In a prospective study with records of heart failure (HF) incidence, we present metabolite profiling data from individuals without HF at baseline. We uncovered the interconnectivity of metabolites using data-driven and causal networks augmented with polygenic factors. Exploring the networks, we identified metabolite broadcasters, receivers, mediators, and subnetworks corresponding to functional classes of metabolites, and provided insights into the link between metabolomic architecture and regulation in health. We incorporated the network structure into the identification of metabolites associated with HF to control the effect of confounding metabolites. We identified metabolites associated with higher or lower risk of HF incidence, the associations that were not confounded by the other metabolites, such as glycine, ureidopropionic and glycocholic acids, and LPC 18:2. We revealed the underlying relationships of the findings. For example, asparagine directly influenced glycine, and both were inversely associated with HF. These two metabolites were influenced by polygenic factors and only essential amino acids which are not synthesized in the human body and come directly from the diet. Metabolites may play a critical role in linking genetic background and lifestyle factors to HF progression. Revealing the underlying connectivity of metabolites associated with HF strengthens the findings and facilitates a mechanistic understanding of HF progression.
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Affiliation(s)
| | | | - Akram Yazdani
- Division of Clinical and Translational Sciences, Department of Internal Medicine, at The University of Texas Health Science Center at Houston, McGovern Medical School
| | - Daniel Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902
| | | | - Mohamad Hadi
- School of Mathematics, University of science and technology of Iran, Tehran
| | - Ahmad Samiei
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA
| | | | | | | | | | | | - Samia Mora
- Brigham and Women's Hospital and Harvard Medical School
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13
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Brown BC, Wang C, Kasela S, Aguet F, Nachun DC, Taylor KD, Tracy RP, Durda P, Liu Y, Johnson WC, Van Den Berg D, Gupta N, Gabriel S, Smith JD, Gerzsten R, Clish C, Wong Q, Papanicolau G, Blackwell TW, Rotter JI, Rich SS, Barr RG, Ardlie KG, Knowles DA, Lappalainen T. Multiset correlation and factor analysis enables exploration of multi-omics data. Cell Genom 2023; 3:100359. [PMID: 37601969 PMCID: PMC10435377 DOI: 10.1016/j.xgen.2023.100359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 08/22/2023]
Abstract
Multi-omics datasets are becoming more common, necessitating better integration methods to realize their revolutionary potential. Here, we introduce multi-set correlation and factor analysis (MCFA), an unsupervised integration method tailored to the unique challenges of high-dimensional genomics data that enables fast inference of shared and private factors. We used MCFA to integrate methylation markers, protein expression, RNA expression, and metabolite levels in 614 diverse samples from the Trans-Omics for Precision Medicine/Multi-Ethnic Study of Atherosclerosis multi-omics pilot. Samples cluster strongly by ancestry in the shared space, even in the absence of genetic information, while private spaces frequently capture dataset-specific technical variation. Finally, we integrated genetic data by conducting a genome-wide association study (GWAS) of our inferred factors, observing that several factors are enriched for GWAS hits and trans-expression quantitative trait loci. Two of these factors appear to be related to metabolic disease. Our study provides a foundation and framework for further integrative analysis of ever larger multi-modal genomic datasets.
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Affiliation(s)
- Brielin C. Brown
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | - Collin Wang
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - François Aguet
- Illumina Incorporated, San Francisco, CA, USA
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Department of Clinical Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Namrata Gupta
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Stacy Gabriel
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Joshua D. Smith
- Northwest Genomics Center, University of Washington, Seattle, WA, USA
| | - Robert Gerzsten
- Beth Israel Deaconess Medical Center, Division of Cardiovascular Medicine, Boston, MA, USA
| | - Clary Clish
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - George Papanicolau
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R. Graham Barr
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - David A. Knowles
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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14
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Sanmarco LM, Rone JM, Polonio CM, Fernandez Lahore G, Giovannoni F, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Faust Akl C, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Stevens NA, Piester G, Chung EN, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Lactate limits CNS autoimmunity by stabilizing HIF-1α in dendritic cells. Nature 2023; 620:881-889. [PMID: 37558878 PMCID: PMC10725186 DOI: 10.1038/s41586-023-06409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Dendritic cells (DCs) have a role in the development and activation of self-reactive pathogenic T cells1,2. Genetic variants that are associated with the function of DCs have been linked to autoimmune disorders3,4, and DCs are therefore attractive therapeutic targets for such diseases. However, developing DC-targeted therapies for autoimmunity requires identification of the mechanisms that regulate DC function. Here, using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies, we identify a regulatory loop of negative feedback that operates in DCs to limit immunopathology. Specifically, we find that lactate, produced by activated DCs and other immune cells, boosts the expression of NDUFA4L2 through a mechanism mediated by hypoxia-inducible factor 1α (HIF-1α). NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs that are involved in the control of pathogenic autoimmune T cells. We also engineer a probiotic that produces lactate and suppresses T cell autoimmunity through the activation of HIF-1α-NDUFA4L2 signalling in DCs. In summary, we identify an immunometabolic pathway that regulates DC function, and develop a synthetic probiotic for its therapeutic activation.
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Affiliation(s)
- Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gonzalo Fernandez Lahore
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kylynne Ferrara
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Cristina Gutierrez-Vazquez
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Ning Li
- Synlogic Therapeutics, Cambridge, MA, USA
| | | | - Agustin Plasencia
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Payal Nanda
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Evelin S Heck
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Claudia M Rejano-Gordillo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Pedro H Fonseca-Castro
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Tomer Illouz
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Linnerbauer
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Rocky M Barilla
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Farrenkopf
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Nikolas A Stevens
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gavin Piester
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth N Chung
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Lucas Dailey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - David Hava
- Synlogic Therapeutics, Cambridge, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roni Nowarski
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Eduardo Balsa
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter JC, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Cell Metab 2023; 35:887-905.e11. [PMID: 37075753 PMCID: PMC10257950 DOI: 10.1016/j.cmet.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 04/21/2023]
Abstract
Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated diseases. However, there are no scalable approaches to comprehensively assess the diverse FFAs circulating in human plasma. Furthermore, assessing how FFA-mediated processes interact with genetic risk for disease remains elusive. Here, we report the design and implementation of fatty acid library for comprehensive ontologies (FALCON), an unbiased, scalable, and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids associated with decreased membrane fluidity. Furthermore, we prioritized genes that reflect the combined effects of harmful FFA exposure and genetic risk for type 2 diabetes (T2D). We found that c-MAF-inducing protein (CMIP) protects cells from FFA exposure by modulating Akt signaling. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.
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Affiliation(s)
- Nicolas Wieder
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Neurology with Experimental Neurology and Berlin Institute of Health, Charité, 10117 Berlin, Germany
| | - Juliana Coraor Fried
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Choah Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Eriene-Heidi Sidhom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthew R Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Carlos Arevalo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Moran Dvela-Levitt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Jonas Sieber
- Department of Endocrinology, Metabolism and Cardiovascular Systems, University of Fribourg, Fribourg, Switzerland
| | | | - Julian Pacheco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Shantanu Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justine C Rutter
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Zon Weng Lai
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Aaron Baublis
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Renuka Subramanian
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranjan Devkota
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonnell Small
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vedagopuram Sreekanth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Myeonghoon Han
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Donghyun Lim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hilary Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Mass General Hospital, Boston, MA 02114, USA
| | - Marcia C Haigis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Sheu
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Bridget K Wagner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jillian L Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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16
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Sanmarco LM, Rone JM, Polonio CM, Giovannoni F, Lahore GF, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Akl CF, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Piester G, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Engineered probiotics limit CNS autoimmunity by stabilizing HIF-1α in dendritic cells. bioRxiv 2023:2023.03.17.532101. [PMID: 36993446 PMCID: PMC10055137 DOI: 10.1101/2023.03.17.532101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Dendritic cells (DCs) control the generation of self-reactive pathogenic T cells. Thus, DCs are considered attractive therapeutic targets for autoimmune diseases. Using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies we identified a negative feedback regulatory pathway that operates in DCs to limit immunopathology. Specifically, we found that lactate, produced by activated DCs and other immune cells, boosts NDUFA4L2 expression through a mechanism mediated by HIF-1α. NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs involved in the control of pathogenic autoimmune T cells. Moreover, we engineered a probiotic that produces lactate and suppresses T-cell autoimmunity in the central nervous system via the activation of HIF-1α/NDUFA4L2 signaling in DCs. In summary, we identified an immunometabolic pathway that regulates DC function, and developed a synthetic probiotic for its therapeutic activation.
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17
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Mehta RS, Mayers JR, Zhang Y, Bhosle A, Glasser NR, Nguyen LH, Ma W, Bae S, Branck T, Song K, Sebastian L, Pacheco JA, Seo HS, Clish C, Dhe-Paganon S, Ananthakrishnan AN, Franzosa EA, Balskus EP, Chan AT, Huttenhower C. Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease. Nat Med 2023; 29:700-709. [PMID: 36823301 PMCID: PMC10928503 DOI: 10.1038/s41591-023-02217-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/10/2023] [Indexed: 02/25/2023]
Abstract
For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.
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Affiliation(s)
- Raaj S Mehta
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jared R Mayers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yancong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Amrisha Bhosle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nathaniel R Glasser
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Long H Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenjie Ma
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sena Bae
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tobyn Branck
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luke Sebastian
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Hyuk-Soo Seo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Emily P Balskus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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18
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Miranda-Maravi S, Hoffman WG, Dev PK, Barber JL, Schwartz CS, Clarkson WA, Robbins JM, Rao P, Mi M, Ghosh S, Clish C, Silbernagel G, Chen YQ, Konrad RJ, Bouchard C, Gerszten RE, Sarzynski MA. Abstract P201: Plasma Proteomic Signatures of Angptl3/8 and 4/8 Before and After Exercise Training. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Introduction:
Angiopoietin like protein (ANGPTL) complexes 3/8 and 4/8 are established inhibitors of lipoprotein lipase and modifiable by regular exercise. However, the molecular biomarkers related to their exercise responses have not been fully elucidated. The purpose of this study was to examine the associations between plasma proteins and ANGPTL3/8 and 4/8 before and after exercise training.
Methods:
Measurements were taken before and after 20 weeks of exercise training in 630 adults (36% Black, 56% women, mean age 35 yrs) of the HERITAGE Family Study. Meso Scale Discovery immunoassays were used to measure ANGPTL3/8 and ANGPTL4/8 complexes in serum. Plasma proteins (n=4979 aptamers) were quantified using SomaScan. Linear mixed models tested the association between plasma proteins and each trait at baseline and post- training with full covariate adjustment. Significance was set to FDR<0.05.
Results:
A total of 862 and 126 proteins were significantly associated with ANGPTL3/8 at baseline or post-training, respectively, with 80 proteins associated at both time points, including PCSK9 and PLTP (
Figure 1A
). Conversely, 46 proteins were only associated with ANGPTL3/8 at post-training, 23 of which whose levels significantly changed with training including NRP1, ghrelin, HHIP, and APOA1. A total of 433 and 71 proteins were significantly associated with ANGPTL4/8 at baseline or post-training, respectively, with 46 proteins associated with both time points (
Figure 1B
). A total of 25 proteins were only associated with ANGPTL4/8 at post-training, 12 of which whose levels significantly changed with training including ghrelin, COL6A2, and MMP16.
Conclusions:
We identified a subset of proteins uniquely associated with exercise-induced changes in ANGPTL3/8 and 4/8. Thus, the responsiveness of ANGPTL3/8 and 4/8 to regular exercise may be related to cholesterol esterification, lipoprotein remodeling, inflammatory response, and regulation of fibrinolysis and coagulation among other biological pathways.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Michael Mi
- Beth Israel Deaconess Med Cntr, Boston, MA
| | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
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19
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Wang F, Tessier AJ, Liang L, Wittenbecher C, Haslam D, Eliassen AH, Rexrode KM, Tobias DK, Li J, Zeleznik O, Stampfer MJ, Grodstein F, Martínez-González M, Salas-Salvado J, Clish C, Lee KH, Sun Q, Hu F, Guasch-Ferré M. Abstract MP22: Plasma Metabolomic Profiles Associated With Mortality and Longevity in a Prospective Study of 13,401 Individuals. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.mp22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Background:
Recent advances in metabolomic studies have shown promise in elucidating the biological pathways underpinning aging processes and mortality in animal models, but data in humans are lacking. We aimed to evaluate the associations between metabolite profiles, all-cause and cause-specific mortality, and longevity.
Methods:
Within three prospective cohorts (Nurses’ Health Study [NHS], NHSII, and Health Professional’s Follow-up Study), we measured plasma metabolites from 11,523 participants (mean age 54 years, 86% female) using high-throughput liquid chromatography-mass spectrometry. Participants were free of cardiovascular disease and cancer at blood collection. Metabolome-wide association analyses were conducted for all-cause, cardiovascular, and cancer mortality using Cox proportional hazards regression and longevity (attaining 85 years of age) using logistic regression. Both pre-defined and data-driven metabolite groups were also evaluated. We further developed a multi-metabolite profile score for all-cause mortality using an elastic-net regularized Cox model and assessed its associations with mortality and longevity. Results for all-cause mortality were replicated among 1878 participants (mean age 67 years, 58% female) from the PREDIMED trial.
Results:
We documented 4252 deaths (including 864 cardiovascular deaths and 1070 cancer deaths) and 3048 achieving longevity over a median follow-up of 22.6 years in the NHS/NHSII/HPFS, and 126 deaths during a follow-up of 4.7 years in the PREDIMED. Higher levels of three nucleosides (N2,N2-dimethylguanosine, pseudouridine, and N4-acetylcytidine), 4-acetamidobutanoic acid, triacylglycerols with ≤56 carbons and ≤3 double bonds, and several other lipids were associated with increased risk of all-cause mortality and corresponding decreased likelihood of longevity; whereas L-serine, L-glutamine, and TAGs with >56 carbons or >3 double bonds were associated with lower mortality risk and higher odds of achieving longevity. A multi-metabolite profile score comprising 73 metabolites was positively associated with all-cause (HR per 1-SD increment=1.25 [95% CI: 1.21, 1.30] in NHS/NHSII/HPFS and 1.47 [95% CI: 1.22, 1.78] in PREDIMED), cardiovascular (HR=1.34 [95% CI:1.24, 1.45]), and cancer mortality (HR=1.15 [95% CI:1.08, 1.24]) and inversely associated with longevity (OR=0.79 [95% CI: 0.74, 0.86]).
Conclusions:
We identified multiple metabolites associated with mortality and longevity. Our findings provide insights into the biological pathways that lead to death and open up new avenues to incorporate these metabolomic markers in clinical and research settings.
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Affiliation(s)
- Fenglei Wang
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | - Liming Liang
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | | | - A H Eliassen
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | | | - Jun Li
- Brigham and Women's Hosp, Boston, MA
| | - Oana Zeleznik
- Brigham and Women’s Hosp and Harvard Med Sch, Boston, MA
| | | | | | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kyu Ha Lee
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Qi Sun
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Frank Hu
- Harvard T.H. Chan Sch of Public Health, Boston, MA
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20
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Tessier AJ, Wang F, Liang L, Wittenbecher C, Haslam DE, Eliassen AH, Sun Q, Tobias DK, Li J, Zeleznik O, Ascherio A, Stampfer MJ, Grodstein F, Rexrode KM, Martinez-Gonzalez MA, Clish C, Chavarro JE, Hu FB, Guasch M. Abstract P203: Healthy Lifestyle Plasma Metabolite Profile and Risk of Mortality in US Prospective Cohort Studies. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Background:
A healthy lifestyle is associated with a lower risk of premature death. Metabolic pathways of a healthy lifestyle and their association with mortality remain to be understood. This study aimed to identify the metabolomic profile of a healthy lifestyle score and examine its prospective association with all-cause and cause-specific mortality, including death from cardiovascular disease (CVD) and cancer.
Methods:
The population included 12,146 participants from the Nurses’ Health Study (NHS), NHS II and Health Professionals Follow-Up Study (HPFS)(83% women, 97% white, aged 55±9y). Plasma metabolites were profiled using high-throughput liquid chromatography mass-spectrometry at baseline (NHS:1989-1990; NHSII:1996-1999; HPFS:1993-1995). The healthy lifestyle score was computed by summing the total number of healthy lifestyle factors participants adhered to from validated questionnaires at baseline: healthy diet (Alternative Healthy Eating Index, upper 40%), moderate alcohol intake (women: 5-15 g/d; men: 5-30 g/d), moderate-to-vigorous physical activity (≥30min/d), never smoking and normal BMI (18.5-24.9kg/m
2
). Deaths were ascertained with death certificates and medical records. The metabolite profile was identified using elastic net regressions with train test validation split (70-30%). Metabolic pathways were determined using Metabolite Set Enrichment Analysis (MSEA). Multivariable-adjusted Cox proportional hazards regressions were used to estimate hazard ratios and 95% confidence intervals (HR[CI]) per unit of score of the healthy lifestyle metabolite profile with mortality risk.
Results:
The identified profile included 88 metabolites and correlated with the healthy lifestyle score (Pearson r=0.43-0.44; p<0.001). Triglyceride and diglyceride metabolite sets were inversely associated with the healthy lifestyle score, whereas cholesteryl ester and phosphatidylcholine plasmalogen sets were directly associated (p<0.001). Among individual lifestyle factors, the profile was most strongly correlated with normal BMI (r
pb
=0.43; p<0.001). Over 32y of follow-up, there were 3,851 deaths, including 749 deaths from CVD and 994 from cancer. Participants with a higher healthy lifestyle metabolite profile score had lower risk of all-cause (HR=0.79[0.73, 0.85]) and CVD mortality (HR=0.77[0.58, 0.95]), but not cancer (HR=0.91[0.77, 1.05]). Significant associations persisted after further adjustment for the healthy lifestyle score.
Conclusions:
In US adults, we identified a metabolite profile related to a healthy lifestyle largely reflecting lipid metabolism pathways. A higher metabolite score was associated with lower subsequent all-cause mortality risk, specifically from CVD. Findings provide novel insights into potential metabolic pathways underlying the association between a healthy lifestyle and lower premature mortality.
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Affiliation(s)
| | - Fenglei Wang
- Harvard TH Chan Sch of Public Health, Boston, MA
| | | | | | | | | | - Qi Sun
- Harvard TH Chan Sch of Public Health, Boston, MA
| | | | - Jun Li
- Harvard Sch of Public Health, Boston, MA
| | | | | | | | | | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Frank B Hu
- Harvard TH Chan Sch of Public Health, Boston, MA
| | - Marta Guasch
- Harvard TH Chan Sch of Public Health, Boston, MA
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21
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Huang T, Zhu Y, Shutta K, Balasubramanian R, Zeleznik O, Rexrode KM, Clish C, Sun Q, Hu F, Kubzansky L, Hankinson S. Abstract MP58: A Plasma Metabolite Score Related to Psychological Distress and Future Diabetes Risk: A Nested Case-Control Study in US Women. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.mp58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Introduction:
Various forms of psychological distress, such as depression and anxiety, have been identified as risk factors for diabetes. However, there is limited evidence from population-based, epidemiologic studies investigating potential molecular mechanisms (e.g., metabolic dysregulation) linking psychological distress and diabetes development.
Hypothesis:
We assessed the hypothesis that a metabolite score reflecting psychological distress-related metabolic dysregulation is predictive of future diabetes risk in women.
Methods:
We conducted a nested case-control study of plasma metabolomics and diabetes risk in the Nurses’ Health Study, including 728 women (mean age: 55.2 years) with incident diabetes and 728 controls matched on age, race, fasting status, and time/date of blood collection. Blood samples were collected between 1989-1990 and incident diabetes was diagnosed between 1990-2012. Based on the metabolomic signature of chronic psychological distress we previously identified and validated in women (including coefficient estimates for individual metabolite associations), we calculated a weighted plasma metabolomic score of psychological distress comprised of 19 metabolites (e.g., serotonin, threonine, hippurate, biliverdin, glutamine, etc.). We used conditional logistic regression accounting for matching factors and other diabetes risk factors to estimate odds ratios (OR) and 95% CI for diabetes risk across quintiles of the distress-related metabolite score.
Results:
After adjusting for sociodemographic factors, family history of diabetes and health behaviors, the OR (95% CI) for diabetes risk across quintiles of the distress-related metabolite score was 1.00 (reference) for Q1, 1.11 (0.77, 1.61) for Q2, 1.64 (1.14, 2.35) for Q3, 2.07 (1.42, 3.01) for Q4, and 2.35 (1.60, 3.47) for Q5. Each 1-unit increase in the score was associated with 26% higher diabetes risk (95% CI: 1.15, 1.38; p-trend<0.0001). This association was moderately attenuated after additional adjustment for baseline body mass index (OR per 1-unit increase: 1.13; 95% CI: 1.02, 1.25; p-trend=0.02). Further, psychological distress assessed via self-report (defined as presence of depression or anxiety) was associated with modestly increased diabetes risk in the same sample (OR: 1.25; 95% CI: 1.01, 1.55). The metabolite score mediated 20.7% (95% CI: 5.1, 56.1) of the association between psychological distress and diabetes risk (p=0.0065).
Conclusions:
Our results suggest that the distress-related metabolite score was significantly associated with diabetes risk in women and partly mediated the association between self-reported psychological distress and diabetes risk. These findings provide supporting evidence that metabolic dysregulation may be an important mechanism underlying the observed association between psychological distress and diabetes risk.
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Affiliation(s)
| | - Yiwen Zhu
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | | | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Qi Sun
- HARVARD SCHOOL OF PUBLIC HEALTH, Boston, MA
| | - Frank Hu
- Harvard Sch of Public Health, Boston, MA
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22
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Dev PK, Miranda-Maravi S, Hoffman W, Barber JL, Schwartz CS, Clarkson WA, Robbins JM, Rao P, Mi M, Ghosh S, Ghosh S, Clish C, Silbernagel G, Chen YQ, Konrad RJ, Bouchard C, Gerszten RE, Sarzynski MA. Abstract P205: Association of Angptl3/8 and 4/8 With Plasma Metabolites Before and After Exercise Training. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Introduction:
Angiopoietin like protein (ANGPTL) complexes 3/8 and 4/8 are established inhibitors of lipoprotein lipase and modifiable by regular exercise. However, the molecular underpinning of these novel biomarkers has not been fully elucidated. The purpose of this study was to examine the associations between plasma metabolites and ANGPTL3/8 and 4/8 before and after exercise training.
Methods:
Measurements were taken before and after 20 weeks of exercise training in 630 adults (36% Black, 56% women, mean age 35 yrs) of the HERITAGE Family Study. Meso Scale Discovery immunoassays were used to measure ANGPTL3/8 and 4/8 in serum. Plasma metabolites (n=300 named) were measured using LC-MS and the HILIC-pos method. Linear mixed models tested the association between metabolites and each trait at baseline and post-training with full covariate adjustment. Significance was set to FDR<0.05.
Results:
A total of 111 and 93 metabolites were significantly associated with ANGPTL3/8 at baseline or post-training, respectively (
Figure 1A
). A total of 69 metabolites were associated with ANGPTL3/8 at both time points, including ketone bodies, acylcarnitines, and DMGV, while 24 metabolites were only associated at post-training including citric acid, methionine, and glycine. A total of 89 and 40 metabolites were significantly associated with ANGPTL4/8 at baseline or post-training, respectively (
Figure 1B
). A total of 13 metabolites were associated with ANGPTL4/8 at both time points including glycine and lysophospholipids, whereas 27 metabolites were associated only at post-training including hydroxyproline, N-Lignoceroyl Taurine, and methylguanidine.
Conclusions:
We identified several plasma metabolites associated with ANGPTL3/8 and 4/8 before and after exercise training. Our findings indicate potential metabolic pathways related to the exercise responsiveness of ANGPTL3/8 and 4/8, including glucose-alanine cycle, urea cycle, and glycine and methionine metabolism.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Michael Mi
- Beth Israel Deaconess Med Cntr, Boston, MA
| | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
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23
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Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter J, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. bioRxiv 2023:2023.02.19.529127. [PMID: 36865221 PMCID: PMC9979987 DOI: 10.1101/2023.02.19.529127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism. Highlights FALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effectsFALCON is applicable to many and diverse cell typesA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidityNew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for diseaseC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling.
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Affiliation(s)
- Nicolas Wieder
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Department of Neurology with Experimental Neurology, Charité, Berlin, Germany
| | - Juliana Coraor Fried
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | - Choah Kim
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | - Eriene-Heidi Sidhom
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | | | | | | | - Moran Dvela-Levitt
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Jonas Sieber
- Department of Endocrinology, Metabolism and Cardiovascular Systems, University of Fribourg, Fribourg, Switzerland
| | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - Justine Rutter
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
| | | | - Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Zon Weng Lai
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston MA 02115 USA
| | - Aaron Baublis
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston MA 02115 USA
| | - Renuka Subramanian
- Laboratory for Surgical and Metabolic Research, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ranjan Devkota
- Broad Institute of MIT and Harvard, Cambridge, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonnell Small
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vedagopuram Sreekanth
- Broad Institute of MIT and Harvard, Cambridge, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Donghyun Lim
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Hilary Finucane
- Broad Institute of MIT and Harvard, Cambridge, USA
- Analytic and Translational Genetics Unit, Mass General Hospital, Boston, MA, USA
| | - Marcia C. Haigis
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Sheu
- Laboratory for Surgical and Metabolic Research, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Boston Children’s Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Bridget K. Wagner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA, USA
| | | | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Lead Contact
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24
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Fritz J, Huang T, Depner CM, Zeleznik OA, Cespedes Feliciano EM, Li W, Stone KL, Manson JE, Clish C, Sofer T, Schernhammer E, Rexrode K, Redline S, Wright KP, Vetter C. Sleep duration, plasma metabolites, and obesity and diabetes: a metabolome-wide association study in US women. Sleep 2023; 46:zsac226. [PMID: 36130143 PMCID: PMC9832513 DOI: 10.1093/sleep/zsac226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
Short and long sleep duration are associated with adverse metabolic outcomes, such as obesity and diabetes. We evaluated cross-sectional differences in metabolite levels between women with self-reported habitual short (<7 h), medium (7-8 h), and long (≥9 h) sleep duration to delineate potential underlying biological mechanisms. In total, 210 metabolites were measured via liquid chromatography-mass spectrometry in 9207 women from the Nurses' Health Study (NHS; N = 5027), the NHSII (N = 2368), and the Women's Health Initiative (WHI; N = 2287). Twenty metabolites were consistently (i.e. praw < .05 in ≥2 cohorts) and/or strongly (pFDR < .05 in at least one cohort) associated with short sleep duration after multi-variable adjustment. Specifically, levels of two lysophosphatidylethanolamines, four lysophosphatidylcholines, hydroxyproline and phenylacetylglutamine were higher compared to medium sleep duration, while levels of one diacylglycerol and eleven triacylglycerols (TAGs; all with ≥3 double bonds) were lower. Moreover, enrichment analysis assessing associations of metabolites with short sleep based on biological categories demonstrated significantly increased acylcarnitine levels for short sleep. A metabolite score for short sleep duration based on 12 LASSO-regression selected metabolites was not significantly associated with prevalent and incident obesity and diabetes. Associations of single metabolites with long sleep duration were less robust. However, enrichment analysis demonstrated significant enrichment scores for four lipid classes, all of which (most markedly TAGs) were of opposite sign than the scores for short sleep. Habitual short sleep exhibits a signature on the human plasma metabolome which is different from medium and long sleep. However, we could not detect a direct link of this signature with obesity and diabetes risk.
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Affiliation(s)
- Josef Fritz
- Circadian and Sleep Epidemiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria
| | - Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher M Depner
- Department of Health and Kinesiology, University of Utah, Salt Lake City, UT, USA
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Wenjun Li
- Department of Public Health, School of Health Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Katie L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Clary Clish
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Eva Schernhammer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Vienna, Austria
| | - Kathryn Rexrode
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Women’s Health, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kenneth P Wright
- Sleep and Chronobiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Céline Vetter
- Circadian and Sleep Epidemiology Laboratory, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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25
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Moreau F, Brunao BB, Liu XY, Tremblay F, Fitzgerald K, Avila-Pacheco J, Clish C, Kahn RC, Softic S. Liver-specific FGFR4 knockdown in mice on an HFD increases bile acid synthesis and improves hepatic steatosis. J Lipid Res 2022; 64:100324. [PMID: 36586437 PMCID: PMC9871743 DOI: 10.1016/j.jlr.2022.100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with increased risk in patients with metabolic syndrome. There are no FDA-approved treatments, but FXR agonists have shown promising results in clinical studies for NAFLD management. In addition to FXR, fibroblast growth factor receptor FGFR4 is a key mediator of hepatic bile acid synthesis. Using N-acetylgalactosamine-conjugated siRNA, we knocked down FGFR4 specifically in the liver of mice on chow or high-fat diet and in mouse primary hepatocytes to determine the role of FGFR4 in metabolic processes and hepatic steatosis. Liver-specific FGFR4 silencing increased bile acid production and lowered serum cholesterol. Additionally, we found that high-fat diet-induced liver steatosis and insulin resistance improved following FGFR4 knockdown. These improvements were associated with activation of the FXR-FGF15 axis in intestinal cells, but not in hepatocytes. We conclude that targeting FGFR4 in the liver to activate the intestinal FXR-FGF15 axis may be a promising strategy for the treatment of NAFLD and metabolic dysfunction.
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Affiliation(s)
- Francois Moreau
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Bruna Brasil Brunao
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Xiang-Yu Liu
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Julian Avila-Pacheco
- Metabolomics Platform of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Metabolomics Platform of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ronald C. Kahn
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Samir Softic
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, and Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, University of Kentucky, Lexington, KY, USA.
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26
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Marsh SE, Murphy S, Kamath T, Gazestani V, Therrien M, Dolan MJ, Jereb S, Reyes M, Gobom J, Clish C, Hacohen N, Zetterberg H, Leinonen V, Macosko E, Stevens B. Multi‐modal Analysis and Modeling of Human Neurodegenerative Disease to Reveal Disease Mechanisms and Biomarkers. Alzheimers Dement 2022. [DOI: 10.1002/alz.061905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Samuel E Marsh
- Boston Children’s Hospital Boston MA USA
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Sarah Murphy
- Boston Children’s Hospital Boston MA USA
- Broad Institute of MIT and Harvard Cambridge MA USA
| | | | | | | | | | - Sasa Jereb
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Miguel Reyes
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Johan Gobom
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg Gothenburg Sweden
| | - Clary Clish
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg Gothenburg Sweden
| | | | - Evan Macosko
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard Cambridge MA USA
- Boston Children Hospital Boston MA USA
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27
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Guo JA, Su J, Jambhale A, Dilly J, Hennessey CJ, Shiau C, Yu P, Wang S, Wang J, Abbassi L, Neiswender J, Bertea T, Yang A, Yu Q, Westcott P, Schenkel J, Kim DY, Hoffman HI, Jaramillo GC, Uribe GA, Wu WW, Mehta A, Ting D, Pacheco JA, Deik A, Clish C, Vazquez F, Wolpin B, Regev A, Freed-Pastor WA, Mancias JD, Jacks T, Hwang WL, Aguirre AJ. Abstract A052: Systematic dissection of transcriptional states in pancreatic cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-a052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Transcriptional states in pancreatic cancer can stratify patients by response to chemotherapy and clinical outcomes. These include the classical and basal-like states as well as a newly identified neural-like progenitor (NRP) state, which we have previously found to be enriched in primary patient tumors treated with neoadjuvant chemotherapy and radiotherapy. While several transcription factor drivers of classical and basal-like identity have been described, key regulators of the NRP state are unknown. Through in silico approaches, we identified candidate transcription factors of the NRP state, including GLIS3, a Krüppel-like zinc finger protein that mediates neuroendocrine fate during pancreatic development and differentiation of human embryonic stem cells into posterior neural progenitor cells. Our understanding of biologic and clinically-relevant attributes of transcriptional cell states remains limited by state-specific biases in various preclinical models. Existing human cell lines maintained as two-dimensional cultures tend to preferentially represent the basal-like state, whereas human three-dimensional organoid models grown in standard culture conditions best reflect the classical state. These phenotypes are therefore impacted by culture conditions as well as underlying genetic features. Furthermore, most murine pancreatic cancer models do not fully reflect the classical vs. basal-like state heterogeneity observed in humans. To enable systematic study of the classical, basal-like and NRP phenotypes, we developed isogenic KP (KrasG12D/+;Trp53FL/FL) murine organoids with a germline dCas9-VPR system to enable facile overexpression of state-specific transcription factors through CRISPR activation approaches. Quantitative PCR, RNA-sequencing, and proteomics confirmed Gata6, deltaN Trp63, and Glis3 as drivers of classical, basal-like, and NRP identity, respectively. DeltaN Trp63 organoids were further differentiated by loss of luminal morphology. Pairwise comparisons of global transcriptional alterations suggest the greatest similarities between the Gata6- and Glis3-overexpressed models, which is consistent with enhanced associations between classical and NRP states in patient tumors. Finally, although basal-like and NRP states are associated with poorer response to multi-agent chemotherapy, state-specific therapeutic sensitivities to other treatments remain incompletely defined. We therefore performed drug sensitivity assays with a panel of targeted therapies and unveiled state-specific sensitivities. These data were corroborated by drug sensitivity profiling of human patient-derived organoids and cell lines. Taken together, these results suggest a framework for defining cell state-specific vulnerabilities that may aid in stratifying and treating pancreatic cancer patients with new therapies.
Citation Format: Jimmy A. Guo, Jennifer Su, Ananya Jambhale, Julien Dilly, Connor J. Hennessey, Carina Shiau, Patrick Yu, Steven Wang, Junning Wang, Laleh Abbassi, James Neiswender, Tate Bertea, Annan Yang, Qijia Yu, Peter Westcott, Jason Schenkel, Daniel Y. Kim, Hannah I. Hoffman, Grissel Cervantes Jaramillo, Giselle A. Uribe, Westley W. Wu, Arnav Mehta, David Ting, Julian A. Pacheco, Amy Deik, Clary Clish, Francisca Vazquez, Brian Wolpin, Aviv Regev, William A. Freed-Pastor, Joseph D. Mancias, Tyler Jacks, William L. Hwang, Andrew J. Aguirre. Systematic dissection of transcriptional states in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A052.
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Affiliation(s)
- Jimmy A. Guo
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | - Carina Shiau
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Patrick Yu
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Steven Wang
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | - Tate Bertea
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Annan Yang
- 3Dana Farber Cancer Institute, Boston, MA,
| | - Qijia Yu
- 3Dana Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | | | | | - Arnav Mehta
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - David Ting
- 6Massachusetts General Hospital, Boston, MA,
| | | | - Amy Deik
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Clary Clish
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
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28
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Rogando AC, Weber KM, Xing J, Xue X, Yohannes T, Morack R, Qi Q, Clish C, Bullock K, Gustafson D, Anastos K, Sharma A, Burgess HJ, French AL. The IDOze Study: The Link Between Sleep Disruption and Tryptophan-Kynurenine Pathway Activation in Women With Human Immunodeficiency Virus. J Infect Dis 2022; 226:1451-1460. [PMID: 35801535 PMCID: PMC9989737 DOI: 10.1093/infdis/jiac287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/07/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Poor sleep is associated with human immunodeficiency virus (HIV), particularly among women with HIV (WWH), although mechanisms are unclear. We explored cross-sectional associations between sleep disruption and tryptophan-kynurenine (T/K) pathway activation, measured by the kynurenine-to-tryptophan ratio (K:T). METHODS HIV-uninfected women (HIV-) and WWH aged 35-70 years and on stable antiretroviral therapy were included. Sleep metrics were measured using wrist actigraphy. Plasma T/K pathway metabolites were measured using liquid chromatography-tandem mass spectrometry. Multivariate linear regression models examined relationships between K:T and actigraphy-based sleep metrics by HIV status. RESULTS WWH (n = 153) and HIV- women (n = 151) were demographically similar. Among WWH, median CD4 was 751 cells/µL; 92% had undetectable HIV RNA. Compared to HIV- women, WWH had higher K:T (P < .001) and kynurenine (P = .01) levels but similar tryptophan levels (P = .25). Higher K:T was associated with more wake bouts (P = .001), more time awake after sleep onset (P = .01), and lower sleep efficiency (P = .03) in WWH only. CONCLUSIONS HIV infection was associated with T/K pathway activation; this activation was associated with poorer sleep efficiency and more fragmented sleep. While longitudinal studies are needed to elucidate the directionality of these associations, these findings may help identify treatments to reduce sleep disruption in WWH by targeting residual inflammation and T/K pathway activation.
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Affiliation(s)
- Andrea C Rogando
- College of Science and Health at Charles R. Drew University of Medicine and Science, Los Angeles, California, USA.,Hektoen Institute of Medicine/CORE Center of Cook County Health, Chicago, Illinois, USA
| | - Kathleen M Weber
- Hektoen Institute of Medicine/CORE Center of Cook County Health, Chicago, Illinois, USA
| | - Jiaqian Xing
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tsion Yohannes
- Hektoen Institute of Medicine/CORE Center of Cook County Health, Chicago, Illinois, USA
| | - Ralph Morack
- Hektoen Institute of Medicine/CORE Center of Cook County Health, Chicago, Illinois, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Clary Clish
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Kevin Bullock
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York, USA
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Helen J Burgess
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County Health, Chicago, Illinois, USA
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29
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Chou C, Mohanty S, Kang HA, Kong L, Avila‐Pacheco J, Joshi SR, Ueda I, Devine L, Raddassi K, Pierce K, Jeanfavre S, Bullock K, Meng H, Clish C, Santori FR, Shaw AC, Xavier RJ. Metabolomic and transcriptomic signatures of influenza vaccine response in healthy young and older adults. Aging Cell 2022; 21:e13682. [PMID: 35996998 PMCID: PMC9470889 DOI: 10.1111/acel.13682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 01/25/2023] Open
Abstract
Seasonal influenza causes mild to severe respiratory infections and significant morbidity, especially in older adults. Transcriptomic analysis in populations across multiple flu seasons has provided insights into the molecular determinants of vaccine response. Still, the metabolic changes that underlie the immune response to influenza vaccination remain poorly characterized. We performed untargeted metabolomics to analyze plasma metabolites in a cohort of younger and older subjects before and after influenza vaccination to identify vaccine-induced molecular signatures. Metabolomic and transcriptomic data were combined to define networks of gene and metabolic signatures indicative of high and low antibody response in these individuals. We observed age-related differences in metabolic baselines and signatures of antibody response to influenza vaccination and the abundance of α-linolenic and linoleic acids, sterol esters, fatty-acylcarnitines, and triacylglycerol metabolism. We identified a metabolomic signature associated with age-dependent vaccine response, finding increased tryptophan and decreased polyunsaturated fatty acids (PUFAs) in young high responders (HRs), while fatty acid synthesis and cholesteryl esters accumulated in older HRs. Integrated metabolomic and transcriptomic analysis shows that depletion of PUFAs, which are building blocks for prostaglandins and other lipid immunomodulators, in young HR subjects at Day 28 is related to a robust immune response to influenza vaccination. Increased glycerophospholipid levels were associated with an inflammatory response in older HRs to flu vaccination. This multi-omics approach uncovered age-related molecular markers associated with influenza vaccine response and provides insight into vaccine-induced metabolic responses that may help guide development of more effective influenza vaccines.
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Affiliation(s)
- Chih‐Hung Chou
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | | | - Lingjia Kong
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Samit R. Joshi
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ikuyo Ueda
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Lesley Devine
- Department of Laboratory MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Khadir Raddassi
- Department of NeurologyYale School of MedicineNew HavenConnecticutUSA
| | - Kerry Pierce
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Kevin Bullock
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Hailong Meng
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Clary Clish
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Fabio R. Santori
- Center for Molecular MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ramnik J. Xavier
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Klarman Cell ObservatoryBroad Institute of Harvard and MITCambridgeMassachusettsUSA
- Center for Computational and Integrative Biology and Department of Molecular BiologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusettsUSA
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Dev PK, Barbar JL, Cai G, Robbins JM, Rao P, Mi M, Ghosh S, Clish C, Katz DH, Gerszten RE, Bouchard C, Sarzynski MA. EXERCISE TRAINING SLOWS DOWN PROTEOMIC AGE ACCELERATION IN MIDDLE-AGED TO OLDER ADULTS- HERITAGE FAMILY STUDY. Med Sci Sports Exerc 2022. [DOI: 10.1249/01.mss.0000875936.05661.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barber JL, Cai G, Robbins JM, Rao P, Mi M, Ghosh S, Clish C, Katz DH, Gerszten RE, Bouchard C, Sarzynski MA. EXERCISE TRAINING-INDUCED CHANGES IN LIPID TRAITS ARE ASSOCIATED WITH CHANGES IN CIRCULATING PROTEINS AND METABOLITES. Med Sci Sports Exerc 2022. [DOI: 10.1249/01.mss.0000878156.71301.7f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Clarkson WA, Barber JL, Robbins JM, Rao P, Mi M, Dev PK, Ghosh S, Clish C, Katz DH, Gerszten RE, Bouchard C, Sarzynski MA. Associations Between Changes In Plasma Proteins And Body Composition Traits In Response To Endurance Training. Med Sci Sports Exerc 2022. [DOI: 10.1249/01.mss.0000877312.49396.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kang JH, Zeleznik O, Frueh L, Lasky-Su J, Eliassen AH, Clish C, Rosner BA, Pasquale LR, Wiggs JL. Prediagnostic Plasma Metabolomics and the Risk of Exfoliation Glaucoma. Invest Ophthalmol Vis Sci 2022; 63:15. [PMID: 35951322 PMCID: PMC9386645 DOI: 10.1167/iovs.63.9.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Purpose The etiology of exfoliation glaucoma (XFG) is poorly understood. We aimed to identify a prediagnostic plasma metabolomic signature associated with XFG. Methods We conducted a 1:1 matched case-control study nested within the Nurses' Health Study and Health Professionals Follow-up Study. We collected blood samples in 1989-1990 (Nurses' Health Study) and 1993-1995 (Health Professionals Follow-up Study). We identified 205 incident XFG cases through 2016 (average time to diagnosis from blood draw = 11.8 years) who self-reported glaucoma and were confirmed as XFG cases with medical records. We profiled plasma metabolites using liquid chromatography-mass spectrometry. We evaluated 379 known metabolites (transformed for normality using probit scores) using multiple conditional logistic models. Metabolite set enrichment analysis was used to identify metabolite classes associated with XFG. To adjust for multiple comparisons, we used number of effective tests (NEF) and the false discovery rate (FDR). Results Mean age of cases (n = 205) at diagnosis was 71 years; 85% were women and more than 99% were Caucasian; controls (n = 205) reported eye examinations as of the matched cases' index date. Thirty-three metabolites were nominally significantly associated with XFG (P < 0.05), and 4 metabolite classes were FDR-significantly associated. We observed positive associations for lysophosphatidylcholines (FDR = 0.02) and phosphatidylethanolamine plasmalogens (FDR = 0.004) and inverse associations for triacylglycerols (FDR < 0.0001) and steroids (FDR = 0.03). In particular, the multivariable-adjusted odds ratio with each 1 standard deviation higher plasma cortisone levels was 0.49 (95% confidence interval, 0.32-0.74; NEF = 0.05). Conclusions In plasma from a decade before diagnosis, lysophosphatidylcholines and phosphatidylethanolamine plasmalogens were positively associated and triacylglycerols and steroids (e.g., cortisone) were inversely associated with XFG risk.
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Affiliation(s)
- Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - Oana Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - Lisa Frueh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
| | - A Heather Eliassen
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
- Departments of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Clary Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States
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Zhang Y, Ngo D, Yu B, Shah N, Chen H, Ramos A, Zee P, Kaplan R, Rotter J, Clish C, Gerszten R, Kristal B, Gharib S, Redline S, Sofer T. 0030 Development and Validation of a Metabolomic Risk Score for Obstructive Sleep Apnea across Race/Ethnicities. Sleep 2022. [DOI: 10.1093/sleep/zsac079.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Obstructive sleep apnea (OSA) is a common disorder characterized by recurrent episodes of upper airway obstruction during sleep resulting in oxygen desaturation and sleep fragmentation, and associated with increased risk of adverse health outcomes. Metabolites are being increasingly used for biomarker discovery and evaluation of disease processes and progression. We aimed to develop a metabolomic risk score (MRS) for OSA and identify individual metabolites associated with OSA to provide insights into the pathogenesis of OSA.
Methods
We studied 219 metabolites and their associations the apnea hypopnea index (AHI) and with OSA, defined as AHI , in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) (n=3507) using two methods: (1) association analysis of individual metabolites, and (2) least absolute shrinkage and selection operator (LASSO) regression to identify a subset of metabolites that are jointly associated with OSA, and develop an MRS. We then validated the results in Multi-Ethnic Study of Atherosclerosis (MESA) (n=475), an independent dataset.
Results
HCHS/SOL participants were 41.72 years old on average, 50.7% female, and 10.2% had OSA. MESA individuals were 68.45 years old on average, 56.2% females, and 46.7% had OSA. When assessing the associations between OSA/AHI and individual metabolites, we identified seven metabolites significantly and positively associated with OSA in HCHS/SOL (FDR p<0.05), of which four associations - glutamate, oleoyl-linoleoyl-glycerol (18:1/18:2) (DAG(36:3)), linoleoyl-linoleoyl-glycerol (18:2/18:2) (DAG(36:4)) and phenylalanine, replicated in MESA (one sided-p value<0.05). The OSA-MRS, composed of 14 metabolites, was associated with 52% increase of risk for moderate to severe OSA (OR=1.52 [95% CI: 1.23-1.87] per 1 SD of OSA-MRS, p<.001) in the discovery dataset of HCHS/SOL and 44% increased risk (OR=1.44 [95% CI: 1.03-2.03] per 1 SD of OSA-MRS, p=0.034) in the validation dataset of MESA, both adjusted for demographic, lifestyle, and comorbidities. Similar albeit less significant associations were observed for AHI modeled continuously.
Conclusion
We developed an MRS that replicated in an independent multi-ethnic dataset, demonstrating the robustness of metabolomic-based OSA risk score to population heterogeneity. Replicated metabolite associations may provide insights into OSA-related molecular and metabolic mechanisms.
Support (If Any)
Support for metabolomics data was graciously provided by the JLH Foundation (Houston, Texas). The Hispanic Community Health Study/Study of Latinos was carried out as a collaborative study supported by contracts from the National Heart, Lung, and Blood Institute (NHLBI) to the University of North Carolina (N01-HC65233), University of Miami (N01-HC65234), Albert Einstein College of Medicine (N01-HC65235), Northwestern University (N01-HC65236), and San Diego State University (N01-HC65237). The following Institutes/Centers/Offices contribute to the HCHS/SOL through a transfer of funds to the NHLBI: National Center on Minority Health and Health Disparities, the National Institute of Deafness and Other Communications Disorders, the National Institute of Dental and Craniofacial Research, the National Institute of Diabetes and Digestive and Kidney Diseases, the National Institute of Neurological Disorders and Stroke, and the Office of Dietary Supplements. The authors thank the staff and participants of HCHS/SOL for their important contributions. MESA and the MESA SHARe project are conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support for MESA is provided by contracts HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420. MESA Family is conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support is provided by grants and contracts R01HL071051, R01HL071205, R01HL071250, R01HL071251, R01HL071258, R01HL071259, and by the National Center for Research Resources, Grant UL1RR033176. The provision of genotyping data was supported in part by the National Center for Advancing Translational Sciences, CTSI grant UL1TR001881, and the National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC) grant DK063491 to the Southern California Diabetes Endocrinology Research Center. Molecular data for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). ). Metabolomics for “NHLBI TOPMed: Multi-Ethnic Study of Atherosclerosis (MESA)” (phs001416) was performed at Broad Institute and Beth Israel Metabolomics Platform (HHSN268201600038I). Core support including centralized genomic read mapping and genotype calling, along with variant quality metrics and filtering were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I). Core support including phenotype harmonization, data management, sample-identity QC, and general program coordination were provided by the TOPMed Data Coordinating Center (R01HL-120393; U01HL-120393; contract HHSN268201800001I). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed. This study was supported by NHLBI grant R35HL135818.
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Affiliation(s)
| | - Debby Ngo
- Beth Israel Deaconess Medical Center
| | - Bing Yu
- School of Public Health, The University of Texas Health Science Center at Houston
| | | | - Han Chen
- School of Public Health, The University of Texas Health Science Center at Houston
| | | | | | | | - Jerome Rotter
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | | | | | | | | | - Susan Redline
- Brigham and Women's Hospital and Harvard Medical School
| | - Tamar Sofer
- Harvard Medical School and Harvard T.H. Chan School of Public Health
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Kachroo P, Stewart ID, Kelly RS, Stav M, Mendez K, Dahlin A, Soeteman DI, Chu SH, Huang M, Cote M, Knihtilä HM, Lee-Sarwar K, McGeachie M, Wang A, Wu AC, Virkud Y, Zhang P, Wareham NJ, Karlson EW, Wheelock CE, Clish C, Weiss ST, Langenberg C, Lasky-Su JA. Metabolomic profiling reveals extensive adrenal suppression due to inhaled corticosteroid therapy in asthma. Nat Med 2022; 28:814-822. [PMID: 35314841 PMCID: PMC9350737 DOI: 10.1038/s41591-022-01714-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
The application of large-scale metabolomic profiling provides new opportunities for realizing the potential of omics-based precision medicine for asthma. By leveraging data from over 14,000 individuals in four distinct cohorts, this study identifies and independently replicates 17 steroid metabolites whose levels were significantly reduced in individuals with prevalent asthma. Although steroid levels were reduced among all asthma cases regardless of medication use, the largest reductions were associated with inhaled corticosteroid (ICS) treatment, as confirmed in a 4-year low-dose ICS clinical trial. Effects of ICS treatment on steroid levels were dose dependent; however, significant reductions also occurred with low-dose ICS treatment. Using information from electronic medical records, we found that cortisol levels were substantially reduced throughout the entire 24-hour daily period in patients with asthma who were treated with ICS compared to those who were untreated and to patients without asthma. Moreover, patients with asthma who were treated with ICS showed significant increases in fatigue and anemia as compared to those without ICS treatment. Adrenal suppression in patients with asthma treated with ICS might, therefore, represent a larger public health problem than previously recognized. Regular cortisol monitoring of patients with asthma treated with ICS is needed to provide the optimal balance between minimizing adverse effects of adrenal suppression while capitalizing on the established benefits of ICS treatment.
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Affiliation(s)
- Priyadarshini Kachroo
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Rachel S Kelly
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meryl Stav
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Mendez
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amber Dahlin
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Djøra I Soeteman
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Health Decision Science, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Su H Chu
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mengna Huang
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Margaret Cote
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanna M Knihtilä
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathleen Lee-Sarwar
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael McGeachie
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alberta Wang
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ann Chen Wu
- Harvard Pilgrim Health Care Institute and Department of Population Medicine, Harvard Medical School, Boston, MA, USA
| | - Yamini Virkud
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pei Zhang
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry 2, Karolinska Institute, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Department of Medicine, Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry 2, Karolinska Institute, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | | | - Scott T Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jessica A Lasky-Su
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Schubert R, Geoffroy E, Gregga I, Mulford AJ, Aguet F, Ardlie K, Gerszten R, Clish C, Van Den Berg D, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy R, Conomos M, Blackwell T, Papanicolaou G, Lappalainen T, Mikhaylova AV, Thornton TA, Cho MH, Gignoux CR, Lange L, Lange E, Rich SS, Rotter JI, Manichaikul A, Im HK, Wheeler HE. Protein prediction for trait mapping in diverse populations. PLoS One 2022; 17:e0264341. [PMID: 35202437 PMCID: PMC8870552 DOI: 10.1371/journal.pone.0264341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. Here, we used the Trans-omics for Precision Medicine (TOPMed) Multi-omics pilot study, which comprises data from Multi-Ethnic Study of Atherosclerosis (MESA), to optimize genetic predictors of the plasma proteome for genetically regulated proteome-wide association studies (PWAS) in diverse populations. We built predictive models for protein abundances using data collected in TOPMed MESA, for which we have measured 1,305 proteins by a SOMAscan assay. We compared predictive models built via elastic net regression to models integrating posterior inclusion probabilities estimated by fine-mapping SNPs prior to elastic net. In order to investigate the transferability of predictive models across ancestries, we built protein prediction models in all four of the TOPMed MESA populations, African American (n = 183), Chinese (n = 71), European (n = 416), and Hispanic/Latino (n = 301), as well as in all populations combined. As expected, fine-mapping produced more significant protein prediction models, especially in African ancestries populations, potentially increasing opportunity for discovery. When we tested our TOPMed MESA models in the independent European INTERVAL study, fine-mapping improved cross-ancestries prediction for some proteins. Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. At current training population sample sizes, performance between baseline and fine-mapped protein prediction models in PWAS was similar, highlighting the utility of elastic net. Our predictive models in diverse populations are publicly available for use in proteome mapping methods at https://doi.org/10.5281/zenodo.4837327.
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Affiliation(s)
- Ryan Schubert
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Elyse Geoffroy
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Isabelle Gregga
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ashley J. Mulford
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Francois Aguet
- Broad Institute, Cambridge, MA, United States of America
| | - Kristin Ardlie
- Broad Institute, Cambridge, MA, United States of America
| | - Robert Gerszten
- Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Clary Clish
- Broad Institute, Cambridge, MA, United States of America
| | - David Van Den Berg
- University of Southern California, Los Angeles, CA, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, United States of America
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Russell Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Matthew Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Tom Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, United States of America
| | - Tuuli Lappalainen
- New York Genome Center and Department of Systems Biology, Columbia University, New York, NY United States of America
| | - Anna V. Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Heather E. Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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El Zarif T, Adib E, Clish C, Shukla SA, Freeman D, Thomas J, Ravi P, Tuff M, McGregor BA, Mantia C, Ravi A, Sonpavde GP. Comprehensive metabolomic profiling of plasma from patients (pts) with metastatic urothelial carcinoma (mUC) receiving immune checkpoint inhibitors (ICI) or platinum-based chemotherapy (PBC). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
565 Background: Metabolomic profiling of plasma from mUC pts has not been comprehensively examined. Plasma metabolomics may capture the effects of interactions between the malignancy, host and therapy. We hypothesized that Identifying metabolites in plasma from patients with mUC receiving an ICI or PBC may shed valuable insights regarding tumor biology and mechanisms of resistance. Methods: We obtained 0.2 ml plasma before and after starting therapy from pts with mUC receiving an ICI or PBC at the Dana-Farber Cancer Institute. Plasma metabolomic profiling was conducted at the Broad Institute using 3 complementary liquid chromatography tandem mass spectrometry (LC-MS)-based metabolomics platforms. We measured 648 metabolites at baseline prior to starting ICI/PBC and at a second time point in each subject following initiation of ICI/PBC. Metabolite levels were assumed to be normally distributed with log transformation to transform distributions to be approximately symmetric. We performed Wilcoxon-rank sum test to compare the levels of metabolites before and after initiation of the ICI or PBC (significance at p < 0.05). Results: Plasma was available at baseline and during therapy in 53 mUC pts (ICI: n = 43; PBC: n = 10). The median age was 68 (range: 39-86) years and 42 (82.3%) were male. The median time from baseline to the second time point was 4.7 months (range: 0.7-90.2). The ICIs administered were atezolizumab (n = 20), pembrolizumab (n = 16), nivolumab (n = 5), and durvalumab + tremelimumab (n = 1). We identified 20 metabolites that were significantly increased in post-PBC plasma samples (vs. pre-PBC) and 19 metabolites increased in post-ICI (vs. pre-ICI) samples (p < 0.05). All altered metabolites except one (Uracil) were exclusive for each treatment group. The most significant metabolites that increased following initiation of the ICI and PBC are shown in the Table. Evaluation of the association of plasma metabolomics with clinical outcomes and toxicities is ongoing. Conclusions: This is the first report, to our knowledge, of comprehensive metabolomic plasma profiling of pre- and post-ICI and PBC pts with mUC. The metabolomic changes after ICI appear distinct from those seen after PBC. Furthermore, our study sheds insights on potential mechanisms of resistance and new therapeutic targets in pts with mUC.[Table: see text]
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Affiliation(s)
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Jonathan Thomas
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | | | | | | | | | | | - Guru P. Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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Wittenbecher C, Guasch-Ferré M, Haslam DE, Dennis C, Li J, Bhupathiraju SN, Lee CH, Qi Q, Liang L, Eliassen AH, Clish C, Sun Q, Hu FB. Changes in metabolomics profiles over ten years and subsequent risk of developing type 2 diabetes: Results from the Nurses' Health Study. EBioMedicine 2021; 75:103799. [PMID: 34979341 PMCID: PMC8733263 DOI: 10.1016/j.ebiom.2021.103799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Metabolomics profiles were consistently associated with type 2 diabetes (T2D) risk, but evidence on long-term metabolite changes and T2D incidence is lacking. We examined the associations of 10-year plasma metabolite changes with subsequent T2D risk. METHODS We conducted a nested T2D case-control study (n=244 cases, n=244 matched controls) within the Nurses' Health Study. Repeated metabolomics profiling (170 targeted metabolites) was conducted in participant blood specimens from 1989/1990 and 2000/2001, and T2D occurred between 2002 and 2008. We related 10-year metabolite changes (Δ-values) to subsequent T2D risk using conditional logistic models, adjusting for baseline metabolite levels and baseline levels and concurrent changes of BMI, diet quality, physical activity, and smoking status. FINDINGS The 10-year changes of thirty-one metabolites were associated with subsequent T2D risk (false discovery rate-adjusted p-values [FDR]<0.05). The top three high T2D risk-associated 10-year changes were (odds ratio [OR] per standard deviation [SD], 95%CI): Δisoleucine (2.72, 1.97-3.79), Δleucine (2.53, 1.86-3.47), and Δvaline (1.93, 1.52-2.44); other high-risk-associated metabolite changes included alanine, tri-/diacylglycerol-fragments, short-chain acylcarnitines, phosphatidylethanolamines, some vitamins, and bile acids (ORs per SD between 1.31and 1.82). The top three low T2D risk-associated 10-year metabolite changes were (OR per SD, 95% CI): ΔN-acetylaspartic acid (0.54, 0.42-0.70), ΔC20:0 lysophosphatidylethanolamine (0.68, 0.56-0.82), and ΔC16:1 sphingomyelin (0.68, 0.56-0.83); 10-year changes of other sphingomyelins, plasmalogens, glutamine, and glycine were also associated with lower subsequent T2D risk (ORs per SD between 0.66 and 0.78). INTERPRETATION Repeated metabolomics profiles reflecting the long-term deterioration of amino acid and lipid metabolism are associated with subsequent risk of T2D.
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Affiliation(s)
- Clemens Wittenbecher
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam Rehbruecke, Nuthetal, Germany,German Center for Diabetes Research (DZD), Neuherberg, Germany,Corresponding authors at: Department of Nutrition, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA
| | - Danielle E. Haslam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA
| | | | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shilpa N. Bhupathiraju
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA
| | - Chih-Hao Lee
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qibin Qi
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Liming Liang
- 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, MA, USA
| | - A. Heather Eliassen
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qi Sun
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Corresponding authors at: Department of Nutrition, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
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Bulló M, Papandreou C, García-Gavilán J, Ruiz-Canela M, Li J, Guasch-Ferré M, Toledo E, Clish C, Corella D, Estruch R, Ros E, Fitó M, Lee CH, Pierce K, Razquin C, Arós F, Serra-Majem L, Liang L, Martínez-González MA, Hu FB, Salas-Salvadó J. Tricarboxylic acid cycle related-metabolites and risk of atrial fibrillation and heart failure. Metabolism 2021; 125:154915. [PMID: 34678258 PMCID: PMC9206868 DOI: 10.1016/j.metabol.2021.154915] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/28/2021] [Accepted: 10/14/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Tricarboxylic acid (TCA) cycle deregulation may predispose to cardiovascular diseases, but the role of TCA cycle-related metabolites in the development of atrial fibrillation (AF) and heart failure (HF) remains unexplored. This study sought to investigate the association of TCA cycle-related metabolites with risk of AF and HF. METHODS We used two nested case-control studies within the PREDIMED study. During a mean follow-up for about 10 years, 512 AF and 334 HF incident cases matched by age (±5 years), sex and recruitment center to 616 controls and 433 controls, respectively, were included in this study. Baseline plasma levels of citrate, aconitate, isocitrate, succinate, malate and d/l-2-hydroxyglutarate were measured with liquid chromatography-tandem mass spectrometry. Multivariable conditional logistic regression models were fitted to estimate odds ratios (OR) and 95% confidence intervals (95% CI) for metabolites and the risk of AF or HF. Potential confounders included smoking, family history of premature coronary heart disease, physical activity, alcohol intake, body mass index, intervention groups, dyslipidemia, hypertension, type 2 diabetes and medication use. RESULTS Comparing extreme quartiles of metabolites, elevated levels of succinate, malate, citrate and d/l-2-hydroxyglutarate were associated with a higher risk of AF [ORQ4 vs. Q1 (95% CI): 1.80 (1.21-2.67), 2.13 (1.45-3.13), 1.87 (1.25-2.81) and 1.95 (1.31-2.90), respectively]. One SD increase in aconitate was directly associated with AF risk [OR (95% CI): 1.16 (1.01-1.34)]. The corresponding ORs (95% CI) for HF comparing extreme quartiles of malate, aconitate, isocitrate and d/l-2-hydroxyglutarate were 2.15 (1.29-3.56), 2.16 (1.25-3.72), 2.63 (1.56-4.44) and 1.82 (1.10-3.04), respectively. These associations were confirmed in an internal validation, except for aconitate and AF. CONCLUSION These findings underscore the potential role of the TCA cycle in the pathogenesis of cardiac outcomes.
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Affiliation(s)
- Mònica Bulló
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Christopher Papandreou
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Jesus García-Gavilán
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Miguel Ruiz-Canela
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA
| | - Estefanía Toledo
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain
| | - Clary Clish
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Ramon Estruch
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Internal Medicine, Department of Endocrinology and Nutrition Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Emilio Ros
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Lipid Clinic, Department of Endocrinology and Nutrition Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Montserrat Fitó
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Cardiovascular and Nutrition Research Group, Institut de Recerca Hospital del Mar, Barcelona, Spain
| | - Chih-Hao Lee
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Molecular Metabolism (C.-H.L.), Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kerry Pierce
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Cristina Razquin
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain
| | - Fernando Arós
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Cardiology, University Hospital of Alava, Vitoria, Spain
| | - Lluís Serra-Majem
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Institute of Health Sciences IUNICS, University of Balearic Islands and Hospital Son Espases, Palma de Mallorca, Spain
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Statistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Miguel A Martínez-González
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Statistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jordi Salas-Salvadó
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain.
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Ferraro G, Ali A, Luengo A, Deik A, Abbott K, Bezwada D, Blanc L, Prideaux B, Jin X, Posada J, Amoozgar Z, Ferreira R, Chen I, Naxerova K, Ng C, Westermark A, Davidson S, Fukumura D, Dartois V, Clish C, Heiden MV, Jain R. TAMI-05. FATTY ACID SYNTHESIS IS REQUIRED FOR HER2+ BREAST CANCER BRAIN METASTASIS. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Brain metastases are refractory to therapies that control systemic disease in patients with human epidermal growth factor receptor 2-positive breast cancer and the brain microenvironment contributes to this therapy resistance. Nutrient availability can vary across tissues, therefore metabolic adaptations required for brain metastatic breast cancer growth may introduce liabilities that can be exploited for therapy. Here we assessed how metabolism differs between breast tumors in brain versus extracranial sites and found that fatty acid synthesis is elevated in breast tumors growing in the brain. We determine that this phenotype is an adaptation to decreased lipid availability in the brain relative to other tissues, resulting in site-specific dependency on fatty acid synthesis for breast tumors growing at this site. Genetic or pharmacological inhibition of fatty acid synthase reduces human epidermal growth factor receptor 2-positive breast tumor growth in the brain, demonstrating that differences in nutrient availability across metastatic sites can result in targetable metabolic dependencies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xin Jin
- Broad Institute, Cambridge, USA
| | | | | | | | - Ivy Chen
- Harvard Medical School / MIT, Boston, USA
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Molsberry S, Bjornevik K, Hughes KC, Zhang ZJ, Jeanfavre S, Clish C, Healy B, Schwarzschild M, Ascherio A. Plasma Metabolomic Markers of Insulin Resistance and Diabetes and Rate of Incident Parkinson's Disease. J Parkinsons Dis 2021; 10:1011-1021. [PMID: 32250318 DOI: 10.3233/jpd-191896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Although there is evidence of shared dysregulated pathways between diabetes and Parkinson's disease, epidemiologic research on an association between the two diseases has produced inconsistent results. OBJECTIVE We aimed to assess whether known metabolomic markers of insulin resistance and diabetes are also associated with Parkinson's disease development. METHODS We conducted a nested case-control study among Nurses' Health Study and Health Professionals Follow-up Study participants who had provided blood samples up to twenty years prior to Parkinson's diagnosis. Cases were matched to risk-set sampled controls by age, sex, fasting status, and time of blood collection. Participants provided covariate information via regularly collected cohort questionnaires. We used conditional logistic regression models to assess whether plasma levels of branched chain amino acids, acylcarnitines, glutamate, or glutamine were associated with incident development of Parkinson's disease. RESULTS A total of 349 case-control pairs were included in this analysis. In the primary analyses, none of the metabolites of interest were associated with Parkinson's disease development. In investigations of the association between each metabolite and Parkinson's disease at different time intervals prior to diagnosis, some metabolites showed marginally significant association but, after correction for multiple testing, only C18 : 2 acylcarnitine was significantly associated with Parkinson's disease among subjects for whom blood was collected less than 60 months prior to case diagnosis. CONCLUSIONS Plasma levels of diabetes-related metabolites did not contribute to predict risk of Parkinson's disease. Further investigation of the relationship between pre-diagnostic levels of diabetes-related metabolites and Parkinson's disease in other populations is needed to confirm these findings.
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Affiliation(s)
- Samantha Molsberry
- Population Health Sciences Program, Harvard University, Cambridge, MA, USA
| | - Kjetil Bjornevik
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Katherine C Hughes
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhongli Joel Zhang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sarah Jeanfavre
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Clary Clish
- Metabolomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Brian Healy
- Partners Multiple Sclerosis Center, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Alberto Ascherio
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Wagner A, Wang C, Fessler J, DeTomaso D, Avila-Pacheco J, Kaminski J, Zaghouani S, Christian E, Thakore P, Schellhaass B, Akama-Garren E, Pierce K, Singh V, Ron-Harel N, Douglas VP, Bod L, Schnell A, Puleston D, Sobel RA, Haigis M, Pearce EL, Soleimani M, Clish C, Regev A, Kuchroo VK, Yosef N. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity. Cell 2021; 184:4168-4185.e21. [PMID: 34216539 PMCID: PMC8621950 DOI: 10.1016/j.cell.2021.05.045] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/15/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Metabolism is a major regulator of immune cell function, but it remains difficult to study the metabolic status of individual cells. Here, we present Compass, an algorithm to characterize cellular metabolic states based on single-cell RNA sequencing and flux balance analysis. We applied Compass to associate metabolic states with T helper 17 (Th17) functional variability (pathogenic potential) and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known Th17/regulatory T cell (Treg) differences, which we validated by metabolic assays. Compass also predicted that Th17 pathogenicity was associated with arginine and downstream polyamine metabolism. Indeed, polyamine-related enzyme expression was enhanced in pathogenic Th17 and suppressed in Treg cells. Chemical and genetic perturbation of polyamine metabolism inhibited Th17 cytokines, promoted Foxp3 expression, and remodeled the transcriptome and epigenome of Th17 cells toward a Treg-like state. In vivo perturbations of the polyamine pathway altered the phenotype of encephalitogenic T cells and attenuated tissue inflammation in CNS autoimmunity.
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Affiliation(s)
- Allon Wagner
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chao Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Johannes Fessler
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David DeTomaso
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - James Kaminski
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah Zaghouani
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elena Christian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Brandon Schellhaass
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elliot Akama-Garren
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kerry Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Noga Ron-Harel
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Vivian Paraskevi Douglas
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Lloyd Bod
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Daniel Puleston
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Raymond A Sobel
- Palo Alto Veteran's Administration Health Care System and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcia Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Manoocher Soleimani
- Department of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87121, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Vijay K Kuchroo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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Oren Y, Tsabar M, Cuoco MS, Amir-Zilberstein L, Cabanos HF, Hütter JC, Hu B, Thakore PI, Tabaka M, Fulco CP, Colgan W, Cuevas BM, Hurvitz SA, Slamon DJ, Deik A, Pierce KA, Clish C, Hata AN, Zaganjor E, Lahav G, Politi K, Brugge JS, Regev A. Cycling cancer persister cells arise from lineages with distinct programs. Nature 2021; 596:576-582. [PMID: 34381210 PMCID: PMC9209846 DOI: 10.1038/s41586-021-03796-6] [Citation(s) in RCA: 194] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure1, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment2. Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.
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Affiliation(s)
- Yaara Oren
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, USA
| | - Michael Tsabar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Systems Biology, Harvard Medical School, Boston, MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Heidie F. Cabanos
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA,Departments of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jan-Christian Hütter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bomiao Hu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Pratiksha I. Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Current address: Bristol Myers Squibb, Cambridge, MA, USA
| | | | - Brandon M. Cuevas
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara A. Hurvitz
- David Geffen School of Medicine, University of California, Los Angeles, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Dennis J. Slamon
- David Geffen School of Medicine, University of California, Los Angeles, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Amy Deik
- Metabolomics Platform, Broad Institute, Cambridge, MA, USA
| | | | - Clary Clish
- Metabolomics Platform, Broad Institute, Cambridge, MA, USA
| | - Aaron N. Hata
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA,Departments of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elma Zaganjor
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Katerina Politi
- Departments of Pathology (Section of Medical Oncology), Yale School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, USA,Ludwig Center at Harvard
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Genentech, South San Francisco, CA, USA.
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Costenbader KH, DiIorio M, Chu SH, Cui J, Sparks JA, Lu B, Moss L, Kelmenson L, Feser M, Edison J, Clish C, Lasky-Su J, Deane KD, Karlson EW. Circulating blood metabolite trajectories and risk of rheumatoid arthritis among military personnel in the Department of Defense Biorepository. Ann Rheum Dis 2021; 80:989-996. [PMID: 33753325 PMCID: PMC8455711 DOI: 10.1136/annrheumdis-2020-219682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 01/14/2023]
Abstract
OBJECTIVES We sought to identify metabolic changes potentially related to rheumatoid arthritis (RA) pathogenesis occurring in the blood prior to its diagnosis. METHODS In a US military biorepository, serum samples collected at two timepoints prior to a diagnosis of RA were identified. These were matched to controls who did not develop RA by subject age, race and time between sample collections and RA diagnosis time to stored serum samples. Relative abundances of 380 metabolites were measured using liquid chromatography-tandem mass spectrometry. We determined whether pre-RA case versus control status predicted metabolite concentration differences and differences over time (trajectories) using linear mixed models, assessing for interactions between time, pre-RA status and metabolite concentrations. We separately examined pre-RA and pre-seropositive RA cases versus matched controls and adjusted for smoking. Multiple comparison adjustment set the false discovery rate to 0.05. RESULTS 291 pre-RA cases (80.8% pre seropositive RA) were matched to 292 controls, all with two serum samples (2.7±1.6 years; 1.0±0.9 years before RA/matched date). 52.0% were women; 52.8% were White, 26.8% Black and 20.4% other race. Mean age was 31.2 (±8.1) years at earliest blood draw. Fourteen metabolites had statistically significant trajectory differences among pre-RA subjects versus controls, including sex steroids, amino acid/lipid metabolism and xenobiotics. Results were similar when limited to pre seropositive RA and after adjusting for smoking. CONCLUSIONS In this military case-control study, metabolite concentration trajectory differences in pre-RA cases versus controls implicated steroidogenesis, lipid/amino acid metabolism and xenobiotics in RA pathogenesis. Metabolites may have potential as biomarkers and/or therapeutic targets preceding RA diagnosis.
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Affiliation(s)
- Karen H Costenbader
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA .,Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael DiIorio
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Su H Chu
- Channing Department of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jing Cui
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Bing Lu
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | - Marie Feser
- University of Colorado, Aurora, Colorado, USA
| | - Jess Edison
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Clary Clish
- Metabolomics Group, Broad Institute, Cambridge, Massachusetts, USA
| | - Jessica Lasky-Su
- Channing Department of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Kevin D Deane
- Division of Rheumatology, Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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45
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Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe 2021; 29:1294-1304.e4. [PMID: 34297922 DOI: 10.1016/j.chom.2021.06.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022]
Abstract
The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/β-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.
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Affiliation(s)
- Jonathan Wei Jie Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore University Medical Center, 5 Lower Kent Ridge Rd, Singapore 119074, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), 14 Medical Drive, MD6-Centre for Translational Medicine, Singapore 117599, Singapore
| | - Damian Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nynke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Helena Lau
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sara M Gregory
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - William Tan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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46
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Papandreou C, Bulló M, Hernández-Alonso P, Ruiz-Canela M, Li J, Guasch-Ferré M, Toledo E, Clish C, Corella D, Estruch R, Ros E, Fitó M, Alonso-Gómez A, Fiol M, Santos-Lozano JM, Serra-Majem L, Liang L, Martínez-González MA, Hu FB, Salas-Salvadó J. Choline Metabolism and Risk of Atrial Fibrillation and Heart Failure in the PREDIMED Study. Clin Chem 2021; 67:288-297. [PMID: 33257943 DOI: 10.1093/clinchem/hvaa224] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Few studies have examined the associations of trimethylamine-N-oxide (TMAO) and its precursors (choline, betaine, dimethylglycine, and L-carnitine) with the risk of atrial fibrillation (AF) and heart failure (HF). This study sought to investigate these associations. METHODS Prospective associations of these metabolites with incident AF and HF were examined among participants at high cardiovascular risk in the PREDIMED study (PREvención con DIeta MEDiterránea) after follow-up for about 10 years. Two nested case-control studies were conducted, including 509 AF incident cases matched to 618 controls and 326 HF incident cases matched to 426 controls. Plasma levels of TMAO and its precursors were semi-quantitatively profiled with liquid chromatography tandem mass spectrometry. Odds ratios were estimated with multivariable conditional logistic regression models. RESULTS After adjustment for classical risk factors and accounting for multiple testing, participants in the highest quartile vs. the lowest quartile of baseline choline and betaine levels had a higher risk of AF [OR (95% CI): 1.85 (1.30-2.63) and 1.57 (1.09-2.24), respectively]. The corresponding OR for AF for extreme quartiles of dimethylglycine was 1.39 (0.99-1.96). One SD increase in log-transformed dimethylglycine was positively associated with AF risk (OR, 1.17; 1.03-1.33). The corresponding ORs for HF for extreme quartiles of choline, betaine, and dimethylglycine were 2.51 (1.57-4.03), 1.65 (1.00-2.71) and 1.65 (1.04-2.61), respectively. TMAO and L-carnitine levels were not associated with AF or HF. CONCLUSIONS Our findings support the role of the choline metabolic pathway in the pathogenesis of AF and HF.
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Affiliation(s)
- Christopher Papandreou
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Mònica Bulló
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Pablo Hernández-Alonso
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
| | - Miguel Ruiz-Canela
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA.,Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Estefanía Toledo
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain
| | - Clary Clish
- Broad Institute of MIT and Harvard University, Cambridge, MA
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Ramon Estruch
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Department of Internal Medicine, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Emilio Ros
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Lipid Clinic, Department of Endocrinology and Nutrition, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Montserrat Fitó
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Cardiovascular and Nutrition Research Group, Institut de Recerca Hospital del Mar, Barcelona, Spain
| | - Angel Alonso-Gómez
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Bioaraba Health Research Institute, Osakidetza Basque Health Service, Araba University Hospital, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miquel Fiol
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Institute of Health Sciences IUNICS, University of Balearic Islands and Hospital Son Espases, Palma de Mallorca, Spain
| | - José M Santos-Lozano
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Department of Family Medicine, Distrito Sanitario Atención Primaria Sevilla, San Pablo Health Center, Sevilla, Spain
| | - Lluís Serra-Majem
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,Research Institute of Biomedical and Health Sciences IUIBS, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Liming Liang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Miguel A Martínez-González
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University of Navarra, Department of Preventive Medicine and Public Health, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Navarra, Spain.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jordi Salas-Salvadó
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Institut de Salud Carlos III, Madrid, Spain.,University Hospital of Sant Joan de Reus, Nutrition Unit, Reus, Spain
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47
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Wang F, Baden MY, Li J, Guasch-Ferré M, Li Y, Wan Y, Bhupathiraju SN, Tobias DK, Clish C, Mucci LA, Eliassen AH, Costenbader K, Karlson EW, Ascherio A, Rimm EB, Manson JE, Liang L, Hu F. Abstract 022: Plasma Metabolome Related To Plant-based Diets And The Association With Type 2 Diabetes: A Prospective Cohort Study. Circulation 2021. [DOI: 10.1161/circ.143.suppl_1.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Plant-based diets have been associated with a lower risk of type 2 diabetes. However, the underlying mechanisms are not completely understood, and the evidence using objective approaches to assess the adherence of plant-based diets is limited.
Methods:
In the Nurses’ Health Study (NHS), NHSII, and Health Professionals Follow-Up Study, we characterized the plasma metabolome related to plant-based diets and examined its association with the incidence of type 2 diabetes among 10 699 participants. Plasma metabolomic profiling was conducted by liquid chromatography-tandem mass spectrometry. Adherence to plant-based diets was assessed by three plant-based diet indices derived from the food frequency questionnaire: an overall plant-based diet index (PDI), a healthful PDI (hPDI), and an unhealthful PDI (uPDI). Metabolomic signatures reflecting the adherence to plant-based diets were created using elastic net regression, and their associations with risk of type 2 diabetes were subsequently evaluated using multivariable Cox proportional hazards regression.
Results:
Among 263 metabolites measured, nearly half were significantly associated with PDI (41.4%, 109 of 263), hPDI (51.7%, 136 of 263), and uPDI (40.3%, 106 of 263) after Bonferroni correction. We developed a metabolomic signature comprising 53 metabolites for PDI, 76 metabolites for hPDI, and 88 metabolites for uPDI, each robustly correlated with the corresponding diet index (r=0.34-0.36 for PDI, 0.43-0.44 for hPDI, and 0.36-0.37 for uPDI). We observed an inverse association of PDI metabolomic signature (HR 0.86, 95% CI 0.79-0.93 per one standard deviation) and hPDI metabolomic signature (0.79, 0.72-0.86) with type 2 diabetes risk after adjustment for body mass index and other potential confounders. These two inverse associations remained significant even further adjusting for the corresponding diet index PDI and hPDI. The metabolomic signature for uPDI was not associated with type 2 diabetes risk (1.00, 0.93-1.09).
Conclusion:
Plasma metabolome can robustly reflect adherence and metabolic response to plant-based diets. Metabolomic signatures reflecting greater adherence to an overall plant-based diet, especially a healthful plant-based diet, were associated with a lower risk of type 2 diabetes. These findings support and provide mechanistic insights on the important role of healthful plant-based diets in diabetes prevention.
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Affiliation(s)
- Fenglei Wang
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Megu Y Baden
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Jun Li
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | - Yanping Li
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Yi Wan
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - A. H Eliassen
- Brigham and Women’s Hosp and Harvard Med Sch, Boston, MA
| | | | | | | | - Eric B Rimm
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | | | - Liming Liang
- Harvard T.H. Chan Sch of Public Health, Boston, MA
| | - Frank Hu
- Harvard T.H. Chan Sch of Public Health, Boston, MA
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48
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Thaker VV, Deng S, Gorski G, Vedantam S, Clish C, Salem R, Hirschhorn JN. Baseline Metabolomic Profile as Potential Biomarker for Weight Change After Roux-en-Y Gastric Bypass Surgery. J Endocr Soc 2021. [PMCID: PMC8265719 DOI: 10.1210/jendso/bvab048.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Introduction: Weight loss surgery (WLS) has emerged as an effective treatment for severe obesity (BMI ≥ 40 kg/m2 in adults) and Type 2 diabetes (T2D). There is a wide spectrum of long-term response, both in weight change and resolution of T2D after WLS. Younger age at surgery, white race and the extent of weight loss prior to surgery are the known traits associated with favorable outcomes. The aim of this study was to investigate untargeted metabolite profile prior to surgery as a potential biomarker for long-term weight change response to WLS. Methods: Latent class growth mixture modeling (LCGMM) was used to classify the longitudinal weight change trajectories in a cohort of individuals who underwent Roux-en-Y gastric bypass (RYGB). Untargeted metabolite profile was done on a 4-module Liquid Chromatography/ Mass Spectroscopy (LC-MS) platform on the pre-surgery fasting plasma samples from subjects with weight regain or sustained weight loss. Metabolite wide association studies followed by pathway analysis was undertaken using Mummichog and GSEA algorithms. Partial least-square discriminant analysis (PLS-DA), a supervised classification framework used for datasets with thousands of correlated variables and a small number of samples that performs variable selection and classification as a one-step procedure, was used to identify the informative features that defined the two groups. Results: LCGMM identified 3-classes of weight change in a cohort of 1589 subjects who had undergone RYGB – a) typical trajectory with significant weight loss by 12 months with plateau at ~80% weight loss (n= 1357, 85.4%), b) sustained weight loss without plateau (SWL, n=116, 7.3%) c) weight regain (RGN, 116, 7.3%). Samples from 80 subjects each with RGN or SWL (age 42.5 ± 10 years, 55% F, Excess body weight 221 ± 40 lbs) were used for untargeted profiling of 37,570 metabolite features (564 known). After QC and adjusting for age, sex, race and fasting time, 1920 features (37 known) were associated with the weight category at nominal significance (p <0.05). Amongst the known metabolites, the pathways represented in RGN were amino acid metabolism, branched chain and other essential amino acids that have been previously identified as markers of insulin resistance and T2D, while those with SWL were from sphingolipid metabolism. Dimethylguanidino valeric acid, a marker of liver fat and predictor of T2D was higher in individuals with SWL. Pathway analysis of the known and unknown metabolites together revealed pathways in urea cycle, pyrimidine, glutamate, essential amino acids, and butyrate metabolism. Features identified by PLS-DA overlapped with these pathways. Conclusions: Untargeted baseline metabolites may serve as predictive biomarkers for weight change after RYGB. Future work will focus on developing a metabolite risk score and replication in other cohorts.
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Affiliation(s)
| | | | | | | | | | - Rany Salem
- University of California at San Diego, San Diego, CA, USA
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49
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Rebholz CM, Gao Y, Talegawkar S, Tucker KL, Colantonio LD, Muntner P, Ngo D, Chen ZZ, Cruz D, Katz D, Tahir UA, Clish C, Gerszten RE, Wilson JG. Metabolomic Markers of Southern Dietary Patterns in the Jackson Heart Study. Mol Nutr Food Res 2021; 65:e2000796. [PMID: 33629508 PMCID: PMC8192080 DOI: 10.1002/mnfr.202000796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/07/2021] [Indexed: 02/02/2023]
Abstract
SCOPE New biomarkers are needed that are representative of dietary intake. METHODS AND RESULTS We assess metabolites associated with Southern dietary patterns in 1401 Jackson Heart Study participants. Three dietary patterns are empirically derived using principal component analysis: meat and fast food, fish and vegetables, and starchy foods. We randomly select two subsets of the study population: two-third sample for discovery (n = 934) and one-third sample for replication (n = 467). Among the 327 metabolites analyzed, 14 are significantly associated with the meat and fast food dietary pattern, four are significantly associated with the fish and vegetables dietary pattern, and none are associated with the starchy foods dietary pattern in the discovery sample. In the replication sample, nine remain associated with the meat and fast food dietary pattern [indole-3-propanoic acid, C24:0 lysophosphatidylcholine (LPC), N-methyl proline, proline betaine, C34:2 phosphatidylethanolamine (PE) plasmalogen, C36:5 PE plasmalogen, C38:5 PE plasmalogen, cotinine, hydroxyproline] and three remain associated with the fish and vegetables dietary pattern [1,7-dimethyluric acid, C22:6 lysophosphatidylethanolamine, docosahexaenoic acid (DHA)]. CONCLUSION Twelve metabolites are discovered and replicated in association with dietary patterns detected in a Southern U.S. African-American population, which could be useful as biomarkers of Southern dietary patterns.
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Affiliation(s)
- Casey M. Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Yan Gao
- The Jackson Heart Study, University of Mississippi Medical Center, Jackson, Mississippi
| | - Sameera Talegawkar
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Katherine L. Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Lisandro D. Colantonio
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Alabama
| | - Paul Muntner
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Alabama
| | - Debby Ngo
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Zsu Zsu Chen
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Daniel Cruz
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Daniel Katz
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Usman A. Tahir
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Robert E. Gerszten
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - James G. Wilson
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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Habra H, Kachman M, Bullock K, Clish C, Evans CR, Karnovsky A. metabCombiner: Paired Untargeted LC-HRMS Metabolomics Feature Matching and Concatenation of Disparately Acquired Data Sets. Anal Chem 2021; 93:5028-5036. [PMID: 33724799 PMCID: PMC9906987 DOI: 10.1021/acs.analchem.0c03693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LC-HRMS experiments detect thousands of compounds, with only a small fraction of them identified in most studies. Traditional data processing pipelines contain an alignment step to assemble the measurements of overlapping features across samples into a unified table. However, data sets acquired under nonidentical conditions are not amenable to this process, mostly due to significant alterations in chromatographic retention times. Alignment of features between disparately acquired LC-MS metabolomics data could aid collaborative compound identification efforts and enable meta-analyses of expanded data sets. Here, we describe metabCombiner, a new computational pipeline for matching known and unknown features in a pair of untargeted LC-MS data sets and concatenating their abundances into a combined table of intersecting feature measurements. metabCombiner groups features by mass-to-charge (m/z) values to generate a search space of possible feature pair alignments, fits a spline through a set of selected retention time ordered pairs, and ranks alignments by m/z, mapped retention time, and relative abundance similarity. We evaluated this workflow on a pair of plasma metabolomics data sets acquired with different gradient elution methods, achieving a mean absolute retention time prediction error of roughly 0.06 min and a weighted per-compound matching accuracy of approximately 90%. We further demonstrate the utility of this method by comprehensively mapping features in urine and muscle metabolomics data sets acquired from different laboratories. metabCombiner has the potential to bridge the gap between otherwise incompatible metabolomics data sets and is available as an R package at https://github.com/hhabra/metabCombiner and Bioconductor.
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Affiliation(s)
- Hani Habra
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Arbor, Michigan 48109, United States
| | - Maureen Kachman
- Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan 48105, United States
| | - Kevin Bullock
- Metabolomics Platform, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Clary Clish
- Metabolomics Platform, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Charles R. Evans
- Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan 48105, United States
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Arbor, Michigan 48109, United States; Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan 48105, United States
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