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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; 20:366-389. [PMID: 38853716 DOI: 10.1039/d3mo00266g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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Brownstein AJ, Wilkinson JD, Liang LL, Channick RN, Saggar R, Kim A. Immature reticulocyte fraction: A novel biomarker of hemodynamic severity in pulmonary arterial hypertension. Pulm Circ 2024; 14:e12421. [PMID: 39105130 PMCID: PMC11298897 DOI: 10.1002/pul2.12421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/09/2024] [Accepted: 07/13/2024] [Indexed: 08/07/2024] Open
Abstract
Various erythropoietic abnormalities are highly prevalent among patients with pulmonary arterial hypertension (PAH) and associated with worse disease severity. Given the poorly understood yet important roles of dysregulated erythropoiesis and iron metabolism in PAH, we sought to further characterize the hematologic and iron profiles in PAH and their relationship to PAH severity. We recruited 67 patients with PAH and 13 healthy controls. Hemodynamics attained within 1 year of blood sample collection were available for 36 patients. Multiple hematologic, iron, and inflammatory parameters were evaluated for their association with hemodynamics. The subset with hemodynamic data consisted of 29 females (81%). The most common etiologies were idiopathic PAH (47%) and connective tissue disease-related PAH (33%). 19 (53%) had functional class 3 or 4 symptomatology, and 12 (33%) were on triple pulmonary vasodilator therapy. Immature reticulocyte fraction (IRF) had significant positive correlations with mean pulmonary artery (PA) pressure (mPAP) (0.59, p < 0.001), pulmonary vascular resistance (0.52, p = 0.001), and right atrial pressure (0.46, p = 0.005), and significant negative correlations with cardiac index (-0.43, p = 0.009), PA compliance (PAC) (-0.60, p < 0.001), stroke volume index (SVI) (-0.57, p < 0.001), and mixed venous oxygen saturation (-0.51, p = 0.003). IRF correlated with markers of iron deficiency (ID) and erythropoiesis. On multivariable linear regression, IRF was associated with elevated mPAP and reduced SVI and PAC independent of EPO levels, transferrin saturation, and soluble transferrin receptor levels. We identified IRF as a novel and potent biomarker of PAH hemodynamic severity, possibly related to its associations with erythropoiesis, ID, and tissue hypoxia.
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Affiliation(s)
- Adam J. Brownstein
- Division of Pulmonary and Critical Care MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jared D. Wilkinson
- Advanced Lung Disease and Transplant Program, Inova Heart and Vascular InstituteInova Fairfax HospitalFalls ChurchVirginiaUSA
| | - Lloyd L. Liang
- Division of Pulmonary and Critical Care MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Richard N. Channick
- Division of Pulmonary and Critical Care MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Rajan Saggar
- Division of Pulmonary and Critical Care MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Airie Kim
- Division of Pulmonary and Critical Care MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
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Sanges S, Tian W, Dubucquoi S, Chang JL, Collet A, Launay D, Nicolls MR. B-cells in pulmonary arterial hypertension: friend, foe or bystander? Eur Respir J 2024; 63:2301949. [PMID: 38485150 PMCID: PMC11043614 DOI: 10.1183/13993003.01949-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/01/2024] [Indexed: 04/22/2024]
Abstract
There is an unmet need for new therapeutic strategies that target alternative pathways to improve the prognosis of patients with pulmonary arterial hypertension (PAH). As immunity has been involved in the development and progression of vascular lesions in PAH, we review the potential contribution of B-cells in its pathogenesis and evaluate the relevance of B-cell-targeted therapies. Circulating B-cell homeostasis is altered in PAH patients, with total B-cell lymphopenia, abnormal subset distribution (expansion of naïve and antibody-secreting cells, reduction of memory B-cells) and chronic activation. B-cells are recruited to the lungs through local chemokine secretion, and activated by several mechanisms: 1) interaction with lung vascular autoantigens through cognate B-cell receptors; 2) costimulatory signals provided by T follicular helper cells (interleukin (IL)-21), type 2 T helper cells and mast cells (IL-4, IL-6 and IL-13); and 3) increased survival signals provided by B-cell activating factor pathways. This activity results in the formation of germinal centres within perivascular tertiary lymphoid organs and in the local production of pathogenic autoantibodies that target the pulmonary vasculature and vascular stabilisation factors (including angiotensin-II/endothelin-1 receptors and bone morphogenetic protein receptors). B-cells also mediate their effects through enhanced production of pro-inflammatory cytokines, reduced anti-inflammatory properties by regulatory B-cells, immunoglobulin (Ig)G-induced complement activation, and IgE-induced mast cell activation. Precision-medicine approaches targeting B-cell immunity are a promising direction for select PAH conditions, as suggested by the efficacy of anti-CD20 therapy in experimental models and a trial of rituximab in systemic sclerosis-associated PAH.
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Affiliation(s)
- Sébastien Sanges
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000 Lille, France
- INSERM, F-59000 Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, F-59000 Lille, France
- Centre National de Référence Maladies Auto-immunes Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), F-59000 Lille, France
- Health Care Provider of the European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ReCONNET), F-59000 Lille, France
- Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Both authors contributed equally and share co-first authorship
| | - Wen Tian
- Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Both authors contributed equally and share co-first authorship
| | - Sylvain Dubucquoi
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000 Lille, France
- INSERM, F-59000 Lille, France
- CHU Lille, Institut d'Immunologie, Pôle de Biologie Pathologie Génétique, F-59000 Lille, France
| | - Jason L Chang
- Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Aurore Collet
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000 Lille, France
- INSERM, F-59000 Lille, France
- CHU Lille, Institut d'Immunologie, Pôle de Biologie Pathologie Génétique, F-59000 Lille, France
| | - David Launay
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000 Lille, France
- INSERM, F-59000 Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, F-59000 Lille, France
- Centre National de Référence Maladies Auto-immunes Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), F-59000 Lille, France
- Health Care Provider of the European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ReCONNET), F-59000 Lille, France
- Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Both authors contributed equally and share co-last authorship
| | - Mark R Nicolls
- Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Both authors contributed equally and share co-last authorship
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Goncharova N, Lapshin K, Berezina A, Simakova M, Marichev A, Zlobina I, Marukyan N, Malikov K, Aseeva A, Zaitsev V, Moiseeva O. Elderly Patients with Idiopathic Pulmonary Hypertension: Clinical Characteristics, Survival, and Risk Stratification in a Single-Center Prospective Registry. Life (Basel) 2024; 14:259. [PMID: 38398770 PMCID: PMC10890450 DOI: 10.3390/life14020259] [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: 12/25/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
INTRODUCTION The predictive value of the risk stratification scales in elderly patients with IPAH might differ from that in younger patients. It is unknown whether young and older IPAH patients have the same survival dependence on PAH-specific therapy numbers. The aim of this study was to evaluate the prognostic relevance of risk stratification scales and PAH medication numbers in elderly IPAH patients in comparison with young IPAH patients. MATERIALS AND METHODS A total of 119 patients from a prospective single-center PAH registry were divided into group I < 60 years old (n = 89) and group II ≥ 60 years old (n = 30). ESC/ERS, REVEAL, and REVEAL 2.0 risk stratification scores were assessed at baseline, as well as H2FpEF score and survival at follow-up. RESULTS During a mean follow-up period of 2.9 years (1.63; 6.0), 42 (35.3%) patients died; at 1, 2, 3, 5, 7, and 10 years, survival was 95%, 88.6%, 78.5%, 61.7%, 48.5%, and 33.7%, respectively. No survival differences were observed between the two groups, despite the use of monotherapy in the elderly patients. The best predictive REVEAL value in elderly patients (IPAH patients ≥ 60 years) was AUC 0.73 (0.56-0.91), p = 0.03; and in patients with LHD comorbidities in the entire cohort, it was AUC 0.73 (0.59-0.87), p < 0.009. Factors independently associated with death in the entire cohort were CKD (p = 0.01, HR 0.2), the right-to-left ventricle dimension ratio (p = 0.0047, HR 5.97), and NT-proBNP > 1400 pg/mL (p = 0.008, HR 3.18). CONCLUSION Risk stratification in the elderly IPAH patients requires a fundamentally different approach than that of younger patients, taking into account the initial limitations in physical performance and comorbidities that interfere with current assessment scores. The REVEAL score reliably stratifies patients at any age and LHD comorbidities. The initial monotherapy seems to be reasonable in patients over 60 years. Selection tools for initial combination PAH therapy in older IPAH patients with comorbidities need to be validated in prospective observational studies.
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Affiliation(s)
- Natalia Goncharova
- Almazov National Medical Research Centre, Ministry of Health of Russia, Saint Petersburg 197341, Russia (A.B.); (A.M.); (I.Z.); (N.M.); (K.M.); (A.A.); (V.Z.); (O.M.)
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Kariotis S, Tan PF, Lu H, Rhodes CJ, Wilkins MR, Lawrie A, Wang D. Omada: robust clustering of transcriptomes through multiple testing. Gigascience 2024; 13:giae039. [PMID: 38991852 PMCID: PMC11238428 DOI: 10.1093/gigascience/giae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/09/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cohort studies increasingly collect biosamples for molecular profiling and are observing molecular heterogeneity. High-throughput RNA sequencing is providing large datasets capable of reflecting disease mechanisms. Clustering approaches have produced a number of tools to help dissect complex heterogeneous datasets, but selecting the appropriate method and parameters to perform exploratory clustering analysis of transcriptomic data requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent. To address this, we have developed Omada, a suite of tools aiming to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning-based functions. FINDINGS The efficiency of each tool was tested with 7 datasets characterized by different expression signal strengths to capture a wide spectrum of RNA expression datasets. Our toolkit's decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Within datasets with less clear biological distinctions, our tools either formed stable subgroups with different expression profiles and robust clinical associations or revealed signs of problematic data such as biased measurements. CONCLUSIONS In conclusion, Omada successfully automates the robust unsupervised clustering of transcriptomic data, making advanced analysis accessible and reliable even for those without extensive machine learning expertise. Implementation of Omada is available at http://bioconductor.org/packages/omada/.
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Affiliation(s)
- Sokratis Kariotis
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
| | - Haiping Lu
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
| | - Christopher J Rhodes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Allan Lawrie
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Dennis Wang
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
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Qian J, Chen Y, Yang X, Wang Q, Zhao J, Deng X, Ding Y, Li S, Liu Y, Tian Z, Shen J, Liao Q, Wang Y, Zuo X, Zhang X, Li M, Cui Y, Yu X, Zeng X. Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension. Arthritis Rheumatol 2023; 75:2207-2215. [PMID: 37382296 DOI: 10.1002/art.42641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
OBJECTIVE Pulmonary arterial hypertension (PAH) is a severe complication of systemic lupus erythematosus (SLE). However, the genetic signatures of SLE-associated PAH have not been well studied. We aimed to identify genetic variants implicated in SLE-associated PAH susceptibility within the major histocompatibility complex (MHC) region and assess the contribution to clinical outcomes. METHODS A total of 172 patients with SLE-associated PAH confirmed by right heart catheterization, 1,303 patients with SLE without PAH, and 9,906 healthy controls were included. Deep sequencing of the MHC region was performed to identify alleles, single-nucleotide polymorphisms, and amino acids. We compared patients with SLE-associated PAH with patients with SLE without PAH and healthy controls. Clinical association study was conducted to explore the contribution to phenotypes. RESULTS A total of 19,881 genetic variants were identified within the MHC region. HLA-DQA1*03:02 was identified as a novel genetic variant associated with SLE-associated PAH in the discovery cohort (P = 5.68 × 10-12 ) and authenticated in an independent replication cohort (P = 1.30 × 10-9 ). The strongest associated amino acid position was mapped to HLA-DQα1 in the region affecting MHC/peptide-CD4+ T cell receptor affinity and antigen binding. Clinical association study demonstrated that patients with SLE-associated PAH with HLA-DQA1*03:02 had significantly lower rates of target role achievement (P = 0.005) and survival (P = 0.04). CONCLUSION This study, based on the largest cohort of SLE-associated PAH, is the first to investigate how MHC region genetic variants contribute to SLE-associated PAH susceptibility. HLA-DQA1*03:02 is a novel genetic risk factor and a prognostic factor in SLE-associated PAH. Patients with SLE with this allele require regular monitoring and careful follow-up for early diagnosis and interventions for potential PAH.
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Affiliation(s)
- Junyan Qian
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | | | - Xinzhuang Yang
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Xiaoyue Deng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yufang Ding
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Shengjie Li
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongtai Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Zhuang Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Yanhong Wang
- Department of Epidemiology and Bio-Statistics, Institute of Basic Medical Sciences, China Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xuejun Zhang
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xueqing Yu
- Division of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
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Vraka A, Diamanti E, Kularatne M, Yerly P, Lador F, Aubert JD, Lechartier B. Risk Stratification in Pulmonary Arterial Hypertension, Update and Perspectives. J Clin Med 2023; 12:4349. [PMID: 37445381 DOI: 10.3390/jcm12134349] [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: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Risk stratification in pulmonary arterial hypertension (PAH) is crucial in assessing patient prognosis. It serves a prominent role in everyday patient care and can be determined using several validated risk assessment scores worldwide. The recently published 2022 European Society of Cardiology (ESC)/European Respiratory Society (ERS) guidelines underline the importance of risk stratification not only at baseline but also during follow-up. Achieving a low-risk status has now become the therapeutic goal, emphasising the importance of personalised therapy. The application of these guidelines is also important in determining the timing for lung transplantation referral. In this review, we summarise the most relevant prognostic factors of PAH as well as the parameters used in PAH risk scores and their evolution in the guidelines over the last decade. Finally, we describe the central role that risk stratification plays in the current guidelines not only in European countries but also in Asian countries.
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Affiliation(s)
- Argyro Vraka
- Pulmonary Division, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Eleni Diamanti
- Pulmonary Division, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mithum Kularatne
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Patrick Yerly
- Division of Cardiology, Cardiovascular Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Frédéric Lador
- Pulmonary Division, Geneva University Hospital, 1211 Geneva, Switzerland
| | - John-David Aubert
- Pulmonary Division, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Benoit Lechartier
- Pulmonary Division, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
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8
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Guignabert C, Savale L, Boucly A, Thuillet R, Tu L, Ottaviani M, Rhodes CJ, De Groote P, Prévot G, Bergot E, Bourdin A, Howard LS, Fadel E, Beurnier A, Roche A, Jevnikar M, Jaïs X, Montani D, Wilkins MR, Sitbon O, Humbert M. Serum and Pulmonary Expression Profiles of the Activin Signaling System in Pulmonary Arterial Hypertension. Circulation 2023; 147:1809-1822. [PMID: 37096577 DOI: 10.1161/circulationaha.122.061501] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/04/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Activins are novel therapeutic targets in pulmonary arterial hypertension (PAH). We therefore studied whether key members of the activin pathway could be used as PAH biomarkers. METHODS Serum levels of activin A, activin B, α-subunit of inhibin A and B proteins, and the antagonists follistatin and follistatin-like 3 (FSTL3) were measured in controls and in patients with newly diagnosed idiopathic, heritable, or anorexigen-associated PAH (n=80) at baseline and 3 to 4 months after treatment initiation. The primary outcome was death or lung transplantation. Expression patterns of the inhibin subunits, follistatin, FSTL3, Bambi, Cripto, and the activin receptors type I (ALK), type II (ACTRII), and betaglycan were analyzed in PAH and control lung tissues. RESULTS Death or lung transplantation occurred in 26 of 80 patients (32.5%) over a median follow-up of 69 (interquartile range, 50-81) months. Both baseline (hazard ratio, 1.001 [95% CI, 1.000-1.001]; P=0.037 and 1.263 [95% CI, 1.049-1.520]; P=0.014, respectively) and follow-up (hazard ratio, 1.003 [95% CI, 1.001-1.005]; P=0.001 and 1.365 [95% CI, 1.185-1.573]; P<0.001, respectively) serum levels of activin A and FSTL3 were associated with transplant-free survival in a model adjusted for age and sex. Thresholds determined by receiver operating characteristic analyses were 393 pg/mL for activin A and 16.6 ng/mL for FSTL3. When adjusted with New York Heart Association functional class, 6-minute walk distance, and N-terminal pro-B-type natriuretic peptide, the hazard ratios for transplant-free survival for baseline activin A <393 pg/mL and FSTL3 <16.6 ng/mL were, respectively, 0.14 (95% CI, 0.03-0.61; P=0.009) and 0.17 (95% CI, 0.06-0.45; P<0.001), and for follow-up measures, 0.23 (95% CI, 0.07-0.78; P=0.019) and 0.27 (95% CI, 0.09-0.78, P=0.015), respectively. Prognostic values of activin A and FSTL3 were confirmed in an independent external validation cohort. Histological analyses showed a nuclear accumulation of the phosphorylated form of Smad2/3, higher immunoreactivities for ACTRIIB, ALK2, ALK4, ALK5, ALK7, Cripto, and FSTL3 in vascular endothelial and smooth muscle layers, and lower immunostaining for inhibin-α and follistatin. CONCLUSIONS These findings offer new insights into the activin signaling system in PAH and show that activin A and FSTL3 are prognostic biomarkers for PAH.
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Affiliation(s)
- Christophe Guignabert
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Laurent Savale
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Athénaïs Boucly
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Raphaël Thuillet
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Ly Tu
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Mina Ottaviani
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Christopher J Rhodes
- National Heart and Lung Institute, Imperial College London, United Kingdom (C.J.R., M.R.W.)
| | - Pascal De Groote
- Université de Lille, Service de cardiologie, CHU Lille, Institut Pasteur de Lille, Inserm U1167, France (P.D.G.)
| | - Grégoire Prévot
- CHU de Toulouse, Hôpital Larrey, Service de pneumologie, France (G.P.)
| | - Emmanuel Bergot
- Unicaen, UFR santé, Service de Pneumologie & Oncologie Thoracique, CHU de Caen, France (E.B.)
| | - Arnaud Bourdin
- Université Montpellier, CHU Montpellier, Department of Respiratory Diseases, France (A. Bourdin)
| | - Luke S Howard
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom (L.S.H.)
| | - Elie Fadel
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Department of Thoracic and Vascular Surgery and Heart-Lung Transplantation, Marie Lannelongue Hospital, Groupe Hospitalier Paris Saint-Joseph, Paris-Saclay University, France (E.F.)
| | - Antoine Beurnier
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Anne Roche
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Mitja Jevnikar
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Xavier Jaïs
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - David Montani
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, United Kingdom (C.J.R., M.R.W.)
| | - Olivier Sitbon
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
| | - Marc Humbert
- INSERM UMR_S 999 "Pulmonary Hypertension: Pathophysiology and Novel Therapies," Hôpital Marie Lannelongue, Le Plessis-Robinson, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Université Paris-Saclay, Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Le Kremlin-Bicêtre, France (C.G., L.S., A. Boucly, R.T., L.T., M.O., E.F., A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
- Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, France (L.S., A. Boucly, A. Beurnier, A.R., M.J., X.J., D.M., O.S., M.H.)
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9
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Zhang Z, Wei X. Artificial intelligence-assisted selection and efficacy prediction of antineoplastic strategies for precision cancer therapy. Semin Cancer Biol 2023; 90:57-72. [PMID: 36796530 DOI: 10.1016/j.semcancer.2023.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The rapid development of artificial intelligence (AI) technologies in the context of the vast amount of collectable data obtained from high-throughput sequencing has led to an unprecedented understanding of cancer and accelerated the advent of a new era of clinical oncology with a tone of precision treatment and personalized medicine. However, the gains achieved by a variety of AI models in clinical oncology practice are far from what one would expect, and in particular, there are still many uncertainties in the selection of clinical treatment options that pose significant challenges to the application of AI in clinical oncology. In this review, we summarize emerging approaches, relevant datasets and open-source software of AI and show how to integrate them to address problems from clinical oncology and cancer research. We focus on the principles and procedures for identifying different antitumor strategies with the assistance of AI, including targeted cancer therapy, conventional cancer therapy, and cancer immunotherapy. In addition, we also highlight the current challenges and directions of AI in clinical oncology translation. Overall, we hope this article will provide researchers and clinicians with a deeper understanding of the role and implications of AI in precision cancer therapy, and help AI move more quickly into accepted cancer guidelines.
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Affiliation(s)
- Zhe Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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10
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Benincasa G, Napoli C, Loscalzo J, Maron BA. Pursuing functional biomarkers in complex disease: Focus on pulmonary arterial hypertension. Am Heart J 2023; 258:96-113. [PMID: 36565787 DOI: 10.1016/j.ahj.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 05/11/2023]
Abstract
A major gap in diagnosis, classification, risk stratification, and prediction of therapeutic response exists in pulmonary arterial hypertension (PAH), driven in part by a lack of functional biomarkers that are also disease-specific. In this regard, leveraging big data-omics analyses using innovative approaches that integrate network medicine and machine learning correlated with clinically useful indices or risk stratification scores is an approach well-positioned to advance PAH precision medicine. For example, machine learning applied to a panel of 48 cytokines, chemokines, and growth factors could prognosticate PAH patients with immune-dominant subphenotypes at elevated or low-risk for mortality. Here, we discuss strengths and weaknesses of the most current studies evaluating omics-derived biomarkers in PAH. Progress in this field is offset by studies with small sample size, pervasive limitations in bioinformatics, and lack of standardized methods for data processing and interpretation. Future success in this field, in turn, is likely to hinge on mechanistic validation of data outputs in order to couple functional biomarker data with target-specific therapeutics in clinical practice.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA.
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11
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Hong J, Wong B, Huynh C, Tang B, Ruffenach G, Li M, Umar S, Yang X, Eghbali M. Tm4sf1-marked Endothelial Subpopulation Is Dysregulated in Pulmonary Arterial Hypertension. Am J Respir Cell Mol Biol 2023; 68:381-394. [PMID: 36252184 PMCID: PMC10112423 DOI: 10.1165/rcmb.2022-0020oc] [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: 01/11/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
The identification and role of endothelial progenitor cells in pulmonary arterial hypertension (PAH) remain controversial. Single-cell omics analysis can shed light on endothelial progenitor cells and their potential contribution to PAH pathobiology. We aim to identify endothelial cells that may have stem/progenitor potential in rat lungs and assess their relevance to PAH. Differential expression, gene set enrichment, cell-cell communication, and trajectory reconstruction analyses were performed on lung endothelial cells from single-cell RNA sequencing of Sugen-hypoxia, monocrotaline, and control rats. Relevance to human PAH was assessed in multiple independent blood and lung transcriptomic data sets. Rat lung endothelial cells were visualized by immunofluorescence in situ, analyzed by flow cytometry, and assessed for tubulogenesis in vitro. A subpopulation of endothelial cells (endothelial arterial type 2 [EA2]) marked by Tm4sf1 (transmembrane 4 L six family member 1), a gene strongly implicated in cancer, harbored a distinct transcriptomic signature enriched for angiogenesis and CXCL12 signaling. Trajectory analysis predicted that EA2 has a less differentiated state compared with other endothelial subpopulations. Analysis of independent data sets revealed that TM4SF1 is downregulated in lungs and endothelial cells from patients and PAH models, is a marker for hematopoietic stem cells, and is upregulated in PAH circulation. TM4SF1+CD31+ rat lung endothelial cells were visualized in distal pulmonary arteries, expressed hematopoietic marker CD45, and formed tubules in coculture with lung fibroblasts. Our study uncovered a novel Tm4sf1-marked subpopulation of rat lung endothelial cells that may have stem/progenitor potential and demonstrated its relevance to PAH. Future studies are warranted to further elucidate the role of EA2 and Tm4sf1 in PAH.
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Affiliation(s)
- Jason Hong
- Division of Pulmonary and Critical Care Medicine
| | - Brenda Wong
- Division of Pulmonary and Critical Care Medicine
| | | | - Brian Tang
- Department of Integrative Biology and Physiology, and
| | - Gregoire Ruffenach
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, California
| | - Min Li
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, California
| | - Soban Umar
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, California
| | - Xia Yang
- Department of Integrative Biology and Physiology, and
| | - Mansoureh Eghbali
- Department of Anesthesiology and Perioperative Medicine, University of California, Los Angeles, Los Angeles, California
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12
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Gu S, Goel K, Forbes LM, Kheyfets VO, Yu YRA, Tuder RM, Stenmark KR. Tensions in Taxonomies: Current Understanding and Future Directions in the Pathobiologic Basis and Treatment of Group 1 and Group 3 Pulmonary Hypertension. Compr Physiol 2023; 13:4295-4319. [PMID: 36715285 PMCID: PMC10392122 DOI: 10.1002/cphy.c220010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the over 100 years since the recognition of pulmonary hypertension (PH), immense progress and significant achievements have been made with regard to understanding the pathophysiology of the disease and its treatment. These advances have been mostly in idiopathic pulmonary arterial hypertension (IPAH), which was classified as Group 1 Pulmonary Hypertension (PH) at the Second World Symposia on PH in 1998. However, the pathobiology of PH due to chronic lung disease, classified as Group 3 PH, remains poorly understood and its treatments thus remain limited. We review the history of the classification of the five groups of PH and aim to provide a state-of-the-art review of the understanding of the pathogenesis of Group 1 PH and Group 3 PH including insights gained from novel high-throughput omics technologies that have revealed heterogeneities within these categories as well as similarities between them. Leveraging the substantial gains made in understanding the genomics, epigenomics, proteomics, and metabolomics of PAH to understand the full spectrum of the complex, heterogeneous disease of PH is needed. Multimodal omics data as well as supervised and unbiased machine learning approaches after careful consideration of the powerful advantages as well as of the limitations and pitfalls of these technologies could lead to earlier diagnosis, more precise risk stratification, better predictions of disease response, new sub-phenotype groupings within types of PH, and identification of shared pathways between PAH and other types of PH that could lead to new treatment targets. © 2023 American Physiological Society. Compr Physiol 13:4295-4319, 2023.
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Affiliation(s)
- Sue Gu
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
- Cardiovascular Pulmonary Research Lab, University of Colorado School of Medicine, Colorado, USA
- National Jewish Health, Denver, Colorodo, USA
| | - Khushboo Goel
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
- National Jewish Health, Denver, Colorodo, USA
| | - Lindsay M. Forbes
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
| | - Vitaly O. Kheyfets
- Cardiovascular Pulmonary Research Lab, University of Colorado School of Medicine, Colorado, USA
| | - Yen-rei A. Yu
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
- Cardiovascular Pulmonary Research Lab, University of Colorado School of Medicine, Colorado, USA
| | - Rubin M. Tuder
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
- Program in Translational Lung Research, Department of Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
| | - Kurt R. Stenmark
- Cardiovascular Pulmonary Research Lab, University of Colorado School of Medicine, Colorado, USA
- Department of Pediatrics Section of Critical Care Medicine, University of Colorado Anschutz Medical Campus, Colorado, USA
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13
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Sonny S, Yuan H, Chen S, Duncan MR, Chen P, Benny M, Young K, Park KK, Schmidt AF, Wu S. GSDMD deficiency ameliorates hyperoxia-induced BPD and ROP in neonatal mice. Sci Rep 2023; 13:143. [PMID: 36599874 DOI: 10.1038/s41598-022-27201-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) and retinopathy of prematurity (ROP) are among the most common morbidities affecting extremely premature infants who receive oxygen therapy. Many clinical studies indicate that BPD is associated with advanced ROP. However, the mechanistic link between hyperoxia, BPD, and ROP remains to be explored. Gasdermin D (GSDMD) is a key executor of inflammasome-induced pyroptosis and inflammation. Inhibition of GSDMD has been shown to attenuate hyperoxia-induced BPD and brain injury in neonatal mice. The objective of this study was to further define the mechanistic roles of GSDMD in the pathogenesis of hyperoxia-induced BPD and ROP in mouse models. Here we show that global GSDMD knockout (GSDMD-KO) protects against hyperoxia-induced BPD by reducing macrophage infiltration, improving alveolarization and vascular development, and decreasing cell death. In addition, GSDMD deficiency prevented hyperoxia-induced ROP by reducing vasoobliteration and neovascularization, improving thinning of multiple retinal tissue layers, and decreasing microglial activation. RNA sequencing analyses of lungs and retinas showed that similar genes, including those from inflammatory, cell death, tissue remodeling, and tissue and vascular developmental signaling pathways, were induced by hyperoxia and impacted by GSDMD-KO in both models. These data highlight the importance of GSDMD in the pathogenesis of BPD and ROP and suggest that targeting GSDMD may be beneficial in preventing and treating BPD and ROP in premature infants.
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Affiliation(s)
- Sarah Sonny
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Huijun Yuan
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Shaoyi Chen
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Matthew R Duncan
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Pingping Chen
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Merline Benny
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Karen Young
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Kevin K Park
- Department of Neurological Surgery, The Miami Project to Cure Paralysis, Miami, FL, USA
| | - Augusto F Schmidt
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA
| | - Shu Wu
- Neonatology and Batchelor Children Research Institute, University of Miami Miller School of Medicine, 1580 NW 10thAve, Miami, FL, 33136, USA.
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14
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Wilkins MR. Pulmonary Hypertension: Dissecting a Complex Phenotype. J Am Coll Cardiol 2022; 80:719-721. [PMID: 35953137 DOI: 10.1016/j.jacc.2022.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.
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15
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Carlsen J, Henriksen HH, Marin de Mas I, Johansson PI. An explorative metabolomic analysis of the endothelium in pulmonary hypertension. Sci Rep 2022; 12:13284. [PMID: 35918401 PMCID: PMC9345936 DOI: 10.1038/s41598-022-17374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Pulmonary hypertension (PH) is classified into five clinical diagnostic groups, including group 1 [idiopathic pulmonary arterial hypertension (IPAH) and connective tissue disease-associated PAH (CTD-aPAH)] and group 4 (chronic thromboembolic pulmonary hypertension (CTEPH)). PH is a progressive, life-threatening, incurable disease. The pathological mechanisms underlying PH remain elusive; recent evidence has revealed that abnormal metabolic activities in the endothelium may play a crucial role. This research introduces a novel approach for studying PH endothelial function, building on the genome-scale metabolic reconstruction of the endothelial cell (EC) to investigate intracellular metabolism. We demonstrate that the intracellular metabolic activities of ECs in PH patients cluster into four phenotypes independent of the PH diagnosis. Notably, the disease severity differs significantly between the metabolic phenotypes, suggesting their clinical relevance. The significant metabolic differences between the PH phenotypes indicate that they may require different therapeutic interventions. In addition, diagnostic capabilities enabling their identification is warranted to investigate whether this opens a novel avenue of precision medicine.
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Affiliation(s)
- J Carlsen
- Department of Cardiology, 2141 Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark. .,CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - H H Henriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - I Marin de Mas
- CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - P I Johansson
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,CAG Center for Endotheliomics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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16
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Jones RJ, De Bie EMDD, Groves E, Zalewska KI, Swietlik EM, Treacy CM, Martin JM, Polwarth G, Li W, Guo J, Baxendale HE, Coleman S, Savinykh N, Coghlan JG, Corris PA, Howard LS, Johnson MK, Church C, Kiely DG, Lawrie A, Lordan JL, Mackenzie Ross RV, Pepke Zaba J, Wilkins MR, Wort SJ, Fiorillo E, Orrù V, Cucca F, Rhodes CJ, Gräf S, Morrell NW, McKinney EF, Wallace C, Toshner M. Autoimmunity Is a Significant Feature of Idiopathic Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2022; 206:81-93. [PMID: 35316153 PMCID: PMC7613913 DOI: 10.1164/rccm.202108-1919oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/16/2022] [Indexed: 12/15/2022] Open
Abstract
Rationale: Autoimmunity is believed to play a role in idiopathic pulmonary arterial hypertension (IPAH). It is not clear whether this is causative or a bystander of disease and if it carries any prognostic or treatment significance. Objectives: To study autoimmunity in IPAH using a large cross-sectional cohort. Methods: Assessment of the circulating immune cell phenotype was undertaken using flow cytometry, and the profile of serum immunoglobulins was generated using a standardized multiplex array of 19 clinically validated autoantibodies in 473 cases and 946 control subjects. Additional glutathione S-transferase fusion array and ELISA data were used to identify a serum autoantibody to BMPR2 (bone morphogenetic protein receptor type 2). Clustering analyses and clinical correlations were used to determine associations between immunogenicity and clinical outcomes. Measurements and Main Results: Flow cytometric immune profiling demonstrates that IPAH is associated with an altered humoral immune response in addition to raised IgG3. Multiplexed autoantibodies were significantly raised in IPAH, and clustering demonstrated three distinct clusters: "high autoantibody," "low autoantibody," and a small "intermediate" cluster exhibiting high concentrations of ribonucleic protein complex. The high-autoantibody cluster had worse hemodynamics but improved survival. A small subset of patients demonstrated immunoglobulin reactivity to BMPR2. Conclusions: This study establishes aberrant immune regulation and presence of autoantibodies as key features in the profile of a significant proportion of patients with IPAH and is associated with clinical outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wei Li
- Heart and Lung Research Institute
| | | | | | | | - Natalia Savinykh
- Cambridge Biomedical Research Centre Phenotyping Hub, Department of Medicine, University of Cambridge
| | - J. Gerry Coghlan
- Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | | | | | - Martin K. Johnson
- Scottish Pulmonary Vascular Unit, Golden Jubilee National Hospital, Glasgow, United Kingdom
| | - Colin Church
- Scottish Pulmonary Vascular Unit, Golden Jubilee National Hospital, Glasgow, United Kingdom
| | - David G. Kiely
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Allan Lawrie
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | | | | | | | - Martin R. Wilkins
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | | | - Christopher J. Rhodes
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | | | - Eoin F. McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Chris Wallace
- Heart and Lung Research Institute
- Medical Research Council Biostatistics Unit
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge, United Kingdom
| | - Mark Toshner
- Heart and Lung Research Institute
- Royal Papworth Hospital, and
| | - the UK National Cohort Study of Idiopathic and Heritable PAH Consortium
- Heart and Lung Research Institute
- Cambridge Biomedical Research Centre Phenotyping Hub, Department of Medicine, University of Cambridge
- Royal Papworth Hospital, and
- Medical Research Council Biostatistics Unit
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Royal Free London National Health Service Foundation Trust, London, United Kingdom
- Freeman Hospital, Newcastle-upon-Tyne, United Kingdom
- Hammersmith Hospital, London, United Kingdom
- Scottish Pulmonary Vascular Unit, Golden Jubilee National Hospital, Glasgow, United Kingdom
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Royal United Hospitals Bath National Health Service Foundation Trust, Bath, United Kingdom
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
- Royal Brompton Hospital, London, United Kingdom
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
- University of Sassari, Sassari, Italy; and
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge, United Kingdom
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17
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Deng L, Han X, Wang Z, Nie X, Bian J. The Landscape of Noncoding RNA in Pulmonary Hypertension. Biomolecules 2022; 12:biom12060796. [PMID: 35740920 PMCID: PMC9220981 DOI: 10.3390/biom12060796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/08/2023] Open
Abstract
The transcriptome of pulmonary hypertension (PH) is complex and highly genetically heterogeneous, with noncoding RNA transcripts playing crucial roles. The majority of RNAs in the noncoding transcriptome are long noncoding RNAs (lncRNAs) with less circular RNAs (circRNAs), which are two characteristics gaining increasing attention in the forefront of RNA research field. These noncoding transcripts (especially lncRNAs and circRNAs) exert important regulatory functions in PH and emerge as potential disease biomarkers and therapeutic targets. Recent technological advancements have established great momentum for discovery and functional characterization of ncRNAs, which include broad transcriptome sequencing such as bulk RNA-sequence, single-cell and spatial transcriptomics, and RNA-protein/RNA interactions. In this review, we summarize the current research on the classification, biogenesis, and the biological functions and molecular mechanisms of these noncoding RNAs (ncRNAs) involved in the pulmonary vascular remodeling in PH. Furthermore, we highlight the utility and challenges of using these ncRNAs as biomarkers and therapeutics in PH.
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Affiliation(s)
- Lin Deng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (L.D.); (Z.W.)
| | - Xiaofeng Han
- Department of Diagnostic and Interventional Radiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China;
| | - Ziping Wang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (L.D.); (Z.W.)
| | - Xiaowei Nie
- Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People’s Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, China
- Correspondence: (X.N.); (J.B.)
| | - Jinsong Bian
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (L.D.); (Z.W.)
- Correspondence: (X.N.); (J.B.)
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18
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Singh N, Ventetuolo CE. Prime Time for Proteomics in Pulmonary Arterial Hypertension Risk Assessment? Am J Respir Crit Care Med 2022; 205:988-990. [PMID: 35143371 PMCID: PMC9851471 DOI: 10.1164/rccm.202201-0040ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Navneet Singh
- Division of Pulmonary, Critical Care and Sleep MedicineBrown UniversityProvidence, Rhode Island
| | - Corey E. Ventetuolo
- Division of Pulmonary, Critical Care and Sleep Medicine,Department of Health Services, Policy and PracticeBrown UniversityProvidence, Rhode Island
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19
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Foley A, Steinberg BE, Goldenberg NM. Inflammasome Activation in Pulmonary Arterial Hypertension. Front Med (Lausanne) 2022; 8:826557. [PMID: 35096915 PMCID: PMC8792742 DOI: 10.3389/fmed.2021.826557] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023] Open
Abstract
Inflammasomes are multi-protein complexes that sense both infectious and sterile inflammatory stimuli, launching a cascade of responses to propagate danger signaling throughout an affected tissue. Recent studies have implicated inflammasome activation in a variety of pulmonary diseases, including pulmonary arterial hypertension (PAH). Indeed, the end-products of inflammasome activation, including interleukin (IL)-1β, IL-18, and lytic cell death (“pyroptosis”) are all key biomarkers of PAH, and are potentially therapeutic targets for human disease. This review summarizes current knowledge of inflammasome activation in immune and vascular cells of the lung, with a focus on the role of these pathways in the pathogenesis of PAH. Special emphasis is placed on areas of potential drug development focused on inhibition of inflammasomes and their downstream effectors.
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Affiliation(s)
- Anna Foley
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Benjamin E Steinberg
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
| | - Neil M Goldenberg
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
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