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Ambade AS, Naranjo M, Tuhy T, Yu R, Marimoutou M, Everett AD, Shimoda LA, Zimmerman SL, Cubero Salazar IM, Simpson CE, Tedford RJ, Hsu S, Hassoun PM, Damico RL. Collagen 18A1/Endostatin Expression in the Progression of Right Ventricular Remodeling and Dysfunction in Pulmonary Arterial Hypertension. Am J Respir Cell Mol Biol 2024; 71:343-355. [PMID: 38861354 PMCID: PMC11376241 DOI: 10.1165/rcmb.2024-0039oc] [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: 01/26/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024] Open
Abstract
Numerous studies have demonstrated that endostatin (ES), a potent angiostatic peptide derived from collagen type XVIII α 1 chain and encoded by COL18A1, is elevated in pulmonary arterial hypertension (PAH). It is important to note that elevated ES has consistently been associated with altered hemodynamics, poor functional status, and adverse outcomes in adult and pediatric PAH. This study used serum samples from patients with Group I PAH and plasma and tissue samples derived from the Sugen/hypoxia rat pulmonary hypertension model to define associations between COL18A1/ES and disease development, including hemodynamics, right ventricle (RV) remodeling, and RV dysfunction. Using cardiac magnetic resonance imaging and advanced hemodynamic assessments with pressure-volume loops in patients with PAH to assess RV-pulmonary arterial coupling, we observed a strong relationship between circulating ES levels and metrics of RV structure and function. Specifically, RV mass and the ventricular mass index were positively associated with ES, whereas RV ejection fraction and RV-pulmonary arterial coupling were inversely associated with ES levels. Our animal data demonstrate that the development of pulmonary hypertension is associated with increased COL18A1/ES in the heart as well as the lungs. Disease-associated increases in COL18A1 mRNA and protein were most pronounced in the RV compared with the left ventricle and lung. COL18A1 expression in the RV was strongly associated with disease-associated changes in RV mass, fibrosis, and myocardial capillary density. These findings indicate that COL18A1/ES increases early in disease development in the RV and implicates COL18A1/ES in pathologic RV dysfunction in PAH.
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Affiliation(s)
| | - Mario Naranjo
- Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, Pennsylvania
| | - Tijana Tuhy
- Division of Pulmonary and Critical Care Medicine
| | - Rose Yu
- Division of Pulmonary Medicine, Johns Hopkins Community Physicians, Columbia, Maryland
| | - Mery Marimoutou
- Institute for In Vitro Sciences, Gaithersburg, Maryland; and
| | | | | | | | | | | | - Ryan J Tedford
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Steven Hsu
- Division of Cardiology, Department of Medicine
| | | | - Rachel L Damico
- Division of Pulmonary and Critical Care Medicine
- Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
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Fadilah A, Putri VYS, Puling IMDR, Willyanto SE. Assessing the precision of machine learning for diagnosing pulmonary arterial hypertension: a systematic review and meta-analysis of diagnostic accuracy studies. Front Cardiovasc Med 2024; 11:1422327. [PMID: 39257851 PMCID: PMC11385608 DOI: 10.3389/fcvm.2024.1422327] [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: 04/23/2024] [Accepted: 07/30/2024] [Indexed: 09/12/2024] Open
Abstract
Introduction Pulmonary arterial hypertension (PAH) is a severe cardiovascular condition characterized by pulmonary vascular remodeling, increased resistance to blood flow, and eventual right heart failure. Right heart catheterization (RHC) is the gold standard diagnostic technique, but due to its invasiveness, it poses risks such as vessel and valve injury. In recent years, machine learning (ML) technologies have offered non-invasive alternatives combined with ML for improving the diagnosis of PAH. Objectives The study aimed to evaluate the diagnostic performance of various methods, such as electrocardiography (ECG), echocardiography, blood biomarkers, microRNA, chest x-ray, clinical codes, computed tomography (CT) scan, and magnetic resonance imaging (MRI), combined with ML in diagnosing PAH. Methods The outcomes of interest included sensitivity, specificity, area under the curve (AUC), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). This study employed the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool for quality appraisal and STATA V.12.0 for the meta-analysis. Results A comprehensive search across six databases resulted in 26 articles for examination. Twelve articles were categorized as low-risk, nine as moderate-risk, and five as high-risk. The overall diagnostic performance analysis demonstrated significant findings, with sensitivity at 81% (95% CI = 0.76-0.85, p < 0.001), specificity at 84% (95% CI = 0.77-0.88, p < 0.001), and an AUC of 89% (95% CI = 0.85-0.91). In the subgroup analysis, echocardiography displayed outstanding results, with a sensitivity value of 83% (95% CI = 0.72-0.91), specificity value of 93% (95% CI = 0.89-0.96), PLR value of 12.4 (95% CI = 6.8-22.9), and DOR value of 70 (95% CI = 23-231). ECG demonstrated excellent accuracy performance, with a sensitivity of 82% (95% CI = 0.80-0.84) and a specificity of 82% (95% CI = 0.78-0.84). Moreover, blood biomarkers exhibited the highest NLR value of 0.50 (95% CI = 0.42-0.59). Conclusion The implementation of echocardiography and ECG with ML for diagnosing PAH presents a promising alternative to RHC. This approach shows potential, as it achieves excellent diagnostic parameters, offering hope for more accessible and less invasive diagnostic methods. Systematic Review Registration PROSPERO (CRD42024496569).
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Affiliation(s)
- Akbar Fadilah
- Brawijaya Cardiovascular Research Center, Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
| | - Valerinna Yogibuana Swastika Putri
- Brawijaya Cardiovascular Research Center, Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
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Zheng Y, Jin W, Zheng Z, Zhang K, Jia J, Lei C, Wang W, Zhu P. Prediction of prognosis in patients with systemic sclerosis based on a machine-learning model. Clin Rheumatol 2024; 43:2573-2584. [PMID: 38937388 DOI: 10.1007/s10067-024-07039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/29/2024]
Abstract
OBJECTIVE The clinical manifestations of systemic sclerosis (SSc) are highly variable, resulting in varied outcomes and complications. Diverse fibrosis of the skin and internal organs, vasculopathy, and dysregulated immune system lead to poor and varied prognoses in patients with SSc subtypes. Therefore, this study aimed to develop a personalized tool for predicting the prognosis of patients with SSc. METHODS A cohort of 517 patients with SSc were recruited between January 2009 and November 2021 at Xijing Hospital in China, and 266 patients completed the follow-up and performed in the survival analysis. Risk factors for death were identified using Cox survival analysis and random survival forest-based machine-learning methods separately. The consistency index, area under the curve (AUC), and integrated Brier scores were used to compare the predictive performance of the different prognostic models. RESULTS The results of Cox-based multivariate regression analysis suggested that pulmonary arterial hypertension, digital ulcer, and Modified Rodnan Skin Score (mRSS) were independent risk factors for poor prognosis in patients with SSc and significant risk factors in random survival forest (RSF) surveys. A nomogram was plotted to evaluate the prognostic risk to facilitate clinical assessment; the RSF model had better predictive performance than the Cox model, with 3- and 5-year AUCs of 0.74 and 0.78, respectively. CONCLUSION Machine-learning models can help us better understand the prognosis of patients with SSc and comprehensively evaluate the clinical characteristics of each individual. The early identification of the characteristics of high-risk patients can improve the prognosis of those with SSc. Key Points • Regarding predictive performance, the random survival forest model was more effective than the Cox model and had unique advantages in analyzing nonlinear effects and variable importance. • Machine learning using the simple clinical features of patients with systemic sclerosis (SSc) to predict mortality can guide attending physicians, and the early identification of high-risk patients with SSc and referral to experts will assist rheumatologists in monitoring and management planning.
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Affiliation(s)
- Yan Zheng
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Wei Jin
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Zhaohui Zheng
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Kui Zhang
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Junfeng Jia
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Cong Lei
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Weitao Wang
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China
| | - Ping Zhu
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Shaanxi Province, No. 15 Changle West Road, Xi'an, 710032, People's Republic of China.
- Science Center for Molecular Medicine, National Translational, Xi'an, People's Republic of China.
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Boxhammer E, Paar V, Kopp K, Gharibeh SX, Bovenkamp-Aberger E, Rezar R, Lichtenauer M, Hoppe UC, Mirna M. Insulin-like Growth Factor-Binding Protein 2 in Severe Aortic Valve Stenosis and Pulmonary Hypertension: A Gender-Based Perspective. Int J Mol Sci 2024; 25:8220. [PMID: 39125788 PMCID: PMC11312253 DOI: 10.3390/ijms25158220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Severe aortic valve stenosis (AS) and pulmonary hypertension (PH) are life-threatening cardiovascular conditions, necessitating early detection and intervention. Recent studies have explored the role of Insulin-like Growth Factor-Binding Protein 2 (IGF-BP2) in cardiovascular pathophysiology. Understanding its involvement may offer novel insights into disease mechanisms and therapeutic targets for these conditions. A total of 102 patients (46 female, 56 male) with severe AS undergoing a transcatheter aortic valve replacement (TAVR) in a single-center study were classified using echocardiography tests to determine systolic pulmonary artery pressure (sPAP) and the presence (sPAP ≥ 40 mmHg) or absence (sPAP < 40 mmHg) of PH. Additionally, serial laboratory determinations of IGF-BP2 before, and at 24 h, 96 h, and 3 months after intervention were conducted in all study participants. Considering the entire cohort, patients with PH had significant and continuously higher serum IGF-BP2 concentrations over time than patients without PH. After subdivision by sex, it could be demonstrated that the above-mentioned results were only verifiable in males, but not in females. In the male patients, baseline IGF-BP2 levels before the TAVR was an isolated risk factor for premature death after intervention and at 1, 3, and 5 years post-intervention. The same was valid for the combination of male and echocardiographically established PH patients. The predictive role of IGF-BP2 in severe AS and concurrent PH remains unknown. A more profound comprehension of IGF-BP2 mechanisms, particularly in males, could facilitate the earlier consideration of the TAVR as a more effective and successful treatment strategy.
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Affiliation(s)
- Elke Boxhammer
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University of Salzburg, 5020 Salzburg, Austria
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Ravipati A, Elman SA. The state of artificial intelligence for systemic dermatoses: Background and applications for psoriasis, systemic sclerosis, and much more. Clin Dermatol 2024:S0738-081X(24)00103-2. [PMID: 38909858 DOI: 10.1016/j.clindermatol.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Artificial intelligence (AI) has been steadily integrated into dermatology, with AI platforms already attempting to identify skin cancers and diagnose benign versus malignant lesions. Although not as widely known, AI programs have also been utilized as diagnostic and prognostic tools for dermatologic conditions with systemic or extracutaneous involvement, especially for diseases with autoimmune etiologies. We have provided a primer on commonly used AI platforms and the practical applicability of these algorithms in dealing with psoriasis, systemic sclerosis, and dermatomyositis as a microcosm for future directions in the field. With a rapidly changing landscape in dermatology and medicine as a whole, AI could be a versatile tool to support clinicians and enhance access to care.
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Affiliation(s)
- Advaitaa Ravipati
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Scott A Elman
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.
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Gao L, Skinner J, Nath T, Lin Q, Griffiths M, Damico RL, Pauciulo MW, Nichols WC, Hassoun PM, Everett AD, Johns RA. Resistin predicts disease severity and survival in patients with pulmonary arterial hypertension. Respir Res 2024; 25:235. [PMID: 38844967 PMCID: PMC11154998 DOI: 10.1186/s12931-024-02861-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Abnormal remodeling of distal pulmonary arteries in patients with pulmonary arterial hypertension (PAH) leads to progressively increased pulmonary vascular resistance, followed by right ventricular hypertrophy and failure. Despite considerable advancements in PAH treatment prognosis remains poor. We aim to evaluate the potential for using the cytokine resistin as a genetic and biological marker for disease severity and survival in a large cohort of patients with PAH. METHODS Biospecimens, clinical, and genetic data for 1121 adults with PAH, including 808 with idiopathic PAH (IPAH) and 313 with scleroderma-associated PAH (SSc-PAH), were obtained from a national repository. Serum resistin levels were measured by ELISA, and associations between resistin levels, clinical variables, and single nucleotide polymorphism genotypes were examined with multivariable regression models. Machine-learning (ML) algorithms were applied to develop and compare risk models for mortality prediction. RESULTS Resistin levels were significantly higher in all PAH samples and PAH subtype (IPAH and SSc-PAH) samples than in controls (P < .0001) and had significant discriminative abilities (AUCs of 0.84, 0.82, and 0.91, respectively; P < .001). High resistin levels (above 4.54 ng/mL) in PAH patients were associated with older age (P = .001), shorter 6-min walk distance (P = .001), and reduced cardiac performance (cardiac index, P = .016). Interestingly, mutant carriers of either rs3219175 or rs3745367 had higher resistin levels (adjusted P = .0001). High resistin levels in PAH patients were also associated with increased risk of death (hazard ratio: 2.6; 95% CI: 1.27-5.33; P < .0087). Comparisons of ML-derived survival models confirmed satisfactory prognostic value of the random forest model (AUC = 0.70, 95% CI: 0.62-0.79) for PAH. CONCLUSIONS This work establishes the importance of resistin in the pathobiology of human PAH. In line with its function in rodent models, serum resistin represents a novel biomarker for PAH prognostication and may indicate a new therapeutic avenue. ML-derived survival models highlighted the importance of including resistin levels to improve performance. Future studies are needed to develop multi-marker assays that improve noninvasive risk stratification.
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Affiliation(s)
- Li Gao
- Department of Medicine, Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview Circle, Room 3B.65B, Baltimore, MD, 21224-6821, USA.
| | - John Skinner
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 361, Baltimore, MD, 21287, USA
| | - Tanmay Nath
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Qing Lin
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 361, Baltimore, MD, 21287, USA
| | - Megan Griffiths
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rachel L Damico
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Paul M Hassoun
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen D Everett
- Division of Pediatric Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roger A Johns
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 361, Baltimore, MD, 21287, USA.
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Momenzadeh A, Kreimer S, Guo D, Ayres M, Berman D, Chyu KY, Shah PK, Milewicz D, Azizzadeh A, Meyer JG, Parker S. Differentiation between descending thoracic aortic diseases using machine learning and plasma proteomic signatures. Clin Proteomics 2024; 21:38. [PMID: 38825704 PMCID: PMC11145886 DOI: 10.1186/s12014-024-09487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/25/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection. METHODS This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases. Quantitatively similar proteins were clustered based on linkage distance from hierarchical clustering and ML models were trained with uncorrelated protein lists across various linkage distances with hyperparameter optimization using fivefold cross validation. Permutation importance (PI) was used for ranking the most important predictor proteins of ML classification between disease states and the proteins among the top 10 PI protein groups were submitted for pathway analysis. RESULTS Of the 1,549 peptides and 198 proteins used in this study, no peptides and only one protein, hemopexin (HPX), were significantly different at an adjusted p < 0.01 between Type B and DTAA cases. The highest performing model on the training set (Support Vector Classifier) and its corresponding linkage distance (0.5) were used for evaluation of the test set, yielding a precision-recall area under the curve of 0.7 to classify between Type B from DTAA cases. The five proteins with the highest PI scores were immunoglobulin heavy variable 6-1 (IGHV6-1), lecithin-cholesterol acyltransferase (LCAT), coagulation factor 12 (F12), HPX, and immunoglobulin heavy variable 4-4 (IGHV4-4). All proteins from the top 10 most important groups generated the following significantly enriched pathways in the plasma of Type B versus DTAA patients: complement activation, humoral immune response, and blood coagulation. CONCLUSIONS We conclude that ML may be useful in differentiating the plasma proteome of highly similar disease states that would otherwise not be distinguishable using statistics, and, in such cases, ML may enable prioritizing important proteins for model prediction.
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Affiliation(s)
- Amanda Momenzadeh
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Simion Kreimer
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Matthew Ayres
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel Berman
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Cedars Sinai Imaging Department, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Kuang-Yuh Chyu
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Prediman K Shah
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dianna Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Ali Azizzadeh
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Jesse G Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
| | - Sarah Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles California, USA.
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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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彭 威, 张 泽, 肖 云. [Research progress on bioinformatics in pulmonary arterial hypertension]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:425-431. [PMID: 38660909 PMCID: PMC11057300 DOI: 10.7499/j.issn.1008-8830.2310076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a severe disease characterized by abnormal pulmonary vascular remodeling and increased right ventricular pressure load, posing a significant threat to patient health. While some pathological mechanisms of PAH have been revealed, the deeper mechanisms of pathogenesis remain to be elucidated. In recent years, bioinformatics has provided a powerful tool for a deeper understanding of the complex mechanisms of PAH through the integration of techniques such as multi-omics analysis, artificial intelligence, and Mendelian randomization. This review focuses on the bioinformatics methods and technologies used in PAH research, summarizing their current applications in the study of disease mechanisms, diagnosis, and prognosis assessment. Additionally, it analyzes the existing challenges faced by bioinformatics and its potential applications in the clinical and basic research fields of PAH in the future.
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Affiliation(s)
| | - 泽盈 张
- 中南大学湘雅二医院心血管内科,湖南长沙410007
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Guerrero L, Vindel-Alfageme J, Hierro L, Stark L, Vicent D, Sorzano CÓS, Corrales FJ. Discrimination of Etiologically Different Cholestasis by Modeling Proteomics Datasets. Int J Mol Sci 2024; 25:3684. [PMID: 38612495 PMCID: PMC11011353 DOI: 10.3390/ijms25073684] [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: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Cholestasis is characterized by disrupted bile flow from the liver to the small intestine. Although etiologically different cholestasis displays similar symptoms, diverse factors can contribute to the progression of the disease and determine the appropriate therapeutic option. Therefore, stratifying cholestatic patients is essential for the development of tailor-made treatment strategies. Here, we have analyzed the liver proteome from cholestatic patients of different etiology. In total, 7161 proteins were identified and quantified, of which 263 were differentially expressed between control and cholestasis groups. These differential proteins point to deregulated cellular processes that explain part of the molecular framework of cholestasis progression. However, the clustering of different cholestasis types was limited. Therefore, a machine learning pipeline was designed to identify a panel of 20 differential proteins that segregate different cholestasis groups with high accuracy and sensitivity. In summary, proteomics combined with machine learning algorithms provides valuable insights into the molecular mechanisms of cholestasis progression and a panel of proteins to discriminate across different types of cholestasis. This strategy may prove useful in developing precision medicine approaches for patient care.
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Affiliation(s)
- Laura Guerrero
- Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain; (L.G.); (J.V.-A.); (C.Ó.S.S.)
| | - Jorge Vindel-Alfageme
- Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain; (L.G.); (J.V.-A.); (C.Ó.S.S.)
| | - Loreto Hierro
- IdiPAZ, Instituto de Investigación Sanitaria (Health Research Institute), Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (L.H.); (L.S.); (D.V.)
| | - Luiz Stark
- IdiPAZ, Instituto de Investigación Sanitaria (Health Research Institute), Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (L.H.); (L.S.); (D.V.)
| | - David Vicent
- IdiPAZ, Instituto de Investigación Sanitaria (Health Research Institute), Hospital Universitario La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain; (L.H.); (L.S.); (D.V.)
| | - Carlos Óscar S. Sorzano
- Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain; (L.G.); (J.V.-A.); (C.Ó.S.S.)
| | - Fernando J. Corrales
- Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain; (L.G.); (J.V.-A.); (C.Ó.S.S.)
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Szabo I, Badii M, Gaál IO, Szabo R, Sîrbe C, Humiță O, Joosten LAB, Crișan TO, Rednic S. Immune Profiling of Patients with Systemic Sclerosis through Targeted Proteomic Analysis. Int J Mol Sci 2023; 24:17601. [PMID: 38139427 PMCID: PMC10744051 DOI: 10.3390/ijms242417601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
High-throughput proteomic analysis could offer new insights into the pathogenesis of systemic sclerosis (SSc) and reveal non-invasive biomarkers for diagnosis and severity. This study aimed to assess the protein signature of patients with SSc compared to that of healthy volunteers, decipher various disease endotypes using circulating proteins, and determine the diagnostic performance of significantly expressed plasma analytes. We performed targeted proteomic profiling in a cohort of fifteen patients with SSc and eighteen controls using the Olink® (Olink Bioscience, Uppsala, Sweden)Target 96 Inflammation Panels. Seventeen upregulated proteins involved in angiogenesis, innate immunity, and co-stimulatory pathways discriminated between patients with SSc and healthy controls (HCs) and further classified them into two clusters, a low-inflammatory and a high-inflammatory endotype. Younger age, shorter disease duration, and lack of reflux esophagitis characterized patients in the low-inflammatory endotype. TNF, CXCL9, TNFRSF9, and CXCL10 positively correlated with disease progression, while the four-protein panel comprising TNF, CXCL9, CXCL10, and CX3CL1 showed high diagnostic performance. Collectively, this study identified a distinct inflammatory signature in patients with SSc that reflects a persistent T helper type 1 (Th 1) immune response irrespective of disease duration, while the multi-protein panel might improve early diagnosis in SSc.
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Affiliation(s)
- Iulia Szabo
- Department of Rheumatology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.S.)
- Department of Rheumatology, County Emergency Hospital, 400347 Cluj-Napoca, Romania
| | - Medeea Badii
- Department of Medical Genetics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ildikó O. Gaál
- Department of Medical Genetics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Robert Szabo
- 2nd Anesthesia Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Anesthesia and Intensive Care, County Emergency Hospital, 400347 Cluj-Napoca, Romania
| | - Claudia Sîrbe
- 2nd Pediatric Discipline, Department of Mother and Child, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- 2nd Pediatric Clinic, Center of Expertise in Pediatric Liver Rare Disorders, Emergency Clinical Hospital for Children, 400177 Cluj-Napoca, Romania
| | - Oana Humiță
- Department of Rheumatology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.S.)
| | - Leo A. B. Joosten
- Department of Medical Genetics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tania O. Crișan
- Department of Medical Genetics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Simona Rednic
- Department of Rheumatology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.S.)
- Department of Rheumatology, County Emergency Hospital, 400347 Cluj-Napoca, Romania
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Momenzadeh A, Kreimer S, Guo D, Ayres M, Berman D, Chyu KY, Shah PK, Milewicz D, Azizzadeh A, Meyer JG, Parker S. Differentiation between Descending Thoracic Aortic Diseases using Machine Learning and Plasma Proteomic Signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538468. [PMID: 37162892 PMCID: PMC10168345 DOI: 10.1101/2023.04.26.538468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection. Methods This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases. Quantitatively similar proteins were clustered based on linkage distance from hierarchical clustering and ML models were trained with uncorrelated protein lists across various linkage distances with hyperparameter optimization using 5-fold cross validation. Permutation importance (PI) was used for ranking the most important predictor proteins of ML classification between disease states and the proteins among the top 10 PI protein groups were submitted for pathway analysis. Results Of the 1,549 peptides and 198 proteins used in this study, no peptides and only one protein, hemopexin (HPX), were significantly different at an adjusted p-value <0.01 between Type B and DTAA cases. The highest performing model on the training set (Support Vector Classifier) and its corresponding linkage distance (0.5) were used for evaluation of the test set, yielding a precision-recall area under the curve of 0.7 to classify between Type B from DTAA cases. The five proteins with the highest PI scores were immunoglobulin heavy variable 6-1 (IGHV6-1), lecithin-cholesterol acyltransferase (LCAT), coagulation factor 12 (F12), HPX, and immunoglobulin heavy variable 4-4 (IGHV4-4). All proteins from the top 10 most important correlated groups generated the following significantly enriched pathways in the plasma of Type B versus DTAA patients: complement activation, humoral immune response, and blood coagulation. Conclusions We conclude that ML may be useful in differentiating the plasma proteome of highly similar disease states that would otherwise not be distinguishable using statistics, and, in such cases, ML may enable prioritizing important proteins for model prediction.
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Affiliation(s)
- Amanda Momenzadeh
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Simion Kreimer
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Matthew Ayres
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Daniel Berman
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Cedars-Sinai Imaging Department, Cedars Sinai Medical Center, Lost Angeles, California, USA
| | - Kuang-Yuh Chyu
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Prediman K Shah
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dianna Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Ali Azizzadeh
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Jesse G. Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Sarah Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles California, USA
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13
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Muruganandam M, Ariza-Hutchinson A, Patel RA, Sibbitt WL. Biomarkers in the Pathogenesis, Diagnosis, and Treatment of Systemic Sclerosis. J Inflamm Res 2023; 16:4633-4660. [PMID: 37868834 PMCID: PMC10590076 DOI: 10.2147/jir.s379815] [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] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Systemic sclerosis (SSc) is a complex autoimmune disease characterized by vascular damage, vasoinstability, and decreased perfusion with ischemia, inflammation, and exuberant fibrosis of the skin and internal organs. Biomarkers are analytic indicators of the biological and disease processes within an individual that can be accurately and reproducibly measured. The field of biomarkers in SSc is complex as recent studies have implicated at least 240 pathways and dysregulated proteins in SSc pathogenesis. Anti-nuclear antibodies (ANA) are classical biomarkers with well-described clinical classifications and are present in more than 90% of SSc patients and include anti-centromere, anti-Th/To, anti-RNA polymerase III, and anti-topoisomerase I antibodies. Transforming growth factor-β (TGF-β) is central to the fibrotic process of SSc and is intimately intertwined with other biomarkers. Tyrosine kinases, interferon-1 signaling, IL-6 signaling, endogenous thrombin, peroxisome proliferator-activated receptors (PPARs), lysophosphatidic acid receptors, and amino acid metabolites are new biomarkers with the potential for developing new therapeutic agents. Other biomarkers implicated in SSc-ILD include signal transducer and activator of transcription 4 (STAT4), CD226 (DNAX accessory molecule 1), interferon regulatory factor 5 (IRF5), interleukin-1 receptor-associated kinase-1 (IRAK1), connective tissue growth factor (CTGF), pyrin domain containing 1 (NLRP1), T-cell surface glycoprotein zeta chain (CD3ζ) or CD247, the NLR family, SP-D (surfactant protein), KL-6, leucine-rich α2-glycoprotein-1 (LRG1), CCL19, genetic factors including DRB1 alleles, the interleukins (IL-1, IL-4, IL-6, IL-8, IL-10 IL-13, IL-16, IL-17, IL-18, IL-22, IL-32, and IL-35), the chemokines CCL (2,3,5,13,20,21,23), CXC (8,9,10,11,16), CX3CL1 (fractalkine), and GDF15. Adiponectin (an indicator of PPAR activation) and maresin 1 are reduced in SSc patients. A new trend has been the use of biomarker panels with combined complex multifactor analysis, machine learning, and artificial intelligence to determine disease activity and response to therapy. The present review is an update of the various biomarker molecules, pathways, and receptors involved in the pathology of SSc.
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Affiliation(s)
- Maheswari Muruganandam
- Department of Internal Medicine, Division of Rheumatology and School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Angie Ariza-Hutchinson
- Department of Internal Medicine, Division of Rheumatology and School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rosemina A Patel
- Department of Internal Medicine, Division of Rheumatology and School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Wilmer L Sibbitt
- Department of Internal Medicine, Division of Rheumatology and School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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Lemmers JMJ, van Caam APM, Kersten B, van den Ende CHM, Knaapen H, van Dijk APJ, Hagmolen of ten Have W, van den Hoogen FHJ, Koenen H, van Leuven SI, Alkema W, Smeets RL, Vonk MC. Nailfold capillaroscopy and candidate-biomarker levels in systemic sclerosis-associated pulmonary hypertension: A cross-sectional study. JOURNAL OF SCLERODERMA AND RELATED DISORDERS 2023; 8:221-230. [PMID: 37744051 PMCID: PMC10515989 DOI: 10.1177/23971983231175213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/23/2023] [Indexed: 09/26/2023]
Abstract
Objectives Pulmonary hypertension is one of the leading causes of death in systemic sclerosis. Early detection and treatment of pulmonary hypertension in systemic sclerosis is crucial. Nailfold capillaroscopy microscopy, vascular autoantibodies AT1R and ETAR, and several candidate-biomarkers have the potential to serve as noninvasive tools to identify systemic sclerosis patients at risk for developing pulmonary hypertension. Here, we explore the classifying potential of nailfold capillaroscopy microscopy characteristics and serum levels of selected candidate-biomarkers in a sample of systemic sclerosis patients with and without different forms of pulmonary hypertension. Methods A total of 81 consecutive systemic sclerosis patients were included, 40 with systemic sclerosis pulmonary hypertension and 41 with no pulmonary hypertension. In each group, quantitative and qualitative nailfold capillaroscopy microscopy characteristics, vascular autoantibodies AT1R and ETAR, and serum levels of 24 soluble serum factors were determined. For evaluation of the nailfold capillaroscopy microscopy characteristics, linear regression analysis accounting for age, sex, and diffusing capacity of the lungs for carbon monoxide percentage predicted was used. Autoantibodies and soluble serum factor levels were compared using two-sample t test with equal variances. Results No statistically significant differences were observed in quantitative or qualitative nailfold capillaroscopy microscopy characteristics, or vascular autoantibody ETAR and AT1R titer between systemic sclerosis-pulmonary hypertension and systemic sclerosis-no pulmonary hypertension. In contrast, several serum levels of soluble factors differed between groups: Endostatin, sVCAM, and VEGFD were increased, and CXCL4, sVEGFR2, and PDGF-AB/BB were decreased in systemic sclerosis-pulmonary hypertension. Random forest classification identified Endostatin and CXCL4 as the most predictive classifiers to distinguish systemic sclerosispulmonary hypertension from systemic sclerosis-no pulmonary hypertension. Conclusion This study shows the potential for several soluble serum factors to distinguish systemic sclerosis-pulmonary hypertension from systemic sclerosis-no pulmonary hypertension. We found no classifying potential for qualitative or quantitative nailfold capillaroscopy microscopy characteristics, or vascular autoantibodies.
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Affiliation(s)
- Jacqueline MJ Lemmers
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan PM van Caam
- Laboratory of Experimental Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigit Kersten
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Hanneke Knaapen
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arie PJ van Dijk
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Hans Koenen
- Laboratory of Clinical Chemistry and Immunology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sander I van Leuven
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wynand Alkema
- Department of Data Science for Life Sciences & Health, Hanze University, Groningen, The Netherlands
| | - Ruben L Smeets
- Laboratory of Clinical Chemistry and Immunology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madelon C Vonk
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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Di Maggio G, Confalonieri P, Salton F, Trotta L, Ruggero L, Kodric M, Geri P, Hughes M, Bellan M, Gilio M, Lerda S, Baratella E, Confalonieri M, Mondini L, Ruaro B. Biomarkers in Systemic Sclerosis: An Overview. Curr Issues Mol Biol 2023; 45:7775-7802. [PMID: 37886934 PMCID: PMC10604992 DOI: 10.3390/cimb45100490] [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: 09/02/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Systemic sclerosis (SSc) is a complex autoimmune disease characterized by significant fibrosis of the skin and internal organs, with the main involvement of the lungs, kidneys, heart, esophagus, and intestines. SSc is also characterized by macro- and microvascular damage with reduced peripheral blood perfusion. Several studies have reported more than 240 pathways and numerous dysregulation proteins, giving insight into how the field of biomarkers in SSc is still extremely complex and evolving. Antinuclear antibodies (ANA) are present in more than 90% of SSc patients, and anti-centromere and anti-topoisomerase I antibodies are considered classic biomarkers with precise clinical features. Recent studies have reported that trans-forming growth factor β (TGF-β) plays a central role in the fibrotic process. In addition, interferon regulatory factor 5 (IRF5), interleukin receptor-associated kinase-1 (IRAK-1), connective tissue growth factor (CTGF), transducer and activator of transcription signal 4 (STAT4), pyrin-containing domain 1 (NLRP1), as well as genetic factors, including DRB1 alleles, are implicated in SSc damage. Several interleukins (e.g., IL-1, IL-6, IL-10, IL-17, IL-22, and IL-35) and chemokines (e.g., CCL 2, 5, 23, and CXC 9, 10, 16) are elevated in SSc. While adiponectin and maresin 1 are reduced in patients with SSc, biomarkers are important in research but will be increasingly so in the diagnosis and therapeutic approach to SSc. This review aims to present and highlight the various biomarker molecules, pathways, and receptors involved in the pathology of SSc.
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Affiliation(s)
- Giuseppe Di Maggio
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Paola Confalonieri
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Francesco Salton
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Liliana Trotta
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Luca Ruggero
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Metka Kodric
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Pietro Geri
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Michael Hughes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester & Salford Royal NHS Foundation Trust, Manchester M6 8HD, UK;
| | - Mattia Bellan
- Department of Translational Medicine, Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- Center for Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- Department of Medicine, Azienda Ospedaliero–Universitaria, Maggiore della Carità, 28100 Novara, Italy
| | - Michele Gilio
- Infectious Disease Unit, San Carlo Hospital, 85100 Potenza, Italy
| | - Selene Lerda
- Graduate School, University of Milan, 20149 Milano, Italy
| | - Elisa Baratella
- Department of Radiology, Cattinara Hospital, University of Trieste, 34149 Trieste, Italy
| | - Marco Confalonieri
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Lucrezia Mondini
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
| | - Barbara Ruaro
- Pulmonology Unit, Department of Medical Surgical and Healt Sciencies, Hospital of Cattinara, University of Trieste, 34149 Trieste, Italy; (G.D.M.); (M.K.); (P.G.); (L.M.)
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16
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Motta F, Tonutti A, Isailovic N, Ceribelli A, Costanzo G, Rodolfi S, Selmi C, De Santis M. Proteomic aptamer analysis reveals serum biomarkers associated with disease mechanisms and phenotypes of systemic sclerosis. Front Immunol 2023; 14:1246777. [PMID: 37753072 PMCID: PMC10518467 DOI: 10.3389/fimmu.2023.1246777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Background Systemic sclerosis (SSc) is an autoimmune connective tissue disease that affects multiple organs, leading to elevated morbidity and mortality with limited treatment options. The early detection of organ involvement is challenging as there is currently no serum marker available to predict the progression of SSc. The aptamer technology proteomic analysis holds the potential to correlate SSc manifestations with serum proteins up to femtomolar concentrations. Methods This is a two-tier study of serum samples from women with SSc (including patients with interstitial lung disease - ILD - at high-resolution CT scan) and age-matched healthy controls (HC) that were first analyzed with aptamer-based proteomic analysis for over 1300 proteins. Proposed associated proteins were validated by ELISA first in an independent cohort of patients with SSc and HC, and selected proteins subject to further validation in two additional cohorts. Results The preliminary aptamer-based proteomic analysis identified 33 proteins with significantly different concentrations in SSc compared to HC sera and 9 associated with SSc-ILD, including proteins involved in extracellular matrix formation and cell-cell adhesion, angiogenesis, leukocyte recruitment, activation, and signaling. Further validations in independent cohorts ultimately confirmed the association of specific proteins with early SSc onset, specific organ involvement, and serum autoantibodies. Conclusions Our multi-tier proteomic analysis identified serum proteins discriminating patients with SSc and HC or associated with different SSc subsets, disease duration, and manifestations, including ILD, skin involvement, esophageal disease, and autoantibodies.
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Affiliation(s)
- Francesca Motta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Antonio Tonutti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Natasa Isailovic
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Angela Ceribelli
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Giovanni Costanzo
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Stefano Rodolfi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Maria De Santis
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- Rheumatology and Clinical Immunology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
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17
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Luo D, Zheng X, Yang Z, Li H, Fei H, Zhang C. Machine learning for clustering and postclosure outcome of adult CHD-PAH patients with borderline hemodynamics. J Heart Lung Transplant 2023; 42:1286-1297. [PMID: 37211333 DOI: 10.1016/j.healun.2023.05.003] [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: 09/14/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND Patients with uncorrected isolated simple shunts associated pulmonary arterial hypertension (PAH) had increased mortality. Treatment strategies for borderline hemodynamics remain controversial. This study aims to investigate preclosure characteristics and its association with postclosure outcome in this group of patients. METHODS Adults with uncorrected isolated simple shunts associated PAH were included. Peak tricuspid regurgitation velocity<2.8 m/sec with normalized cardiac structures was defined as the favorable study outcome. We applied unsupervised and supervised machine learning for clustering analysis and model constructions. RESULTS Finally, 246 patients were included. During a median follow-up of 414days, 58.49% (62/106) of patients with pretricuspid shunts achieved favorable outcome while 32.22% (46/127) of patients with post-tricuspid shunts. In unsupervised learning, two clusters were identified in both types of shunts. Generally, the oxygen saturation, pulmonary blood flow, cardiac index, dimensions of the right and left atrium, were the major features that characterized the identified clusters. Specifically, mean right atrial pressure, right ventricular dimension, and right ventricular outflow tract helped differentiate clusters in pretricuspid shunts while age, aorta dimension, and systemic vascular resistance helped differentiate clusters for post-tricuspid shunts. Notably, cluster 1 had better postclosure outcome than cluster 2 (70.83% vs 32.55%, p < .001 for pretricuspid and 48.10% vs 16.67%, p < .001 for post-tricuspid). However, models constructed from supervised learning methods did not achieve good accuracy for predicting the postclosure outcome. CONCLUSIONS There were two main clusters in patients with borderline hemodynamics, in which one cluster had better postclosure outcome than the other.
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Affiliation(s)
- Dongling Luo
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xinpeng Zheng
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Ziyang Yang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hezhi Li
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hongwen Fei
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
| | - Caojin Zhang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
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Khan SL, Mathai SC. Scleroderma pulmonary arterial hypertension: the same as idiopathic pulmonary arterial hypertension? Curr Opin Pulm Med 2023; 29:380-390. [PMID: 37461869 PMCID: PMC11334969 DOI: 10.1097/mcp.0000000000001001] [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] [Indexed: 08/03/2023]
Abstract
PURPOSE OF REVIEW Pulmonary arterial hypertension (PAH) is a common complication of systemic sclerosis (SSc), which confers significant morbidity and mortality. The current therapies and treatment strategies for SSc-associated PAH (SSc-PAH) are informed by those used to treat patients with idiopathic PAH (IPAH). There are, however, important differences between these two diseases that impact diagnosis, treatment, and outcomes. RECENT FINDINGS Both SSc-PAH and IPAH are incompletely understood with ongoing research into the underlying cellular biology that characterize and differentiate the two diseases. Additional research seeks to improve identification among SSc patients in order to diagnose patients earlier in the course of their disease. Novel therapies specifically for SSc-PAH such as rituximab and dimethyl fumarate are under investigation. SUMMARY Although patients with SSc-PAH and IPAH present with similar symptoms, there are significant differences between these two forms of PAH that warrant further investigation and characterization of optimal detection strategies, treatment algorithms, and outcomes assessment.
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Affiliation(s)
- Sarah L Khan
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Atzeni IM, Al-Adwi Y, Doornbos-van der Meer B, Roozendaal C, Stel A, van Goor H, Gan CT, Dickinson M, Timens W, Smit AJ, Westra J, Mulder DJ. The soluble receptor for advanced glycation end products is potentially predictive of pulmonary arterial hypertension in systemic sclerosis. Front Immunol 2023; 14:1189257. [PMID: 37409127 PMCID: PMC10318928 DOI: 10.3389/fimmu.2023.1189257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Pulmonary arterial hypertension (PAH) and interstitial lung disease (ILD) are the leading causes of death in systemic sclerosis (SSc). Until now, no prospective biomarker to predict new onset of SSc-ILD or SSc-PAH in patients with SSc has reached clinical application. In homeostasis, the receptor for advanced glycation end products (RAGE) is expressed in lung tissue and involved in cell-matrix adhesion, proliferation and migration of alveolar epithelial cells, and remodeling of the pulmonary vasculature. Several studies have shown that sRAGE levels in serum and pulmonary tissue vary according to the type of lung-related complication. Therefore, we investigated levels of soluble RAGE (sRAGE) and its ligand high mobility group box 1 (HMGB1) in SSc and their abilities to predict SSc-related pulmonary complications. Methods One hundred eighty-eight SSc patients were followed retrospectively for the development of ILD, PAH, and mortality for 8 years. Levels of sRAGE and HMGB1 were measured in serum by ELISA. Kaplan-Meier survival curves were performed to predict lung events and mortality and event rates were compared with a log-rank test. Multiple linear regression analysis was performed to examine the association between sRAGE and important clinical determinants. Results At baseline, levels of sRAGE were significantly higher in SSc-PAH-patients (median 4099.0 pg/ml [936.3-6365.3], p = 0.011) and lower in SSc-ILD-patients (735.0 pg/ml [IQR 525.5-1988.5], p = 0.001) compared to SSc patients without pulmonary involvement (1444.5 pg/ml [966.8-2276.0]). Levels of HMGB1 were not different between groups. After adjusting for age, gender, ILD, chronic obstructive pulmonary disease, anti-centromere antibodies, the presence of puffy fingers or sclerodactyly, use of immunosuppression, antifibrotic therapy, or glucocorticoids, and use of vasodilators, higher sRAGE levels remained independently associated with PAH. After a median follow-up of 50 months (25-81) of patients without pulmonary involvement, baseline sRAGE levels in the highest quartile were predictive of development of PAH (log-rank p = 0.01) and of PAH-related mortality (p = 0.001). Conclusions High systemic sRAGE at baseline might be used as a prospective biomarker for patients with SSc at high risk to develop new onset of PAH. Moreover, high sRAGE levels could predict lower survival rates due to PAH in patients with SSc.
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Affiliation(s)
- Isabella M. Atzeni
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Yehya Al-Adwi
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Berber Doornbos-van der Meer
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Caroline Roozendaal
- Department of Laboratory Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Alja Stel
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Harry van Goor
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - C. Tji Gan
- Department of Pulmonary Diseases and Tuberculosis, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Michael Dickinson
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Andries J. Smit
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Johanna Westra
- Department of Rheumatology and Clinical Immunology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Douwe J. Mulder
- Department of Internal Medicine, Division of Vascular Medicine, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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20
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Ma J, Li Y, Yang X, Liu K, Zhang X, Zuo X, Ye R, Wang Z, Shi R, Meng Q, Chen X. Signaling pathways in vascular function and hypertension: molecular mechanisms and therapeutic interventions. Signal Transduct Target Ther 2023; 8:168. [PMID: 37080965 PMCID: PMC10119183 DOI: 10.1038/s41392-023-01430-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/03/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023] Open
Abstract
Hypertension is a global public health issue and the leading cause of premature death in humans. Despite more than a century of research, hypertension remains difficult to cure due to its complex mechanisms involving multiple interactive factors and our limited understanding of it. Hypertension is a condition that is named after its clinical features. Vascular function is a factor that affects blood pressure directly, and it is a main strategy for clinically controlling BP to regulate constriction/relaxation function of blood vessels. Vascular elasticity, caliber, and reactivity are all characteristic indicators reflecting vascular function. Blood vessels are composed of three distinct layers, out of which the endothelial cells in intima and the smooth muscle cells in media are the main performers of vascular function. The alterations in signaling pathways in these cells are the key molecular mechanisms underlying vascular dysfunction and hypertension development. In this manuscript, we will comprehensively review the signaling pathways involved in vascular function regulation and hypertension progression, including calcium pathway, NO-NOsGC-cGMP pathway, various vascular remodeling pathways and some important upstream pathways such as renin-angiotensin-aldosterone system, oxidative stress-related signaling pathway, immunity/inflammation pathway, etc. Meanwhile, we will also summarize the treatment methods of hypertension that targets vascular function regulation and discuss the possibility of these signaling pathways being applied to clinical work.
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Affiliation(s)
- Jun Ma
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yanan Li
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xiangyu Yang
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Kai Liu
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xin Zhang
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xianghao Zuo
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Runyu Ye
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Ziqiong Wang
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Rufeng Shi
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qingtao Meng
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Xiaoping Chen
- Department of Cardiology, West China Hospital, Sichuan University, No. 37, Guo Xue District, Chengdu, Sichuan, 610041, People's Republic of China.
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21
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Kong X, Sun H, Wei K, Meng L, Lv X, Liu C, Lin F, Gu X. WGCNA combined with machine learning algorithms for analyzing key genes and immune cell infiltration in heart failure due to ischemic cardiomyopathy. Front Cardiovasc Med 2023; 10:1058834. [PMID: 37008314 PMCID: PMC10064046 DOI: 10.3389/fcvm.2023.1058834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
BackgroundIschemic cardiomyopathy (ICM) induced heart failure (HF) is one of the most common causes of death worldwide. This study aimed to find candidate genes for ICM-HF and to identify relevant biomarkers by machine learning (ML).MethodsThe expression data of ICM-HF and normal samples were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between ICM-HF and normal group were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and gene ontology (GO) annotation analysis, protein–protein interaction (PPI) network, gene pathway enrichment analysis (GSEA), and single-sample gene set enrichment analysis (ssGSEA) were performed. Weighted gene co-expression network analysis (WGCNA) was applied to screen for disease-associated modules, and relevant genes were derived using four ML algorithms. The diagnostic values of candidate genes were assessed using receiver operating characteristic (ROC) curves. The immune cell infiltration analysis was performed between the ICM-HF and normal group. Validation was performed using another gene set.ResultsA total of 313 DEGs were identified between ICM-HF and normal group of GSE57345, which were mainly enriched in biological processes and pathways related to cell cycle regulation, lipid metabolism pathways, immune response pathways, and intrinsic organelle damage regulation. GSEA results showed positive correlations with pathways such as cholesterol metabolism in the ICM-HF group compared to normal group and lipid metabolism in adipocytes. GSEA results also showed a positive correlation with pathways such as cholesterol metabolism and a negative correlation with pathways such as lipolytic presentation in adipocytes compared to normal group. Combining multiple ML and cytohubba algorithms yielded 11 relevant genes. After validation using the GSE42955 validation sets, the 7 genes obtained by the machine learning algorithm were well verified. The immune cell infiltration analysis showed significant differences in mast cells, plasma cells, naive B cells, and NK cells.ConclusionCombined analysis using WGCNA and ML identified coiled-coil-helix-coiled-coil-helix domain containing 4 (CHCHD4), transmembrane protein 53 (TMEM53), acid phosphatase 3 (ACPP), aminoadipate-semialdehyde dehydrogenase (AASDH), purinergic receptor P2Y1 (P2RY1), caspase 3 (CASP3) and aquaporin 7 (AQP7) as potential biomarkers of ICM-HF. ICM-HF may be closely related to pathways such as mitochondrial damage and disorders of lipid metabolism, while the infiltration of multiple immune cells was identified to play a critical role in the progression of the disease.
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Affiliation(s)
- XiangJin Kong
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - HouRong Sun
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - KaiMing Wei
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - LingWei Meng
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Lv
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - ChuanZhen Liu
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - FuShun Lin
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - XingHua Gu
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, China
- Correspondence: XingHua Gu
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22
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Dimitsaki S, Gavriilidis GI, Dimitriadis VK, Natsiavas P. Benchmarking of Machine Learning classifiers on plasma proteomic for COVID-19 severity prediction through interpretable artificial intelligence. Artif Intell Med 2023; 137:102490. [PMID: 36868685 PMCID: PMC9846931 DOI: 10.1016/j.artmed.2023.102490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
The SARS-CoV-2 pandemic highlighted the need for software tools that could facilitate patient triage regarding potential disease severity or even death. In this article, an ensemble of Machine Learning (ML) algorithms is evaluated in terms of predicting the severity of their condition using plasma proteomics and clinical data as input. An overview of AI-based technical developments to support COVID-19 patient management is presented outlining the landscape of relevant technical developments. Based on this review, the use of an ensemble of ML algorithms that analyze clinical and biological data (i.e., plasma proteomics) of COVID-19 patients is designed and deployed to evaluate the potential use of AI for early COVID-19 patient triage. The proposed pipeline is evaluated using three publicly available datasets for training and testing. Three ML "tasks" are defined, and several algorithms are tested through a hyperparameter tuning method to identify the highest-performance models. As overfitting is one of the typical pitfalls for such approaches (mainly due to the size of the training/validation datasets), a variety of evaluation metrics are used to mitigate this risk. In the evaluation procedure, recall scores ranged from 0.6 to 0.74 and F1-score from 0.62 to 0.75. The best performance is observed via Multi-Layer Perceptron (MLP) and Support Vector Machines (SVM) algorithms. Additionally, input data (proteomics and clinical data) were ranked based on corresponding Shapley additive explanation (SHAP) values and evaluated for their prognosticated capacity and immuno-biological credence. This "interpretable" approach revealed that our ML models could discern critical COVID-19 cases predominantly based on patient's age and plasma proteins on B cell dysfunction, hyper-activation of inflammatory pathways like Toll-like receptors, and hypo-activation of developmental and immune pathways like SCF/c-Kit signaling. Finally, the herein computational workflow is corroborated in an independent dataset and MLP superiority along with the implication of the abovementioned predictive biological pathways are corroborated. Regarding limitations of the presented ML pipeline, the datasets used in this study contain less than 1000 observations and a significant number of input features hence constituting a high-dimensional low-sample (HDLS) dataset which could be sensitive to overfitting. An advantage of the proposed pipeline is that it combines biological data (plasma proteomics) with clinical-phenotypic data. Thus, in principle, the presented approach could enable patient triage in a timely fashion if used on already trained models. However, larger datasets and further systematic validation are needed to confirm the potential clinical value of this approach. The code is available on Github: https://github.com/inab-certh/Predicting-COVID-19-severity-through-interpretable-AI-analysis-of-plasma-proteomics.
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Affiliation(s)
- Stella Dimitsaki
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thermi, Thessaloniki, Greece.
| | - George I Gavriilidis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thermi, Thessaloniki, Greece
| | - Vlasios K Dimitriadis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thermi, Thessaloniki, Greece
| | - Pantelis Natsiavas
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thermi, Thessaloniki, Greece
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23
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Sanges S, Rice L, Tu L, Valenzi E, Cracowski JL, Montani D, Mantero JC, Ternynck C, Marot G, Bujor AM, Hachulla E, Launay D, Humbert M, Guignabert C, Lafyatis R. Biomarkers of haemodynamic severity of systemic sclerosis-associated pulmonary arterial hypertension by serum proteome analysis. Ann Rheum Dis 2023; 82:365-373. [PMID: 36600187 PMCID: PMC9918672 DOI: 10.1136/ard-2022-223237] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To mine the serum proteome of patients with systemic sclerosis-associated pulmonary arterial hypertension (SSc-PAH) and to detect biomarkers that may assist in earlier and more effective diagnosis and treatment. METHODS Patients with limited cutaneous SSc, no extensive interstitial lung disease and no PAH-specific therapy were included. They were classified as cases if they had PAH confirmed by right heart catheterisation (RHC) and serum collected on the same day as RHC; and as controls if they had no clinical evidence of PAH. RESULTS Patients were mostly middle-aged females with anticentromere-associated SSc. Among 1129 proteins assessed by a high-throughput proteomic assay (SOMAscan), only 2 were differentially expressed and correlated significantly with pulmonary vascular resistance (PVR) in SSc-PAH patients (n=15): chemerin (ρ=0.62, p=0.01) and SET (ρ=0.62, p=0.01). To validate these results, serum levels of chemerin were measured by ELISA in an independent cohort. Chemerin levels were confirmed to be significantly higher (p=0.01) and correlate with PVR (ρ=0.42, p=0.04) in SSc-PAH patients (n=24). Chemerin mRNA expression was detected in fibroblasts, pulmonary artery smooth muscle cells (PA-SMCs)/pericytes and mesothelial cells in SSc-PAH lungs by single-cell RNA-sequencing. Confocal immunofluorescence revealed increased expression of a chemerin receptor, CMKLR1, on SSc-PAH PA-SMCs. SSc-PAH serum seemed to induce higher PA-SMC proliferation than serum from SSc patients without PAH. This difference appeared neutralised when adding the CMKLR1 inhibitor α-NETA. CONCLUSION Chemerin seems an interesting surrogate biomarker for PVR in SSc-PAH. Increased chemerin serum levels and CMKLR1 expression by PA-SMCs may contribute to SSc-PAH pathogenesis by inducing PA-SMC proliferation.
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Affiliation(s)
- Sébastien Sanges
- Boston University School of Medicine, E5 Arthritis Center, Boston, Massachusetts, USA
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- INSERM, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Lille, France
- Centre National de Référence Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France
- Health Care Provider of the European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ReCONNET), Lille, France
| | - Lisa Rice
- Boston University School of Medicine, E5 Arthritis Center, Boston, Massachusetts, USA
| | - Ly Tu
- Université Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999, Hôpital Marie-Lannelongue, Le Plessis-Robinson, France
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - David Montani
- Université Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999, Hôpital Marie-Lannelongue, Le Plessis-Robinson, France
- AP-HP, Department of Respiratory and Intensive Care Medicine, Hôpital Bicêtre, Kremlin-Bicêtre, France
| | - Julio C Mantero
- Boston University School of Medicine, E5 Arthritis Center, Boston, Massachusetts, USA
| | - Camille Ternynck
- Univ. Lille, CHU Lille, ULR 2694 - METRICS: Évaluation des technologies de santé et des pratiques médicales, Lille, France
| | - Guillemette Marot
- Univ. Lille, CHU Lille, ULR 2694 - METRICS: Évaluation des technologies de santé et des pratiques médicales, Lille, France
- Inria, MODAL: MOdels for Data Analysis and Learning, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UAR 2014 - US 41 - PLBS, bilille, Lille, France
| | - Andreea M Bujor
- Boston University School of Medicine, E5 Arthritis Center, Boston, Massachusetts, USA
| | - Eric Hachulla
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- INSERM, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Lille, France
- Centre National de Référence Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France
- Health Care Provider of the European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ReCONNET), Lille, France
| | - David Launay
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- INSERM, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Lille, France
- Centre National de Référence Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France
- Health Care Provider of the European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ReCONNET), Lille, France
| | - Marc Humbert
- Université Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999, Hôpital Marie-Lannelongue, Le Plessis-Robinson, France
- AP-HP, Department of Respiratory and Intensive Care Medicine, Hôpital Bicêtre, Kremlin-Bicêtre, France
| | - Christophe Guignabert
- Université Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999, Hôpital Marie-Lannelongue, Le Plessis-Robinson, France
| | - Robert Lafyatis
- Division of Rheumatology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Moccaldi B, De Michieli L, Binda M, Famoso G, Depascale R, Perazzolo Marra M, Doria A, Zanatta E. Serum Biomarkers in Connective Tissue Disease-Associated Pulmonary Arterial Hypertension. Int J Mol Sci 2023; 24:ijms24044178. [PMID: 36835590 PMCID: PMC9967966 DOI: 10.3390/ijms24044178] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a life-threatening complication of connective tissue diseases (CTDs) characterised by increased pulmonary arterial pressure and pulmonary vascular resistance. CTD-PAH is the result of a complex interplay among endothelial dysfunction and vascular remodelling, autoimmunity and inflammatory changes, ultimately leading to right heart dysfunction and failure. Due to the non-specific nature of the early symptoms and the lack of consensus on screening strategies-except for systemic sclerosis, with a yearly transthoracic echocardiography as recommended-CTD-PAH is often diagnosed at an advanced stage, when the pulmonary vessels are irreversibly damaged. According to the current guidelines, right heart catheterisation is the gold standard for the diagnosis of PAH; however, this technique is invasive, and may not be available in non-referral centres. Hence, there is a need for non-invasive tools to improve the early diagnosis and disease monitoring of CTD-PAH. Novel serum biomarkers may be an effective solution to this issue, as their detection is non-invasive, has a low cost and is reproducible. Our review aims to describe some of the most promising circulating biomarkers of CTD-PAH, classified according to their role in the pathophysiology of the disease.
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Affiliation(s)
- Beatrice Moccaldi
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, 35128 Padova, Italy
| | - Laura De Michieli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padova University Hospital, 35128 Padova, Italy
| | - Marco Binda
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, 35128 Padova, Italy
| | - Giulia Famoso
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padova University Hospital, 35128 Padova, Italy
| | - Roberto Depascale
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, 35128 Padova, Italy
| | - Martina Perazzolo Marra
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padova University Hospital, 35128 Padova, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, 35128 Padova, Italy
- Correspondence: ; Tel.: +39-0498212190
| | - Elisabetta Zanatta
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, 35128 Padova, Italy
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25
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Fioretto BS, Rosa I, Matucci-Cerinic M, Romano E, Manetti M. Current Trends in Vascular Biomarkers for Systemic Sclerosis: A Narrative Review. Int J Mol Sci 2023; 24:ijms24044097. [PMID: 36835506 PMCID: PMC9965592 DOI: 10.3390/ijms24044097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Systemic sclerosis (SSc, scleroderma) is a multifaceted rare connective tissue disease whose pathogenesis is dominated by immune dysregulation, small vessel vasculopathy, impaired angiogenesis, and both cutaneous and visceral fibrosis. Microvascular impairment represents the initial event of the disease, preceding fibrosis by months or years and accounting for the main disabling and/or life-threatening clinical manifestations, including telangiectasias, pitting scars, periungual microvascular abnormalities (e.g., giant capillaries, hemorrhages, avascular areas, ramified/bushy capillaries) clinically detectable by nailfold videocapillaroscopy, ischemic digital ulcers, pulmonary arterial hypertension, and scleroderma renal crisis. Despite a variety of available treatment options, treatment of SSc-related vascular disease remains problematic, even considering SSc etherogenity and the quite narrow therapeutic window. In this context, plenty of studies have highlighted the great usefulness in clinical practice of vascular biomarkers allowing clinicians to assess the evolution of the pathological process affecting the vessels, as well as to predict the prognosis and the response to therapy. The current narrative review provides an up-to-date overview of the main candidate vascular biomarkers that have been proposed for SSc, focusing on their main reported associations with characteristic clinical vascular features of the disease.
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Affiliation(s)
- Bianca Saveria Fioretto
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Irene Rosa
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Marco Matucci-Cerinic
- Section of Internal Medicine, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Eloisa Romano
- Section of Internal Medicine, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Mirko Manetti
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Imaging Platform, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Correspondence:
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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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Kheyfets VO, Sweatt AJ, Gomberg-Maitland M, Ivy DD, Condliffe R, Kiely DG, Lawrie A, Maron BA, Zamanian RT, Stenmark KR. Computational platform for doctor-artificial intelligence cooperation in pulmonary arterial hypertension prognostication: a pilot study. ERJ Open Res 2023; 9:00484-2022. [PMID: 36776484 PMCID: PMC9907150 DOI: 10.1183/23120541.00484-2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pulmonary arterial hypertension (PAH) is a heterogeneous and complex pulmonary vascular disease associated with substantial morbidity. Machine-learning algorithms (used in many PAH risk calculators) can combine established parameters with thousands of circulating biomarkers to optimise PAH prognostication, but these approaches do not offer the clinician insight into what parameters drove the prognosis. The approach proposed in this study diverges from other contemporary phenotyping methods by identifying patient-specific parameters driving clinical risk. Methods We trained a random forest algorithm to predict 4-year survival risk in a cohort of 167 adult PAH patients evaluated at Stanford University, with 20% withheld for (internal) validation. Another cohort of 38 patients from Sheffield University were used as a secondary (external) validation. Shapley values, borrowed from game theory, were computed to rank the input parameters based on their importance to the predicted risk score for the entire trained random forest model (global importance) and for an individual patient (local importance). Results Between the internal and external validation cohorts, the random forest model predicted 4-year risk of death/transplant with sensitivity and specificity of 71.0-100% and 81.0-89.0%, respectively. The model reinforced the importance of established prognostic markers, but also identified novel inflammatory biomarkers that predict risk in some PAH patients. Conclusion These results stress the need for advancing individualised phenotyping strategies that integrate clinical and biochemical data with outcome. The computational platform presented in this study offers a critical step towards personalised medicine in which a clinician can interpret an algorithm's assessment of an individual patient.
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Affiliation(s)
- Vitaly O. Kheyfets
- Paediatric Critical Care Medicine, Developmental Lung Biology and CVP Research Laboratories, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Andrew J. Sweatt
- Division of Pulmonary and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | | | - Dunbar D. Ivy
- Department of Paediatric Cardiology, Children's Hospital Colorado, Aurora, CO, USA
| | - Robin Condliffe
- Sheffield Pulmonary Vascular Disease Unit, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - David G. Kiely
- Sheffield Pulmonary Vascular Disease Unit, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
- Insigneo Institute for in-silico Medicine, University of Sheffield, Sheffield, UK
| | - Allan Lawrie
- Sheffield Pulmonary Vascular Disease Unit, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
- Insigneo Institute for in-silico Medicine, University of Sheffield, Sheffield, UK
| | - Bradley A. Maron
- Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard University, Boston, MA, USA
| | - Roham T. Zamanian
- Division of Pulmonary and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | - Kurt R. Stenmark
- Paediatric Critical Care Medicine, Developmental Lung Biology and CVP Research Laboratories, School of Medicine, University of Colorado, Aurora, CO, USA
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Barrios JP, Tison GH. Advancing cardiovascular medicine with machine learning: Progress, potential, and perspective. Cell Rep Med 2022; 3:100869. [PMID: 36543095 PMCID: PMC9798021 DOI: 10.1016/j.xcrm.2022.100869] [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: 08/03/2022] [Revised: 10/26/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
Recent advances in machine learning (ML) have made it possible to analyze high-dimensional and complex data-such as free text, images, waveforms, videos, and sound-in an automated manner by successfully learning complex associations within these data. Cardiovascular medicine is particularly well poised to take advantage of these ML advances, due to the widespread digitization of medical data and the large number of diagnostic tests used to evaluate cardiovascular disease. Various ML approaches have successfully been applied to cardiovascular tests and diseases to automate interpretation, accurately perform measurements, and, in some cases, predict novel diagnoses from less invasive tests, effectively expanding the utility of more widely accessible diagnostic tests. Here, we present examples of some impactful advances in cardiovascular medicine using ML across a variety of modalities, with a focus on deep learning applications.
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Affiliation(s)
- Joshua P. Barrios
- Department of Medicine, Division of Cardiology, University of California, San Francisco, 555 Mission Bay Blvd South Box 3120, San Francisco, CA 94158, USA
| | - Geoffrey H. Tison
- Department of Medicine, Division of Cardiology, University of California, San Francisco, 555 Mission Bay Blvd South Box 3120, San Francisco, CA 94158, USA,Bakar Computational Health Sciences Institute, University of California, San Francisco, 555 Mission Bay Blvd South Box 3120, San Francisco, CA 94158, USA,Corresponding author
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Xu J, Liang C, Li J. A signal recognition particle-related joint model of LASSO regression, SVM-RFE and artificial neural network for the diagnosis of systemic sclerosis-associated pulmonary hypertension. Front Genet 2022; 13:1078200. [PMID: 36518216 PMCID: PMC9742487 DOI: 10.3389/fgene.2022.1078200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 08/18/2023] Open
Abstract
Background: Systemic sclerosis-associated pulmonary hypertension (SSc-PH) is one of the most common causes of death in patients with systemic sclerosis (SSc). The complexity of SSc-PH and the heterogeneity of clinical features in SSc-PH patients contribute to the difficulty of diagnosis. Therefore, there is a pressing need to develop and optimize models for the diagnosis of SSc-PH. Signal recognition particle (SRP) deficiency has been found to promote the progression of multiple cancers, but the relationship between SRP and SSc-PH has not been explored. Methods: First, we obtained the GSE19617 and GSE33463 datasets from the Gene Expression Omnibus (GEO) database as the training set, GSE22356 as the test set, and the SRP-related gene set from the MSigDB database. Next, we identified differentially expressed SRP-related genes (DE-SRPGs) and performed unsupervised clustering and gene enrichment analyses. Then, we used least absolute shrinkage and selection operator (LASSO) regression and support vector machine-recursive feature elimination (SVM-RFE) to identify SRP-related diagnostic genes (SRP-DGs). We constructed an SRP scoring system and a nomogram model based on the SRP-DGs and established an artificial neural network (ANN) for diagnosis. We used receiver operating characteristic (ROC) curves to identify the SRP-related signature in the training and test sets. Finally, we analyzed immune features, signaling pathways, and drugs associated with SRP and investigated SRP-DGs' functions using single gene batch correlation analysis-based GSEA. Results: We obtained 30 DE-SRPGs and found that they were enriched in functions and pathways such as "protein targeting to ER," "cytosolic ribosome," and "coronavirus disease-COVID-19". Subsequently, we identified seven SRP-DGs whose expression levels and diagnostic efficacy were validated in the test set. As one signature, the area under the ROC curve (AUC) values for seven SRP-DGs were 0.769 and 1.000 in the training and test sets, respectively. Predictions made using the nomogram model are likely beneficial for SSc-PH patients. The AUC values of the ANN were 0.999 and 0.860 in the training and test sets, respectively. Finally, we discovered that some immune cells and pathways, such as activated dendritic cells, complement activation, and heme metabolism, were significantly associated with SRP-DGs and identified ten drugs targeting SRP-DGs. Conclusion: We constructed a reliable SRP-related ANN model for the diagnosis of SSc-PH and investigated the possible role of SRP in the etiopathogenesis of SSc-PH by bioinformatics methods to provide a basis for precision and personalized medicine.
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Affiliation(s)
- Jingxi Xu
- North Sichuan Medical College, Nanchong, China
- Department of Rheumatology and Immunology, The First People’s Hospital of Yibin, Yibin, China
| | - Chaoyang Liang
- Department of Rheumatology and Immunology, The First People’s Hospital of Yibin, Yibin, China
| | - Jiangtao Li
- Department of Rheumatology and Immunology, The First People’s Hospital of Yibin, Yibin, China
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Bellocchi C, Chung A, Volkmann ER. Predicting the Progression of Very Early Systemic Sclerosis: Current Insights. Open Access Rheumatol 2022; 14:171-186. [PMID: 36133926 PMCID: PMC9484572 DOI: 10.2147/oarrr.s285409] [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] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Systemic sclerosis (SSc) is a complex autoimmune connective tissue disease with distinct pathological hallmarks (ie, inflammation, vasculopathy, fibrosis) that may predominate at different stages in the disease course with varying severity. Initial efforts to classify patients with SSc identified a subset of patients with very early SSc. These patients possessed signs of SSc (eg, Raynaud phenomenon, SSc specific autoantibodies and/or nailfold capillary abnormalities) without fulfilling complete SSc classification criteria. Recognizing the inherent value in early diagnosis and intervention in SSc, researchers have endeavored to identify risk factors for progression from very early SSc to definite SSc. The present review summarizes the clinical phenotype of patients with very early and early SSc. Through a scoping review of recent literature, this review also describes risk factors for progression to definite SSc with a focus on the specific clinical features that arise early in the SSc disease course (eg, diffuse cutaneous sclerosis, interstitial lung disease, esophageal dysfunction, renal crisis, cardiac involvement). In addition to clinical risk factors, this review provides evidence for how biological data (ie, serological, genomic, proteomic profiles, skin bioengineering methods) can be integrated into risk assessment models in the future. Furthering our understanding of biological features of very early SSc will undoubtedly provide novel insights into SSc pathogenesis and may illuminate new therapeutic targets to prevent progression of SSc.
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Affiliation(s)
- Chiara Bellocchi
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, University of Milan, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Augustine Chung
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Elizabeth R Volkmann
- Division of Rheumatology, Department of Medicine, University of California, David Geffen School of Medicine, Los Angeles, CA, USA
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Bonomi F, Peretti S, Lepri G, Venerito V, Russo E, Bruni C, Iannone F, Tangaro S, Amedei A, Guiducci S, Matucci Cerinic M, Bellando Randone S. The Use and Utility of Machine Learning in Achieving Precision Medicine in Systemic Sclerosis: A Narrative Review. J Pers Med 2022; 12:1198. [PMID: 35893293 PMCID: PMC9331823 DOI: 10.3390/jpm12081198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a rare connective tissue disease that can affect different organs and has extremely heterogenous presentations. This complexity makes it difficult to perform an early diagnosis and a subsequent subclassification of the disease. This hinders a personalized approach in clinical practice. In this context, machine learning (ML), a branch of artificial intelligence (AI), is able to recognize relationships in data and predict outcomes. METHODS Here, we performed a narrative review concerning the application of ML in SSc to define the state of art and evaluate its role in a precision medicine context. RESULTS Currently, ML has been used to stratify SSc patients and identify those at high risk of severe complications. Additionally, ML may be useful in the early detection of organ involvement. Furthermore, ML might have a role in target therapy approach and in predicting drug response. CONCLUSION Available evidence about the utility of ML in SSc is sparse but promising. Future improvements in this field could result in a big step toward precision medicine. Further research is needed to define ML application in clinical practice.
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Affiliation(s)
- Francesco Bonomi
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Silvia Peretti
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Gemma Lepri
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Vincenzo Venerito
- Rheumatology Unit, Department of Emergency and Organ Transplantations, University of Bari Aldo Moro, 70121 Bari, Italy; (V.V.); (F.I.)
| | - Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Cosimo Bruni
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
- Department of Rheumatology, University Hospital of Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - Florenzo Iannone
- Rheumatology Unit, Department of Emergency and Organ Transplantations, University of Bari Aldo Moro, 70121 Bari, Italy; (V.V.); (F.I.)
| | - Sabina Tangaro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70121 Bari, Italy;
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Serena Guiducci
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Marco Matucci Cerinic
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Silvia Bellando Randone
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
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Romano E, Rosa I, Fioretto BS, Matucci-Cerinic M, Manetti M. Circulating Neurovascular Guidance Molecules and Their Relationship with Peripheral Microvascular Impairment in Systemic Sclerosis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071056. [PMID: 35888144 PMCID: PMC9316343 DOI: 10.3390/life12071056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Systemic sclerosis (SSc, scleroderma) is a complex connective tissue disease whose earliest clinical manifestations are microvascular tone dysregulation and peripheral microcirculatory abnormalities. Following previous evidence of an association between circulating neurovascular guidance molecules and SSc disturbed angiogenesis, here, we measured the levels of soluble neuropilin 1 (sNRP1), semaphorin 3E (Sema3E), and Slit2 by enzyme-linked immunosorbent assay in serum samples from a large case series of 166 SSc patients vs. 110 healthy controls. We focused on their possible correlation with vascular disease clinical features and applied logistic regression analysis to determine which of them could better reflect disease activity and severity. Our results demonstrate that, in SSc: (i) sNRP1 is significantly decreased, with lower sNRP1 serum levels correlating with the severity of nailfold videocapillaroscopy (NVC) abnormalities and the presence of ischemic digital ulcers (DUs); (ii) both Sema3E and Slit2 are increased, with Sema3E better reflecting early NVC abnormalities; and (iii) higher Sema3E correlates with the absence of DUs, while augmented Slit2 associates with the presence of DUs. Receiver operator characteristics curve analysis revealed that both circulating sNRP1 and Sema3E show a moderate diagnostic accuracy. Moreover, logistic regression analysis allowed to identify sNRP1 and Sema3E as more suitable independent biomarkers reflecting the activity and severity of SSc-related peripheral microvasculopathy.
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Affiliation(s)
- Eloisa Romano
- Division of Rheumatology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.R.); (B.S.F.); (M.M.-C.)
| | - Irene Rosa
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy;
| | - Bianca Saveria Fioretto
- Division of Rheumatology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.R.); (B.S.F.); (M.M.-C.)
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy;
| | - Marco Matucci-Cerinic
- Division of Rheumatology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.R.); (B.S.F.); (M.M.-C.)
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Mirko Manetti
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy;
- Correspondence: ; Tel.: +39-055-275-8073
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Zhou J, Chou OHI, Wong KHG, Lee S, Leung KSK, Liu T, Cheung BMY, Wong ICK, Tse G, Zhang Q. Development of an Electronic Frailty Index for Predicting Mortality and Complications Analysis in Pulmonary Hypertension Using Random Survival Forest Model. Front Cardiovasc Med 2022; 9:735906. [PMID: 35872897 PMCID: PMC9304657 DOI: 10.3389/fcvm.2022.735906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background The long-term prognosis of the cardio-metabolic and renal complications, in addition to mortality in patients with newly diagnosed pulmonary hypertension, are unclear. This study aims to develop a scalable predictive model in the form of an electronic frailty index (eFI) to predict different adverse outcomes. Methods This was a population-based cohort study of patients diagnosed with pulmonary hypertension between January 1st, 2000 and December 31st, 2017, in Hong Kong public hospitals. The primary outcomes were mortality, cardiovascular complications, renal diseases, and diabetes mellitus. The univariable and multivariable Cox regression analyses were applied to identify the significant risk factors, which were fed into the non-parametric random survival forest (RSF) model to develop an eFI. Results A total of 2,560 patients with a mean age of 63.4 years old (interquartile range: 38.0–79.0) were included. Over a follow-up, 1,347 died and 1,878, 437, and 684 patients developed cardiovascular complications, diabetes mellitus, and renal disease, respectively. The RSF-model-identified age, average readmission, anti-hypertensive drugs, cumulative length of stay, and total bilirubin were among the most important risk factors for predicting mortality. Pair-wise interactions of factors including diagnosis age, average readmission interval, and cumulative hospital stay were also crucial for the mortality prediction. Patients who developed all-cause mortality had higher values of the eFI compared to those who survived (P < 0.0001). An eFI ≥ 9.5 was associated with increased risks of mortality [hazard ratio (HR): 1.90; 95% confidence interval [CI]: 1.70–2.12; P < 0.0001]. The cumulative hazards were higher among patients who were 65 years old or above with eFI ≥ 9.5. Using the same cut-off point, the eFI predicted a long-term mortality over 10 years (HR: 1.71; 95% CI: 1.53–1.90; P < 0.0001). Compared to the multivariable Cox regression, the precision, recall, area under the curve (AUC), and C-index were significantly higher for RSF in the prediction of outcomes. Conclusion The RSF models identified the novel risk factors and interactions for the development of complications and mortality. The eFI constructed by RSF accurately predicts the complications and mortality of patients with pulmonary hypertension, especially among the elderly.
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Affiliation(s)
- Jiandong Zhou
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oscar Hou In Chou
- Frailty Assessment Unit, Cardiovascular Analytics Group, Hong Kong, Hong Kong SAR, China
- Division of Clincal Pharmacology, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ka Hei Gabriel Wong
- Frailty Assessment Unit, Cardiovascular Analytics Group, Hong Kong, Hong Kong SAR, China
| | - Sharen Lee
- Frailty Assessment Unit, Cardiovascular Analytics Group, Hong Kong, Hong Kong SAR, China
| | | | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Bernard Man Yung Cheung
- Division of Clincal Pharmacology, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ian Chi Kei Wong
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Medicines Optimisation Research and Education, UCL School of Pharmacy, London, United Kingdom
| | - Gary Tse
- Frailty Assessment Unit, Cardiovascular Analytics Group, Hong Kong, Hong Kong SAR, China
- Kent and Medway Medical School, Canterbury, United Kingdom
- *Correspondence: Qingpeng Zhang
| | - Qingpeng Zhang
- School of Data Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Gary Tse ;
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Rhodes CJ, Wharton J, Swietlik EM, Harbaum L, Girerd B, Coghlan JG, Lordan J, Church C, Pepke-Zaba J, Toshner M, Wort SJ, Kiely DG, Condliffe R, Lawrie A, Gräf S, Montani D, Boucly A, Sitbon O, Humbert M, Howard LS, Morrell NW, Wilkins MR. Using the Plasma Proteome for Risk Stratifying Patients with Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2022; 205:1102-1111. [PMID: 35081018 PMCID: PMC9851485 DOI: 10.1164/rccm.202105-1118oc] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rationale: NT-proBNP (N-terminal pro-brain natriuretic peptide), a biomarker of cardiac origin, is used to risk stratify patients with pulmonary arterial hypertension (PAH). Its limitations include poor sensitivity to early vascular pathology. Other biomarkers of vascular or systemic origin may also be useful in the management of PAH. Objectives: Identify prognostic proteins in PAH that complement NT-proBNP and clinical risk scores. Methods: An aptamer-based assay (SomaScan version 4) targeting 4,152 proteins was used to measure plasma proteins in patients with idiopathic, heritable, or drug-induced PAH from the UK National Cohort of PAH (n = 357) and the French EFORT (Evaluation of Prognostic Factors and Therapeutic Targets in PAH) study (n = 79). Prognostic proteins were identified in discovery-replication analyses of UK samples. Proteins independent of 6-minute-walk distance and NT-proBNP entered least absolute shrinkage and selection operator modeling, and the best combination in a single score was evaluated against clinical targets in EFORT. Measurements and Main Results: Thirty-one proteins robustly informed prognosis independent of NT-proBNP and 6-minute-walk distance in the UK cohort. A weighted combination score of six proteins was validated at baseline (5-yr mortality; area under the curve [AUC], 0.73; 95% confidence interval [CI], 0.63-0.85) and follow-up in EFORT (AUC, 0.84; 95% CI, 0.75-0.94; P = 9.96 × 10-6). The protein score risk stratified patients independent of established clinical targets and risk equations. The addition of the six-protein model score to NT-proBNP improved prediction of 5-year outcomes from AUC 0.762 (0.702-0.821) to 0.818 (0.767-0.869) by receiver operating characteristic analysis (P = 0.00426 for difference in AUC) in the UK replication and French samples combined. Conclusions: The plasma proteome informs prognosis beyond established factors in PAH and may provide a more sensitive measure of therapeutic response.
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Affiliation(s)
- Christopher J Rhodes
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - John Wharton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Emilia M Swietlik
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lars Harbaum
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Barbara Girerd
- Université Paris-Saclay, AP-HP, INSERM UMR_S 999, Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Centre, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - J Gerry Coghlan
- Department of Cardiology, Royal Free Campus, University College London, London, United Kingdom
| | - James Lordan
- University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom
| | - Colin Church
- University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joanna Pepke-Zaba
- Pulmonary Vascular Disease Unit, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Mark Toshner
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephen J Wort
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - David G Kiely
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom.,Sheffield Pulmonary Vascular Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom; and
| | - Robin Condliffe
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom.,Sheffield Pulmonary Vascular Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom; and
| | - Allan Lawrie
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,BioResource for Translational Research, National Institute for Health Research Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - David Montani
- Université Paris-Saclay, AP-HP, INSERM UMR_S 999, Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Centre, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Athénaïs Boucly
- Université Paris-Saclay, AP-HP, INSERM UMR_S 999, Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Centre, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Olivier Sitbon
- Université Paris-Saclay, AP-HP, INSERM UMR_S 999, Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Centre, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Marc Humbert
- Université Paris-Saclay, AP-HP, INSERM UMR_S 999, Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Centre, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Luke S Howard
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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35
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Rhodes CJ, Sweatt AJ, Maron BA. Harnessing Big Data to Advance Treatment and Understanding of Pulmonary Hypertension. Circ Res 2022; 130:1423-1444. [PMID: 35482840 PMCID: PMC9070103 DOI: 10.1161/circresaha.121.319969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pulmonary hypertension is a complex disease with multiple causes, corresponding to phenotypic heterogeneity and variable therapeutic responses. Advancing understanding of pulmonary hypertension pathogenesis is likely to hinge on integrated methods that leverage data from health records, imaging, novel molecular -omics profiling, and other modalities. In this review, we summarize key data sets generated thus far in the field and describe analytical methods that hold promise for deciphering the molecular mechanisms that underpin pulmonary vascular remodeling, including machine learning, network medicine, and functional genetics. We also detail how genetic and subphenotyping approaches enable earlier diagnosis, refined prognostication, and optimized treatment prediction. We propose strategies that identify functionally important molecular pathways, bolstered by findings across multi-omics platforms, which are well-positioned to individualize drug therapy selection and advance precision medicine in this highly morbid disease.
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Affiliation(s)
- Christopher J Rhodes
- Department of Medicine, National Heart and Lung Institute, Imperial College London, United Kingdom (C.J.R.)
| | - Andrew J Sweatt
- Department of Medicine, National Heart and Lung Institute, Imperial College London, United Kingdom (C.J.R.)
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (B.A.M.).,Division of Cardiology, VA Boston Healthcare System, West Roxbury, MA (B.A.M.)
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36
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Shi B, Zhou T, Lv S, Wang M, Chen S, Heidari AA, Huang X, Chen H, Wang L, Wu P. An evolutionary machine learning for pulmonary hypertension animal model from arterial blood gas analysis. Comput Biol Med 2022; 146:105529. [PMID: 35594682 DOI: 10.1016/j.compbiomed.2022.105529] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/03/2022]
Abstract
Pulmonary hypertension (PH) is a rare and fatal condition that leads to right heart failure and death. The pathophysiology of PH and potential therapeutic approaches are yet unknown. PH animal models' development and proper evaluation are critical to PH research. This work presents an effective analysis technology for PH from arterial blood gas analysis utilizing an evolutionary kernel extreme learning machine with multiple strategies integrated slime mould algorithm (MSSMA). In MSSMA, two efficient bee-foraging learning operators are added to the original slime mould algorithm, ensuring a suitable trade-off between intensity and diversity. The proposed MSSMA is evaluated on thirty IEEE benchmarks and the statistical results show that the search performance of the MSSMA is significantly improved. The MSSMA is utilised to develop a kernel extreme learning machine (MSSMA-KELM) on PH from arterial blood gas analysis. Comprehensively, the proposed MSSMA-KELM can be used as an effective analysis technology for PH from arterial Blood gas analysis with an accuracy of 93.31%, Matthews coefficient of 90.13%, Sensitivity of 91.12%, and Specificity of 90.73%. MSSMA-KELM can be treated as an effective approach for evaluating mouse PH models.
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Affiliation(s)
- Beibei Shi
- Affiliated People's Hospital of Jiangsu University, 8 Dianli Road, Zhenjiang, Jiangsu, 212000, China.
| | - Tao Zhou
- The First Clinical College, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Shushu Lv
- The First Clinical College, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Mingjing Wang
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, 325035, China.
| | - Siyuan Chen
- Affiliated People's Hospital of Jiangsu University, 8 Dianli Road, Zhenjiang, Jiangsu, 212000, China.
| | - Ali Asghar Heidari
- School of Surveying and Geospatial Engineering, College of Engineering, University of Tehran, Tehran, Iran; Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore.
| | - Xiaoying Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, 325035, China.
| | - Liangxing Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Peiliang Wu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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37
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Qu C, Feng W, Zhao Q, Liu Q, Luo X, Wang G, Sun M, Yao Z, Sun Y, Hou S, Zhao C, Zhang R, Qu X. Effect of Levosimendan on Acute Decompensated Right Heart Failure in Patients With Connective Tissue Disease-Associated Pulmonary Arterial Hypertension. Front Med (Lausanne) 2022; 9:778620. [PMID: 35308558 PMCID: PMC8931274 DOI: 10.3389/fmed.2022.778620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Aims Acute decompensated right heart failure (RHF) in chronic precapillary pulmonary hypertension is often typified by a swiftly progressive syndrome involving systemic congestion. This results from the impairment of the right ventricular filling and/or a reduction in the flow output of the right ventricle, which has been linked to a dismal prognosis of short duration. Despite this, there are limited therapeutic data regarding these acute incidents. This study examined the effect of levosimendan on acute decompensated RHF in patients with connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH). Methods This retrospective study included 87 patients with confirmed CTD-PAH complicated acute decompensated RHF between November 2015 and April 2021. We collected biological, clinical, and demographic data, as well as therapy data, from patients with acute decompensated RHF who required levosimendan treatment in the cardiac care unit (CCU) for CTD-PAH. The patients were divided into two groups according to the levosimendan treatment. Patient information between the two groups was systematically compared in hospital and at follow-up. Results Oxygen saturation of mixed venose blood (SvO2), estimated glomerular filtration rate (eGFR), 24-h urine output, and tricuspid annular plane systolic excursion (TAPSE) were found to be considerably elevated in the levosimendan cohort compared with the control cohort. Patients in the levosimendan cohort exhibited considerably reduced levels of C-reactive protein (CRP), white blood cell (WBC), troponin I, creatinine, NT-proBNP, and RV diameter compared with those in the control cohort. A higher survival rate was observed in the levosimendan cohort. Conclusions Levosimendan treatment could effectively improve acute decompensated RHF and systemic hemodynamics in CTD-PAH patients, with positive effects on survival in hospital and can, therefore, be considered as an alternative treatment option for improving clinical short-term outcomes.
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Affiliation(s)
- Chao Qu
- Department of Cardiology, Heilongjiang Provincial People's Hospital, Harbin, China
| | - Wei Feng
- Department of Cardiology, 1st Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Zhao
- Department of Cardiology, 1st Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Liu
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xing Luo
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, China
| | - Gang Wang
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, China
| | - Meng Sun
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, China
| | - Zhibo Yao
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, China
| | - Yufei Sun
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, China
| | - Shenglong Hou
- Department of Cardiology, Heilongjiang Provincial People's Hospital, Harbin, China
| | - Chunyang Zhao
- Department of Cardiology, Harbin 242 Hospital, Harbin, China
| | - Ruoxi Zhang
- Department of Cardiology, Harbin Yinghua Hospital, Harbin, China
- *Correspondence: Ruoxi Zhang
| | - Xiufen Qu
- Department of Cardiology, 1st Affiliated Hospital of Harbin Medical University, Harbin, China
- Xiufen Qu
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38
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Zhang Y, Qin D, Qin L, Yang X, Luo Q, Wang H. Diagnostic value of cardiac natriuretic peptide on pulmonary hypertension in systemic sclerosis: A systematic review and meta-analysis. Joint Bone Spine 2021; 89:105287. [PMID: 34601113 DOI: 10.1016/j.jbspin.2021.105287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Pulmonary arterial hypertension (PAH) is a major cause of morbidity and mortality in systemic sclerosis (SSc). Many risk factors and predictors of outcomes have been identified in these patients. B-type natriuretic peptide (BNP) and N-terminal pro-BNP (NT-proBNP) serum levels are often elevated in SSc patients with early PAH. We conducted this systematic review and meta-analysis to estimate the diagnostic value of BNP/NT-proBNP in systemic sclerosis secondary pulmonary arterial hypertension (SSc-PAH). METHODS A systematic search was performed through PubMed, Embase, and Cochrane Library databases up to January 30, 2021. Stata 16.0 (Stata Corp, College Station, TX) was used to conduct the meta-analysis. RESULTS A total of 9 studies involving 220 SSc-PAH patients and 259 non-SSc-PAH controls were included. The values of sensitivity and specificity using BNP and NT-ProBNP as diagnostic tools were pooled in the diagnostic meta-analysis. The overall performance of BNP/NT-ProBNP detection was: pooled sensitivity, 0.67 (95% CI: 0.52 to 0.79); pooled specificity, 0.84 (95% CI: 0.75 to 0.91); pooled positive likelihood ratio, 4.3 (95% CI: 3 to 6.1); and pooled negative likelihood ratio, 0.39 (95% CI: 0.28 to 0.55). The subgroup analysis showed similar results. Funnel plots indicate that there is no evidence for publication bias. CONCLUSIONS Our results revealed that NT-proBNP has certain diagnostic value for PAH due to its better specificity and moderate sensitivity, but its clinical application value remains suboptimal and can not be a stand-alone decision-making diagnostic tool of SSc-PAH.
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Affiliation(s)
- Yiwen Zhang
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China
| | - Dimao Qin
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China
| | - Li Qin
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China
| | - Xiaoqian Yang
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China
| | - Qiang Luo
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China
| | - Han Wang
- Department of Cardiology, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, 82 Qinglong St. Chengdu, Sichuan, China.
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39
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Diagnostic and prognostic significance of serum angiopoietin-1 and -2 concentrations in patients with pulmonary hypertension. Sci Rep 2021; 11:15502. [PMID: 34326408 PMCID: PMC8322335 DOI: 10.1038/s41598-021-94907-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
Several biomarkers for detecting pulmonary hypertension (PH) have been reported. However, these biomarkers are deemed insufficient to detect PH in its early stages. We evaluated the utility of serum angiopoietin (ANGP), a glycoprotein related to angiogenesis, as a diagnostic and prognostic biomarker of PH. Patients with PH who underwent right-heart catheterization, were retrospectively studied. Serum concentrations of ANGP-1 and ANGP-2 were measured using an enzyme-linked immunosorbent assay in patients with PH (n = 32), those with idiopathic pulmonary fibrosis (IPF) without PH (as a disease control, n = 75), and age-matched healthy controls (HC, n = 60). Nineteen patients (59.4%) with PH had World Health Organization group 3 PH. Serum ANGP-2 concentration, but not ANGP-1, in patients with PH was significantly higher compared with that in HC (p = 0.025) and in patients with IPF without PH (p = 0.008). Serum ANGP-2 concentration in patients with PH positively and significantly correlated with N-terminal pro-B-type natriuretic peptide (r = 0.769, p < 0.001), right ventricular diameter on echocardiography (r = 0.565, p = 0.035), and mean pulmonary arterial pressure (r = 0.449, p = 0.032) and pulmonary vascular resistance (r = 0.451, p = 0.031) on right-heart catheterization. ANGP-1 and ANGP-2 were expressed on lung vascular endothelial cells, as shown by immunohistochemistry. Patients with PH with higher ANGP-2 concentration (≥ 2.48 ng/mL) had significantly worse survival (p = 0.022). Higher ANGP-2 concentration was a significant worse prognostic factor (hazard ratio = 6.063, p = 0.037), while serum ANGP-1 concentration was not. In conclusion, serum ANGP-2 may be a useful diagnostic and prognostic biomarker in patients with PH, especially in patients with group 3 PH.
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40
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Sweatt AJ, Reddy R, Rahaghi FN, Al-Naamani N. What's new in pulmonary hypertension clinical research: lessons from the best abstracts at the 2020 American Thoracic Society International Conference. Pulm Circ 2021; 11:20458940211040713. [PMID: 34471517 PMCID: PMC8404658 DOI: 10.1177/20458940211040713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
In this conference paper, we review the 2020 American Thoracic Society International Conference session titled, "What's New in Pulmonary Hypertension Clinical Research: Lessons from the Best Abstracts". This virtual mini-symposium took place on 21 October 2020, in lieu of the annual in-person ATS International Conference which was cancelled due to the COVID-19 pandemic. Seven clinical research abstracts were selected for presentation in the session, which encompassed five major themes: (1) standardizing diagnosis and management of pulmonary hypertension, (2) improving risk assessment in pulmonary arterial hypertension, (3) evaluating biomarkers of disease activity, (4) understanding metabolic dysregulation across the spectrum of pulmonary hypertension, and (5) advancing knowledge in chronic thromboembolic pulmonary hypertension. Focusing on these five thematic contexts, we review the current state of knowledge, summarize presented research abstracts, appraise their significance and limitations, and then discuss relevant future directions in pulmonary hypertension clinical research.
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Affiliation(s)
- Andrew J. Sweatt
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Raju Reddy
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Farbod N. Rahaghi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Nadine Al-Naamani
- Division of Pulmonary and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - on behalf of the American Thoracic Society Pulmonary Circulation Assembly Early Career Working Group
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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41
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Launay D, Sanges S, Sobanski V. Time for precision medicine in systemic sclerosis-associated pulmonary arterial hypertension. Eur Respir J 2021; 57:57/6/2100205. [PMID: 34168056 DOI: 10.1183/13993003.00205-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 11/05/2022]
Affiliation(s)
- David Launay
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France .,Inserm, Lille, France.,CHU Lille, Service de Médecine Interne et Immunologie Clinique, Centre de référence des maladies autoimmunes systémiques rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France
| | - Sébastien Sanges
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France.,Inserm, Lille, France.,CHU Lille, Service de Médecine Interne et Immunologie Clinique, Centre de référence des maladies autoimmunes systémiques rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France
| | - Vincent Sobanski
- Univ. Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France.,Inserm, Lille, France.,CHU Lille, Service de Médecine Interne et Immunologie Clinique, Centre de référence des maladies autoimmunes systémiques rares du Nord et Nord-Ouest de France (CeRAINO), Lille, France.,Institut Universitaire de France (IUF), Lille, France
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