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Simpson CE, Ledford JG, Liu G. Application of Metabolomics across the Spectrum of Pulmonary and Critical Care Medicine. Am J Respir Cell Mol Biol 2024; 71:1-9. [PMID: 38547373 DOI: 10.1165/rcmb.2024-0080ps] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/28/2024] [Indexed: 07/02/2024] Open
Abstract
In recent years, metabolomics, the systematic study of small-molecule metabolites in biological samples, has yielded fresh insights into the molecular determinants of pulmonary diseases and critical illness. The purpose of this article is to orient the reader to this emerging field by discussing the fundamental tenets underlying metabolomics research, the tools and techniques that serve as foundational methodologies, and the various statistical approaches to analysis of metabolomics datasets. We present several examples of metabolomics applied to pulmonary and critical care medicine to illustrate the potential of this avenue of research to deepen our understanding of pathophysiology. We conclude by reviewing recent advances in the field and future research directions that stand to further the goal of personalizing medicine to improve patient care.
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Affiliation(s)
- Catherine E Simpson
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Julie G Ledford
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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2
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Choudhury P, Dasgupta S, Bhattacharyya P, Roychowdhury S, Chaudhury K. Understanding pulmonary hypertension: the need for an integrative metabolomics and transcriptomics approach. Mol Omics 2024. [PMID: 38853716 DOI: 10.1039/d3mo00266g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Pulmonary hypertension (PH), characterised by mean pulmonary arterial pressure (mPAP) >20 mm Hg at rest, is a complex pathophysiological disorder associated with multiple clinical conditions. The high prevalence of the disease along with increased mortality and morbidity makes it a global health burden. Despite major advances in understanding the disease pathophysiology, much of the underlying complex molecular mechanism remains to be elucidated. Lack of a robust diagnostic test and specific therapeutic targets also poses major challenges. This review provides a comprehensive update on the dysregulated pathways and promising candidate markers identified in PH patients using the transcriptomics and metabolomics approach. The review also highlights the need of using an integrative multi-omics approach for obtaining insight into the disease at a molecular level. The integrative multi-omics/pan-omics approach envisaged to help in bridging the gap from genotype to phenotype is outlined. Finally, the challenges commonly encountered while conducting omics-driven studies are also discussed.
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Affiliation(s)
- Priyanka Choudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
| | - Sanjukta Dasgupta
- Department of Biotechnology, Brainware University, Barasat, West Bengal, India
| | | | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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Bahi M, Li C, Wang G, Korman BD. Systemic Sclerosis-Associated Pulmonary Arterial Hypertension: From Bedside to Bench and Back Again. Int J Mol Sci 2024; 25:4728. [PMID: 38731946 PMCID: PMC11084945 DOI: 10.3390/ijms25094728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024] Open
Abstract
Systemic sclerosis (SSc) is a heterogeneous disease characterized by autoimmunity, vasculopathy, and fibrosis which affects the skin and internal organs. One key aspect of SSc vasculopathy is pulmonary arterial hypertension (SSc-PAH) which represents a leading cause of morbidity and mortality in patients with SSc. The pathogenesis of pulmonary hypertension is complex, with multiple vascular cell types, inflammation, and intracellular signaling pathways contributing to vascular pathology and remodeling. In this review, we focus on shared molecular features of pulmonary hypertension and those which make SSc-PAH a unique entity. We highlight advances in the understanding of the clinical and translational science pertinent to this disease. We first review clinical presentations and phenotypes, pathology, and novel biomarkers, and then highlight relevant animal models, key cellular and molecular pathways in pathogenesis, and explore emerging treatment strategies in SSc-PAH.
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Affiliation(s)
| | | | | | - Benjamin D. Korman
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 695, Rochester, NY 14642, USA; (M.B.)
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Gu C, Bernstein N, Mittal N, Kurnool S, Schwartz H, Loomba R, Malhotra A. Potential Therapeutic Targets in Obesity, Sleep Apnea, Diabetes, and Fatty Liver Disease. J Clin Med 2024; 13:2231. [PMID: 38673503 PMCID: PMC11050527 DOI: 10.3390/jcm13082231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Obesity and metabolic syndrome affect the majority of the US population. Patients with obesity are at increased risk of developing type 2 diabetes (T2DM), obstructive sleep apnea (OSA), and metabolic dysfunction-associated steatotic liver disease (MASLD), each of which carry the risk of further complications if left untreated and lead to adverse outcomes. The rising prevalence of obesity and its comorbidities has led to increased mortality, decreased quality of life, and rising healthcare expenditures. This phenomenon has resulted in the intensive investigation of exciting therapies for obesity over the past decade, including more treatments that are still in the pipeline. In our present report, we aim to solidify the relationships among obesity, T2DM, OSA, and MASLD through a comprehensive review of current research. We also provide an overview of the surgical and pharmacologic treatment classes that target these relationships, namely bariatric surgery, the glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic polypeptide (GIP), and glucagon receptor agonists.
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Affiliation(s)
- Christina Gu
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
| | - Nicole Bernstein
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
| | - Nikita Mittal
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
| | - Soumya Kurnool
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
| | - Hannah Schwartz
- Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA;
| | - Rohit Loomba
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
| | - Atul Malhotra
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA; (N.B.); (N.M.); (S.K.); (R.L.)
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Alotaibi M, Harvey LD, Nichols WC, Pauciulo MW, Hemnes A, Long T, Watrous JD, Begzati A, Tuomilehto J, Havulinna AS, Niiranen TJ, Jousilahti P, Salomaa V, Bertero T, Kim NH, Desai AA, Malhotra A, Yuan JXJ, Cheng S, Chan SY, Jain M. Pulmonary primary oxysterol and bile acid synthesis as a predictor of outcomes in pulmonary arterial hypertension. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576474. [PMID: 38328113 PMCID: PMC10849469 DOI: 10.1101/2024.01.20.576474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a rare and fatal vascular disease with heterogeneous clinical manifestations. To date, molecular determinants underlying the development of PAH and related outcomes remain poorly understood. Herein, we identify pulmonary primary oxysterol and bile acid synthesis (PPOBAS) as a previously unrecognized pathway central to PAH pathophysiology. Mass spectrometry analysis of 2,756 individuals across five independent studies revealed 51 distinct circulating metabolites that predicted PAH-related mortality and were enriched within the PPOBAS pathway. Across independent single-center PAH studies, PPOBAS pathway metabolites were also associated with multiple cardiopulmonary measures of PAH-specific pathophysiology. Furthermore, PPOBAS metabolites were found to be increased in human and rodent PAH lung tissue and specifically produced by pulmonary endothelial cells, consistent with pulmonary origin. Finally, a poly-metabolite risk score comprising 13 PPOBAS molecules was found to not only predict PAH-related mortality but also outperform current clinical risk scores. This work identifies PPOBAS as specifically altered within PAH and establishes needed prognostic biomarkers for guiding therapy in PAH.
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Affiliation(s)
- Mona Alotaibi
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lloyd D. Harvey
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - William C. Nichols
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Michael W. Pauciulo
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Anna Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tao Long
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jeramie D. Watrous
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Arjana Begzati
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | - Teemu J. Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
- Department of Internal Medicine, University of Turku, Turku, Finland
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Nick H. Kim
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ankit A. Desai
- Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jason X.-J. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen Y. Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Bassareo PP, D’Alto M. Metabolomics in Pulmonary Hypertension-A Useful Tool to Provide Insights into the Dark Side of a Tricky Pathology. Int J Mol Sci 2023; 24:13227. [PMID: 37686034 PMCID: PMC10487467 DOI: 10.3390/ijms241713227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Pulmonary hypertension (PH) is a multifaceted illness causing clinical manifestations like dyspnea, fatigue, and cyanosis. If left untreated, it often evolves into irreversible pulmonary arterial hypertension (PAH), leading to death. Metabolomics is a laboratory technique capable of providing insights into the metabolic pathways that are responsible for a number of physiologic or pathologic events through the analysis of a biological fluid (such as blood, urine, and sputum) using proton nuclear magnetic resonance spectroscopy or mass spectrometry. A systematic review was finalized according to the PRISMA scheme, with the goal of providing an overview of the research papers released up to now on the application of metabolomics to PH/PAH. So, eighty-five papers were identified, of which twenty-four concerning PH, and sixty-one regarding PAH. We found that, from a metabolic standpoint, the hallmarks of the disease onset and progression are an increase in glycolysis and impaired mitochondrial respiration. Oxidation is exacerbated as well. Specific metabolic fingerprints allow the characterization of some of the specific PH and PAH subtypes. Overall, metabolomics provides insights into the biological processes happening in the body of a subject suffering from PH/PAH. The disarranged metabolic pathways underpinning the disease may be the target of new therapeutic agents. Metabolomics will allow investigators to make a step forward towards personalized medicine.
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Affiliation(s)
- Pier Paolo Bassareo
- Mater Misercordiae University Hospital, D07 R2WY Dublin, Ireland
- Children’s Health Ireland at Crumlin, D12 N512 Dublin, Ireland
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Michele D’Alto
- Pulmonary Hypertension Unit, Dipartimento di Cardiologia, Università della Campania “Luigi Vanvitelli”, Ospedale Monaldi, 80131 Naples, Italy;
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Alotaibi M, Liu Y, Magalang GA, Kwan AC, Ebinger JE, Nichols WC, Pauciulo MW, Jain M, Cheng S. Deriving Convergent and Divergent Metabolomic Correlates of Pulmonary Arterial Hypertension. Metabolites 2023; 13:802. [PMID: 37512509 PMCID: PMC10386502 DOI: 10.3390/metabo13070802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
High-dimensional metabolomics analyses may identify convergent and divergent markers, potentially representing aligned or orthogonal disease pathways that underly conditions such as pulmonary arterial hypertension (PAH). Using a comprehensive PAH metabolomics dataset, we applied six different conventional and statistical learning techniques to identify analytes associated with key outcomes and compared the results. We found that certain conventional techniques, such as Bonferroni/FDR correction, prioritized metabolites that tended to be highly intercorrelated. Statistical learning techniques generally agreed with conventional techniques on the top-ranked metabolites, but were also more inclusive of different metabolite groups. In particular, conventional methods prioritized sterol and oxylipin metabolites in relation to idiopathic versus non-idiopathic PAH, whereas statistical learning methods tended to prioritize eicosanoid, bile acid, fatty acid, and fatty acyl ester metabolites. Our findings demonstrate how conventional and statistical learning techniques can offer both concordant or discordant results. In the case of a rare yet morbid condition, such as PAH, convergent metabolites may reflect common pathways to shared disease outcomes whereas divergent metabolites could signal either distinct etiologic mechanisms, different sub-phenotypes, or varying stages of disease progression. Notwithstanding the need to investigate the mechanisms underlying the observed results, our main findings suggest that a multi-method approach to statistical analyses of high-dimensional human metabolomics datasets could effectively broaden the scientific yield from a given study design.
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Affiliation(s)
- Mona Alotaibi
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yunxian Liu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gino A. Magalang
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alan C. Kwan
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - William C. Nichols
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael W. Pauciulo
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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