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Shi Y, Bao L, Li Y, Ou D, Li J, Liu X, Deng N, Deng C, Huang X, Zhang W, Ding H. Multi-omics combined to investigate potential druggable therapeutic targets for stroke: A systematic Mendelian randomization study and transcriptome verification. J Affect Disord 2024; 366:196-209. [PMID: 39214372 DOI: 10.1016/j.jad.2024.08.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/15/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Stroke is a highly prevalent and disabling disease whose disease mechanisms are not fully understood. The discovery of disease-associated proteins with genetic evidence of pathogenicity provides an opportunity to identify new therapeutic targets. METHOD We examined the observed and causal associations of thousands of plasma and inflammatory proteins that were measured using affinity-based proteomic assays. First, we pooled >3000 relevant proteins using a fixed-effects meta-analysis of 2 population-based studies involving 48,383 participants, then investigated the causal effects of stroke and its subtype-associated proteins by forward Mendelian randomization using cis-protein quantitative locus genetic tools identified from genome-wide association studies of these >48,000 individuals. To improve the accuracy of causal estimation, we implemented a systematic Mendelian randomization model that accounts for cascading imbalances between instruments and tested the robustness of causal estimation through multi-method analyses. To further validate the hypothesis that ginsenoside Rg1 monomer acts on the five protein targets screened for drug-targeted regulation, we conducted a comparative analysis of the mRNA (gene) expression levels of a limited number of genes in the brain tissues of different groups of SD rats. The druggability of the candidate proteins was investigated and the mechanism of action and potential targeting side effects were explored by Phenome-wide MR. RESULTS Six circulating proteins were identified to have a significant genetic association with stroke (PFDR < 0.05). For example, in patients with cardioembolic stroke, higher genetically predicted APRT was associated with a lower risk of cardioembolic stroke (ORivw [95 % CI] = 0.641 [0.517, 0.795]; P = 5.25 × 10-5, ORSMR [95 % CI] = 0.572, [0.397, 0.825], PSMR = 0.003). Mediation analyses suggested that atrial fibrillation, angina pectoris, and heart failure may mediate the association of CD40L, LIFR, and UPA with stroke. Molecular docking revealed promising interactions between the identified proteins and glycosides. Transcriptomic sequencing in animal models indicated that ginsenoside Rg1 may act through APRT, IL15RA, and VSIR pathways, with APRT showing significant variability in mRNA sequencing expression. Phenome-wide MR of the six target proteins showed an overwhelming predominance of PFDR > 0.05, indicating less toxicity. CONCLUSIONS The present study provides genetic evidence to support the potential efficacy of targeting the three druggable protein targets for the treatment of stroke. This is achieved by triangulating population genomic and proteomic data. Furthermore, the study validates the pathway mechanisms by which APRT, IL15RA, and VSIR dock ginsenoside Rg1 in animal models. This will help to prioritize stroke drug development.
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Affiliation(s)
- Yiming Shi
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Le Bao
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Yanling Li
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Dian Ou
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Jiating Li
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Xiaodan Liu
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Nujiao Deng
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Changqing Deng
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China
| | - Xiaoping Huang
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China.
| | - Wei Zhang
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China.
| | - Huang Ding
- Hunan University of Chinese Medicine, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Changsha, China.
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Peng W, Shi L, Huang Q, Li T, Jian W, Zhao L, Xu R, Liu T, Zhang B, Wang H, Tong L, Tang H, Wang Y. Metabolite profiles of distinct obesity phenotypes integrating impacts of altitude and their association with diet and metabolic disorders in Tibetans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174754. [PMID: 39032745 DOI: 10.1016/j.scitotenv.2024.174754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/20/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
OBJECTIVE Improved understanding of metabolic obesity phenotypes holds great promise for personalized strategies to combat obesity and its co-morbidities. Such investigation is however lacking in Tibetans with unique living environments and lifestyle in the highlands. Effects of altitude on heterogeneous metabolic obesity phenotypes remain unexplored. METHODS We defined metabolic obesity phenotypes i.e., metabolically healthy/unhealthy and obesity/normal weight in Tibetans (n = 1204) living at 2800 m in the suburb or over 4000 m in pastoral areas. 129 lipoprotein parameters and 25 low-molecular-weight metabolites were quantified and their associations with each phenotype were assessed using logistic regression models adjusting for potential confounders. The metabolic BMI (mBMI) was generated using a machine learning strategy and its relationship with prevalence of obesity co-morbidities and dietary exposures were investigated. RESULTS Ultrahigh altitude positively associated with the metabolically healthy and non-obese phenotype and had a tendency towards a negative association with metabolically unhealthy phenotype. Phenotype-specific associations were found for 107 metabolites (e.g., lipoprotein subclasses, N-acetyl-glycoproteins, amino acids, fatty acids and lactate, p < 0.05), among which 55 were manipulated by altitude. The mBMI showed consistent yet more pronounced associations with cardiometabolic outcomes than BMI. The ORs for diabetes, prediabetes and hypertriglyceridemia were reduced in individuals residing at ultrahigh altitude compared to those residing at high altitude. The mBMI mediated the negative association between pastoral diet and prevalence of prediabetes, hypertension and hypertriglyceridemia, respectively. CONCLUSIONS We found metabolite markers representing distinct obesity phenotypes associated with obesity co-morbidities and the modification effect of altitude, deciphering mechanisms underlying protective effect of ultrahigh altitude and the pastoral diet on metabolic health.
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Affiliation(s)
- Wen Peng
- Department of Public Health, Qinghai University Medical College, No. 16 Kunlun Rd, Xining, 810008, China; Nutrition and Health Promotion Center, Qinghai University Medical College, No. 16 Kunlun Rd, Xining 810008, China; Qinghai Provincial Key Laboratory of Prevention and Control of Glucolipid Metabolic Diseases with Traditional Chinese Medicine, Medical College, Qinghai University, No. 16 Kunlun Rd, Xining 810008, China.
| | - Lin Shi
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 199 Chang'an South Rd, Xi'an, Shaanxi 710062, China
| | - Qingxia Huang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, No. 825 Zhangheng Rd, Shanghai 200438, China
| | - Tiemei Li
- Department of Public Health, Qinghai University Medical College, No. 16 Kunlun Rd, Xining, 810008, China; Nutrition and Health Promotion Center, Qinghai University Medical College, No. 16 Kunlun Rd, Xining 810008, China
| | - Wenxiu Jian
- Department of Public Health, Qinghai University Medical College, No. 16 Kunlun Rd, Xining, 810008, China; Nutrition and Health Promotion Center, Qinghai University Medical College, No. 16 Kunlun Rd, Xining 810008, China
| | - Lei Zhao
- Department of Public Health, Qinghai University Medical College, No. 16 Kunlun Rd, Xining, 810008, China; Nutrition and Health Promotion Center, Qinghai University Medical College, No. 16 Kunlun Rd, Xining 810008, China
| | - Ruijie Xu
- Global Health Institute, School of Public Health, Xi'an Jiaotong University, Room 3104, No. 21 Hongren Building, West China Science and Technology lnnovation Harbour (iHarbour), Xi'an 710061, China
| | - Tianqi Liu
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 199 Chang'an South Rd, Xi'an, Shaanxi 710062, China
| | - Bin Zhang
- School of Mathematics and Statistics, Qinghai Nationalities University, No. 3 Bayi Middle Rd, Xining 810007, China
| | - Haijing Wang
- Department of Public Health, Qinghai University Medical College, No. 16 Kunlun Rd, Xining, 810008, China; Nutrition and Health Promotion Center, Qinghai University Medical College, No. 16 Kunlun Rd, Xining 810008, China
| | - Li Tong
- Qinghai Provincial Key Laboratory of Prevention and Control of Glucolipid Metabolic Diseases with Traditional Chinese Medicine, Medical College, Qinghai University, No. 16 Kunlun Rd, Xining 810008, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, No. 825 Zhangheng Rd, Shanghai 200438, China.
| | - Youfa Wang
- Global Health Institute, School of Public Health, Xi'an Jiaotong University, Room 3104, No. 21 Hongren Building, West China Science and Technology lnnovation Harbour (iHarbour), Xi'an 710061, China.
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Kim JW, Choi SA, Dan K, Koh EJ, Ha S, Phi JH, Kim KH, Han D, Kim SK. Proteomic profiling of cerebrospinal fluid reveals TKT as a potential biomarker for medulloblastoma. Sci Rep 2024; 14:21053. [PMID: 39251709 PMCID: PMC11383936 DOI: 10.1038/s41598-024-71738-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
Cerebrospinal fluid (CSF) plays an important role in brain tumors, including medulloblastoma (MBL). Recent advancements in mass spectrometry systems and 'Omics' data analysis methods enable unbiased, high proteome depth research. We conducted proteomic profiling of the total CSF in MBL patients with the purpose of finding a potential diagnostic biomarker for MBL. We quantified 1112 proteins per CSF sample. Feature selection identified four elevated soluble proteins (SPTBN1, HSP90AA1, TKT, and NME1-NME2) in MBL CSF. Validation with ELISA confirmed that TKT was significantly elevated in MBL. Additionally, TKT-positive extracellular vesicles were significantly enriched in MBL CSF and correlated with the burden of leptomeningeal seeding. Our results provide insights into the proteomics data of the total CSF of MBL patients. Furthermore, we identified the significance of TKT within the total CSF and its presence within circulating EVs in the CSF. We suggest that TKT may serve as a biomarker for MBL.
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Affiliation(s)
- Joo Whan Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Saehim Ha
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Hyun Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea.
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul, 03082, South Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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D’Amato M, Grignano MA, Iadarola P, Rampino T, Gregorini M, Viglio S. The Impact of Serum/Plasma Proteomics on SARS-CoV-2 Diagnosis and Prognosis. Int J Mol Sci 2024; 25:8633. [PMID: 39201322 PMCID: PMC11354567 DOI: 10.3390/ijms25168633] [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: 06/17/2024] [Revised: 07/19/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
While COVID-19's urgency has diminished since its emergence in late 2019, it remains a significant public health challenge. Recent research reveals that the molecular intricacies of this virus are far more complex than initially understood, with numerous post-translational modifications leading to diverse proteoforms and viral particle heterogeneity. Mass spectrometry-based proteomics of patient serum/plasma emerges as a promising complementary approach to traditional diagnostic methods, offering insights into SARS-CoV-2 protein dynamics and enhancing understanding of the disease and its long-term consequences. This article highlights key findings from three years of pandemic-era proteomics research. It delves into biomarker discovery, diagnostic advancements, and drug development efforts aimed at monitoring COVID-19 onset and progression and exploring treatment options. Additionally, it examines global protein abundance and post-translational modification profiling to elucidate signaling pathway alterations and protein-protein interactions during infection. Finally, it explores the potential of emerging multi-omics analytic strategies in combatting SARS-CoV-2.
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Affiliation(s)
- Maura D’Amato
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
| | - Maria Antonietta Grignano
- Unit of Nephrology, Dialysis and Transplantation, IRCCS Policlinico San Matteo Foundation, 27100 Pavia, Italy; (M.A.G.); (T.R.); (M.G.)
| | - Paolo Iadarola
- Department of Biology and Biotechnologies “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Teresa Rampino
- Unit of Nephrology, Dialysis and Transplantation, IRCCS Policlinico San Matteo Foundation, 27100 Pavia, Italy; (M.A.G.); (T.R.); (M.G.)
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy
| | - Marilena Gregorini
- Unit of Nephrology, Dialysis and Transplantation, IRCCS Policlinico San Matteo Foundation, 27100 Pavia, Italy; (M.A.G.); (T.R.); (M.G.)
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
- Lung Transplantation Unit, IRCCS Policlinico San Matteo Foundation, 27100 Pavia, Italy
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Bao A, Ma E, Cornman H, Kambala A, Manjunath J, Kollhoff AL, Imo BU, Kwatra MM, Kwatra SG. Dupilumab Therapy Modulates Circulating Inflammatory Mediators in Patients with Prurigo Nodularis. JID INNOVATIONS 2024; 4:100281. [PMID: 38947360 PMCID: PMC11214504 DOI: 10.1016/j.xjidi.2024.100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/16/2024] [Accepted: 03/31/2024] [Indexed: 07/02/2024] Open
Abstract
Prurigo nodularis (PN) is a chronic inflammatory skin disease characterized by intense pruritus and skin nodules. Beyond the skin, PN involves circulating blood inflammation that may contribute to systemic disease comorbidities. Dupilumab was recently approved for treatment of PN, but its effects on systemic inflammation are unknown. Thus, we aimed to characterize changes in plasma concentrations of inflammatory proteins after dupilumab treatment. In this exploratory study, plasma samples were collected from 3 patients with moderate-to-severe PN before and after ≥6 months of dupilumab treatment. All patients exhibited clinically significant improvements after treatment. Of the 2569 proteins tested, 186 were differentially expressed after treatment (q < 0.1, fold change > 1.3). Downregulated proteins included cytokines associated with T helper (Th) 1 (IFN-γ, TNF-α), Th2 (IL-4, IL-13), and Th17/Th22 (IL-6, IL-22) signaling. Markers of innate immunity (IL-19, toll-like receptor 1, nitric oxide synthase 2), immune cell migration (CCL20, CD177), and fibrosis (IL-11, IL-22) were also decreased (q < 0.1). Gene set variation analysis of Th2, Th17, and epithelial-mesenchymal transition gene sets showed reduced pathway expression in the post-treatment cohort (P < .05). Plasma cytokine levels of IL-11, nitric oxide synthase 2, IL-13, IL-4, and IFNG (R2 > 0.75, q < 0.10) showed the strongest correlations with pruritus severity. Dupilumab may reduce systemic inflammatory proteins associated with multiple immune and fibrosis pathways in patients with PN, potentially modulating the development of systemic disease comorbidities.
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Affiliation(s)
- Aaron Bao
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily Ma
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hannah Cornman
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anusha Kambala
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jaya Manjunath
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander L. Kollhoff
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brenda Umenita Imo
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Madan M. Kwatra
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Shawn G. Kwatra
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Maryland Itch Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Bishop CR, Yan K, Nguyen W, Rawle DJ, Tang B, Larcher T, Suhrbier A. Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung. Front Immunol 2024; 15:1382655. [PMID: 38803494 PMCID: PMC11128561 DOI: 10.3389/fimmu.2024.1382655] [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: 02/06/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis, with a growing body of concern surrounding the potential impacts on human health. Methods Using a mouse model of mild COVID-19, we describe herein the effects of azide-free 1 μm polystyrene MP beads, co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum. The effect of MPs on the host response to SARS-CoV-2 infection was analysed using histopathology and RNA-Seq at 2 and 6 days post-infection (dpi). Results Although infection reduced clearance of MPs from the lung, virus titres and viral RNA levels were not significantly affected by MPs, and overt MP-associated clinical or histopathological changes were not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 dpi and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the 'cytokine release syndrome' signature observed in some COVID-19 patients. Discussion The findings are consistent with the recent finding that MPs can inhibit phagocytosis of apoptotic cells via binding of Tim4. They also add to a growing body of literature suggesting that MPs can dysregulate inflammatory processes in specific disease settings.
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Affiliation(s)
- Cameron R. Bishop
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kexin Yan
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Wilson Nguyen
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel J. Rawle
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bing Tang
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thibaut Larcher
- Institut National de Recherche Agronomique, Unité Mixte de Recherche, Oniris, Nantes, France
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Global Virus Network (GVN) Center of Excellence, Brisbane, QLD, Australia
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Torshin IY, Gromova OA, Chuchalin AG. [Prevention and treatment of COVID-19 based on post-genomic pharmacological analysis: Systematic computer analysis of 290,000 scientific articles on COVID-19]. TERAPEVT ARKH 2024; 96:205-211. [PMID: 38713033 DOI: 10.26442/00403660.2024.03.202635] [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: 06/21/2023] [Accepted: 03/30/2024] [Indexed: 05/08/2024]
Abstract
The COVID-19 pandemic has highlighted pressing challenges in biomedical research methodology. It has become obvious that the rapid and effective development of treatments for "new" viral infections is impossible without the coordination of interdisciplinary research and in-depth analysis of data obtained within the framework of the post-genomic paradigm. Presents the results of a systematic computer analysis of 290,000 scientific articles on COVID-19, with an emphasis on the results of post-genomic studies of SARS-CoV-2. The futility of the overly simplified approach, which considers only one "most important receptor protein", only one "key virus gene", etc., is shown. It is shown how post-genomic technologies will make it possible to find informative biomarkers of severe coronavirus infection, including those based on complex immune disorders associated with COVID-19.
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Affiliation(s)
- I Y Torshin
- Federal Research Center "Computer Science and Control" of the Russian Academy of Sciences
| | - O A Gromova
- Federal Research Center "Computer Science and Control" of the Russian Academy of Sciences
| | - A G Chuchalin
- Pirogov Russian National Research Medical University
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Singla A, Harun N, Dilling DF, Merchant K, McMahan S, Ingledue R, French A, Corral JA, Korbee L, Kopras EJ, Gupta N. Safety and efficacy of sirolimus in hospitalised patients with COVID-19 pneumonia. Respir Investig 2024; 62:216-222. [PMID: 38211546 DOI: 10.1016/j.resinv.2023.12.009] [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: 10/12/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND There is a critical need to develop novel therapies for COVID-19. METHODS We conducted a phase 2, multicentre, placebo-controlled, double-blind, randomised trial; hospitalised patients with hypoxemic respiratory failure due to COVID-19 and at least one poor prognostic biomarker, were given sirolimus (6 mg on Day 1 followed by 2 mg daily for 14 days or hospital discharge, whichever happens first) or placebo, in a 2:1 randomization scheme favouring sirolimus. Primary outcome was the proportion of patients alive and free from advanced respiratory support measures at Day 28. RESULTS Between April 2020 and April 2021, 32 patients underwent randomization and 28 received either sirolimus (n = 18) or placebo (n = 10). Mean age was 57 years and 75 % of the subjects were men. Twenty-two subjects had at least one co-existing condition (Diabetes, hypertension, obesity, CHF, or asthma/COPD) associated with worse prognosis. Mean FiO2 requirement was 0.35. There was no difference in the proportion of patients who were alive and free from advanced respiratory support measures in the sirolimus group (n = 15, 83 %) compared with the placebo group (n = 8, 80 %). Although patients in the sirolimus group demonstrated faster improvement in oxygenation and spent less time in the hospital, these differences were not statistically significant. There was no between-group difference in the rate of change in serum biomarkers such as LDH, ferritin, d-dimer or lymphocyte count. There was a decreased risk of thromboembolic complications in patients on sirolimus compared with placebo. CONCLUSIONS Larger studies are warranted to evaluate the role sirolimus in COVID-19 infection.
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Affiliation(s)
- Abhishek Singla
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA
| | - Nusrat Harun
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Centre, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Daniel F Dilling
- Division of Pulmonary and Critical Care Medicine, Loyola University Medical Centre, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Karim Merchant
- Division of Pulmonary and Critical Care Medicine, Keck Hospital of University of Southern California, IRD Building 7th Floor, 2020 Zonal Ave, Los Angeles, CA, 90033, USA
| | - Susan McMahan
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA
| | - Rebecca Ingledue
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA
| | - Alexandria French
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA
| | - Josefina A Corral
- Clinical Research Office, Loyola University Chicago, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Leslie Korbee
- Academic Regulatory & Monitoring Services LLC, 7806 Gapstow Bridge, Cincinnati, OH, 45231, USA
| | - Elizabeth J Kopras
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA
| | - Nishant Gupta
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati, 231 Albert Sabin Way, ML0564, Cincinnati, OH, 45267, USA.
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9
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Pushalkar S, Wu S, Maity S, Pressler M, Rendleman J, Vitrinel B, Jeffery L, Abdelhadi R, Chen M, Ross T, Carlock M, Choi H, Vogel C. Complex changes in serum protein levels in COVID-19 convalescents. Sci Rep 2024; 14:4479. [PMID: 38396092 PMCID: PMC10891133 DOI: 10.1038/s41598-024-54534-7] [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: 11/03/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
The COVID-19 pandemic, triggered by severe acute respiratory syndrome coronavirus 2, has affected millions of people worldwide. Much research has been dedicated to our understanding of COVID-19 disease heterogeneity and severity, but less is known about recovery associated changes. To address this gap in knowledge, we quantified the proteome from serum samples from 29 COVID-19 convalescents and 29 age-, race-, and sex-matched healthy controls. Samples were acquired within the first months of the pandemic. Many proteins from pathways known to change during acute COVID-19 illness, such as from the complement cascade, coagulation system, inflammation and adaptive immune system, had returned to levels seen in healthy controls. In comparison, we identified 22 and 15 proteins with significantly elevated and lowered levels, respectively, amongst COVID-19 convalescents compared to healthy controls. Some of the changes were similar to those observed for the acute phase of the disease, i.e. elevated levels of proteins from hemolysis, the adaptive immune systems, and inflammation. In contrast, some alterations opposed those in the acute phase, e.g. elevated levels of CETP and APOA1 which function in lipid/cholesterol metabolism, and decreased levels of proteins from the complement cascade (e.g. C1R, C1S, and VWF), the coagulation system (e.g. THBS1 and VWF), and the regulation of the actin cytoskeleton (e.g. PFN1 and CFL1) amongst COVID-19 convalescents. We speculate that some of these shifts might originate from a transient decrease in platelet counts upon recovery from the disease. Finally, we observed race-specific changes, e.g. with respect to immunoglobulins and proteins related to cholesterol metabolism.
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Affiliation(s)
- Smruti Pushalkar
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Shaohuan Wu
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Shuvadeep Maity
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Birla Institute of Technology and Science-Pilani (BITS Pilani), Hyderabad, India
| | - Matthew Pressler
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Justin Rendleman
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Burcu Vitrinel
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Lauren Jeffery
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Ryah Abdelhadi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Mechi Chen
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Ted Ross
- Cleveland Clinic Florida Research & Innovation Center, Port St. Lucie, FL, USA
| | - Michael Carlock
- Cleveland Clinic Florida Research & Innovation Center, Port St. Lucie, FL, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christine Vogel
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
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10
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Duijvelaar E, Gisby J, Peters JE, Bogaard HJ, Aman J. Longitudinal plasma proteomics reveals biomarkers of alveolar-capillary barrier disruption in critically ill COVID-19 patients. Nat Commun 2024; 15:744. [PMID: 38272877 PMCID: PMC10811341 DOI: 10.1038/s41467-024-44986-w] [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: 04/28/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
The pathobiology of respiratory failure in COVID-19 consists of a complex interplay between viral cytopathic effects and a dysregulated host immune response. In critically ill patients, imatinib treatment demonstrated potential for reducing invasive ventilation duration and mortality. Here, we perform longitudinal profiling of 6385 plasma proteins in 318 hospitalised patients to investigate the biological processes involved in critical COVID-19, and assess the effects of imatinib treatment. Nine proteins measured at hospital admission accurately predict critical illness development. Next to dysregulation of inflammation, critical illness is characterised by pathways involving cellular adhesion, extracellular matrix turnover and tissue remodelling. Imatinib treatment attenuates protein perturbations associated with inflammation and extracellular matrix turnover. These proteomic alterations are contextualised using external pulmonary RNA-sequencing data of deceased COVID-19 patients and imatinib-treated Syrian hamsters. Together, we show that alveolar capillary barrier disruption in critical COVID-19 is reflected in the plasma proteome, and is attenuated with imatinib treatment. This study comprises a secondary analysis of both clinical data and plasma samples derived from a clinical trial that was registered with the EU Clinical Trials Register (EudraCT 2020-001236-10, https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-001236-10/NL ) and Netherlands Trial Register (NL8491, https://www.trialregister.nl/trial/8491 ).
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Affiliation(s)
- Erik Duijvelaar
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
| | - Jack Gisby
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - James E Peters
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - Harm Jan Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Jurjan Aman
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
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11
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Harriott NC, Ryan AL. Proteomic profiling identifies biomarkers of COVID-19 severity. Heliyon 2024; 10:e23320. [PMID: 38163173 PMCID: PMC10755324 DOI: 10.1016/j.heliyon.2023.e23320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
SARS-CoV-2 infection remains a major public health concern, particularly for the aged and those individuals with co-morbidities at risk for developing severe COVID-19. Understanding the pathogenesis and biomarkers associated with responses to SARS-CoV-2 infection remain critical components in developing effective therapeutic approaches, especially in cases of severe and long-COVID-19. In this study blood plasma protein expression was compared in subjects with mild, moderate, and severe COVID-19 disease. Evaluation of an inflammatory protein panel confirms upregulation of proteins including TNFβ, IL-6, IL-8, IL-12, already associated with severe cytokine storm and progression to severe COVID-19. Importantly, we identify several proteins not yet associated with COVID-19 disease, including mesothelin (MSLN), that are expressed at significantly higher levels in severe COVID-19 subjects. In addition, we find a subset of markers associated with T-cell and dendritic cell responses to viral infection that are significantly higher in mild cases and decrease in expression as severity of COVID-19 increases, suggesting that an immediate and effective activation of T-cells is critical in modulating disease progression. Together, our findings identify new targets for further investigation as therapeutic approaches for the treatment of SARS-CoV-2 infection and prevention of complications of severe COVID-19.
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Affiliation(s)
- Noa C. Harriott
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City IA 52240, USA
| | - Amy L. Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City IA 52240, USA
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12
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Castro-Pearson S, Samorodnitsky S, Yang K, Lotfi-Emran S, Ingraham NE, Bramante C, Jones EK, Greising S, Yu M, Steffen BT, Svensson J, Åhlberg E, Österberg B, Wacker D, Guan W, Puskarich M, Smed-Sörensen A, Lusczek E, Safo SE, Tignanelli CJ. Development of a proteomic signature associated with severe disease for patients with COVID-19 using data from 5 multicenter, randomized, controlled, and prospective studies. Sci Rep 2023; 13:20315. [PMID: 37985892 PMCID: PMC10661735 DOI: 10.1038/s41598-023-46343-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Significant progress has been made in preventing severe COVID-19 disease through the development of vaccines. However, we still lack a validated baseline predictive biologic signature for the development of more severe disease in both outpatients and inpatients infected with SARS-CoV-2. The objective of this study was to develop and externally validate, via 5 international outpatient and inpatient trials and/or prospective cohort studies, a novel baseline proteomic signature, which predicts the development of moderate or severe (vs mild) disease in patients with COVID-19 from a proteomic analysis of 7000 + proteins. The secondary objective was exploratory, to identify (1) individual baseline protein levels and/or (2) protein level changes within the first 2 weeks of acute infection that are associated with the development of moderate/severe (vs mild) disease. For model development, samples collected from 2 randomized controlled trials were used. Plasma was isolated and the SomaLogic SomaScan platform was used to characterize protein levels for 7301 proteins of interest for all studies. We dichotomized 113 patients as having mild or moderate/severe COVID-19 disease. An elastic net approach was used to develop a predictive proteomic signature. For validation, we applied our signature to data from three independent prospective biomarker studies. We found 4110 proteins measured at baseline that significantly differed between patients with mild COVID-19 and those with moderate/severe COVID-19 after adjusting for multiple hypothesis testing. Baseline protein expression was associated with predicted disease severity with an error rate of 4.7% (AUC = 0.964). We also found that five proteins (Afamin, I-309, NKG2A, PRS57, LIPK) and patient age serve as a signature that separates patients with mild COVID-19 and patients with moderate/severe COVID-19 with an error rate of 1.77% (AUC = 0.9804). This panel was validated using data from 3 external studies with AUCs of 0.764 (Harvard University), 0.696 (University of Colorado), and 0.893 (Karolinska Institutet). In this study we developed and externally validated a baseline COVID-19 proteomic signature associated with disease severity for potential use in both outpatients and inpatients with COVID-19.
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Affiliation(s)
- Sandra Castro-Pearson
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Sarah Samorodnitsky
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kaifeng Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Sahar Lotfi-Emran
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Carolyn Bramante
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Emma K Jones
- Department of Surgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Sarah Greising
- School of Kinesiology, University of Minnesota, Minneapolis, MN, USA
| | - Meng Yu
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Brian T Steffen
- Department of Surgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Julia Svensson
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Eric Åhlberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Björn Österberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - David Wacker
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Michael Puskarich
- Department of Emergency Medicine, University of Minnesota, Minneapolis, MN, USA
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elizabeth Lusczek
- Department of Surgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Sandra E Safo
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Christopher J Tignanelli
- Department of Surgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN, 55455, USA.
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA.
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13
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Dang T, Fermin ASR, Machizawa MG. oFVSD: a Python package of optimized forward variable selection decoder for high-dimensional neuroimaging data. Front Neuroinform 2023; 17:1266713. [PMID: 37829329 PMCID: PMC10566623 DOI: 10.3389/fninf.2023.1266713] [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: 07/25/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
The complexity and high dimensionality of neuroimaging data pose problems for decoding information with machine learning (ML) models because the number of features is often much larger than the number of observations. Feature selection is one of the crucial steps for determining meaningful target features in decoding; however, optimizing the feature selection from such high-dimensional neuroimaging data has been challenging using conventional ML models. Here, we introduce an efficient and high-performance decoding package incorporating a forward variable selection (FVS) algorithm and hyper-parameter optimization that automatically identifies the best feature pairs for both classification and regression models, where a total of 18 ML models are implemented by default. First, the FVS algorithm evaluates the goodness-of-fit across different models using the k-fold cross-validation step that identifies the best subset of features based on a predefined criterion for each model. Next, the hyperparameters of each ML model are optimized at each forward iteration. Final outputs highlight an optimized number of selected features (brain regions of interest) for each model with its accuracy. Furthermore, the toolbox can be executed in a parallel environment for efficient computation on a typical personal computer. With the optimized forward variable selection decoder (oFVSD) pipeline, we verified the effectiveness of decoding sex classification and age range regression on 1,113 structural magnetic resonance imaging (MRI) datasets. Compared to ML models without the FVS algorithm and with the Boruta algorithm as a variable selection counterpart, we demonstrate that the oFVSD significantly outperformed across all of the ML models over the counterpart models without FVS (approximately 0.20 increase in correlation coefficient, r, with regression models and 8% increase in classification models on average) and with Boruta variable selection algorithm (approximately 0.07 improvement in regression and 4% in classification models). Furthermore, we confirmed the use of parallel computation considerably reduced the computational burden for the high-dimensional MRI data. Altogether, the oFVSD toolbox efficiently and effectively improves the performance of both classification and regression ML models, providing a use case example on MRI datasets. With its flexibility, oFVSD has the potential for many other modalities in neuroimaging. This open-source and freely available Python package makes it a valuable toolbox for research communities seeking improved decoding accuracy.
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Affiliation(s)
- Tung Dang
- Center for Brain, Mind, and KANSEI Sciences Research, Hiroshima University, Hiroshima, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Alan S. R. Fermin
- Center for Brain, Mind, and KANSEI Sciences Research, Hiroshima University, Hiroshima, Japan
| | - Maro G. Machizawa
- Center for Brain, Mind, and KANSEI Sciences Research, Hiroshima University, Hiroshima, Japan
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14
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for Mining Protein Dysregulation in Patients with COVID-19. J Proteome Res 2023; 22:2847-2859. [PMID: 37555633 DOI: 10.1021/acs.jproteome.3c00092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 still has limited treatment options. Our understanding of the molecular dysregulations that occur in response to infection remains incomplete. We developed a web application COVIDpro (https://www.guomics.com/covidPro/) that includes proteomics data obtained from 41 original studies conducted in 32 hospitals worldwide, involving 3077 patients and covering 19 types of clinical specimens, predominantly plasma and serum. The data set encompasses 53 protein expression matrices, comprising a total of 5434 samples and 14,403 unique proteins. We identified a panel of proteins that exhibit significant dysregulation, enabling the classification of COVID-19 patients into severe and non-severe disease categories. The proteomic signatures achieved promising results in distinguishing severe cases, with a mean area under the curve of 0.87 and accuracy of 0.80 across five independent test sets. COVIDpro serves as a valuable resource for testing hypotheses and exploring potential targets for novel treatments in COVID-19 patients.
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Affiliation(s)
- Fangfei Zhang
- Fudan University, 220 Handan Road, Shanghai 200433, China
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Augustin Luna
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tingting Tan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Yingdan Chen
- Westlake Omics (Hangzhou) Biotechnology Company Limited, Hangzhou, Zhejiang Province 310024, China
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
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15
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Van Damme KFA, Hoste L, Declercq J, De Leeuw E, Maes B, Martens L, Colman R, Browaeys R, Bosteels C, Verwaerde S, Vermeulen N, Lameire S, Debeuf N, Deckers J, Stordeur P, Depuydt P, Van Braeckel E, Vandekerckhove L, Guilliams M, Schetters STT, Haerynck F, Tavernier SJ, Lambrecht BN. A complement atlas identifies interleukin-6-dependent alternative pathway dysregulation as a key druggable feature of COVID-19. Sci Transl Med 2023; 15:eadi0252. [PMID: 37611083 DOI: 10.1126/scitranslmed.adi0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Improvements in COVID-19 treatments, especially for the critically ill, require deeper understanding of the mechanisms driving disease pathology. The complement system is not only a crucial component of innate host defense but can also contribute to tissue injury. Although all complement pathways have been implicated in COVID-19 pathogenesis, the upstream drivers and downstream effects on tissue injury remain poorly defined. We demonstrate that complement activation is primarily mediated by the alternative pathway, and we provide a comprehensive atlas of the complement alterations around the time of respiratory deterioration. Proteomic and single-cell sequencing mapping across cell types and tissues reveals a division of labor between lung epithelial, stromal, and myeloid cells in complement production, in addition to liver-derived factors. We identify IL-6 and STAT1/3 signaling as an upstream driver of complement responses, linking complement dysregulation to approved COVID-19 therapies. Furthermore, an exploratory proteomic study indicates that inhibition of complement C5 decreases epithelial damage and markers of disease severity. Collectively, these results support complement dysregulation as a key druggable feature of COVID-19.
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Affiliation(s)
- Karel F A Van Damme
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Jozefien Declercq
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Elisabeth De Leeuw
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bastiaan Maes
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Liesbet Martens
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
| | - Roos Colman
- Biostatistics Unit, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Robin Browaeys
- Bioinformatics Expertise Unit, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Cédric Bosteels
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Respiratory Infection and Defense Lab, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stijn Verwaerde
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Nicky Vermeulen
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Sahine Lameire
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Nincy Debeuf
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Julie Deckers
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Patrick Stordeur
- Belgian National Reference Center for the Complement System, Laboratory of Immunology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Pieter Depuydt
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Intensive Care Unit, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Respiratory Infection and Defense Lab, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
| | - Sjoerd T T Schetters
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Simon J Tavernier
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, Netherlands
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16
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Iosef C, Knauer MJ, Nicholson M, Van Nynatten LR, Cepinskas G, Draghici S, Han VKM, Fraser DD. Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function. J Transl Med 2023; 21:377. [PMID: 37301958 PMCID: PMC10257382 DOI: 10.1186/s12967-023-04149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023] Open
Abstract
AIMS Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis and treatment. METHODS Plasma proteome from Long-COVID outpatients was analyzed in comparison to matched acutely ill COVID-19 (mild and severe) inpatients and healthy control subjects. The expression of 3072 protein biomarkers was determined with proximity extension assays and then deconvoluted with multiple bioinformatics tools into both cell types and signaling mechanisms, as well as organ specificity. RESULTS Compared to age- and sex-matched acutely ill COVID-19 inpatients and healthy control subjects, Long-COVID outpatients showed natural killer cell redistribution with a dominant resting phenotype, as opposed to active, and neutrophils that formed extracellular traps. This potential resetting of cell phenotypes was reflected in prospective vascular events mediated by both angiopoietin-1 (ANGPT1) and vascular-endothelial growth factor-A (VEGFA). Several markers (ANGPT1, VEGFA, CCR7, CD56, citrullinated histone 3, elastase) were validated by serological methods in additional patient cohorts. Signaling of transforming growth factor-β1 with probable connections to elevated EP/p300 suggested vascular inflammation and tumor necrosis factor-α driven pathways. In addition, a vascular proliferative state associated with hypoxia inducible factor 1 pathway suggested progression from acute COVID-19 to Long-COVID. The vasculo-proliferative process predicted in Long-COVID might contribute to changes in the organ-specific proteome reflective of neurologic and cardiometabolic dysfunction. CONCLUSIONS Taken together, our findings point to a vasculo-proliferative process in Long-COVID that is likely initiated either prior hypoxia (localized or systemic) and/or stimulatory factors (i.e., cytokines, chemokines, growth factors, angiotensin, etc). Analyses of the plasma proteome, used as a surrogate for cellular signaling, unveiled potential organ-specific prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Cristiana Iosef
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
| | - Michael J Knauer
- Department of Pathology and Laboratory Medicine, London, ON, N6A 5C1, Canada
| | - Michael Nicholson
- Department of Medicine, Western University, London, ON, N6A 5C1, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
- Department of Medical Biophysics, Western University, London, ON, N6A 5C1, Canada
| | - Sorin Draghici
- Department of Computer Science College of Engineering, Wayne State University, Ann Arbor, MI, 48202, USA
- Advaita Bioinformatics, Ann Arbor, 48105-2552, USA
- National Science Foundation, Alexandria, VA, 22314, USA
| | - Victor K M Han
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada
| | - Douglas D Fraser
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada.
- Department of Physiology & Pharmacology, Western University, London, ON, N6A 5C1, Canada.
- Department of Clinical Neurological Sciences, Western University, London, ON, N6A 5C1, Canada.
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17
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El-Agnaf O, Bensmail I, Al-Nesf MAY, Flynn J, Taylor M, Majbour NK, Abdi IY, Vaikath NN, Farooq A, Vemulapalli PB, Schmidt F, Ouararhni K, Al-Siddiqi HH, Arredouani A, Wijten P, Al-Maadheed M, Mohamed-Ali V, Decock J, Abdesselem HB. Uncovering a neurological protein signature for severe COVID-19. Neurobiol Dis 2023; 182:106147. [PMID: 37178811 PMCID: PMC10174474 DOI: 10.1016/j.nbd.2023.106147] [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: 02/16/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has sparked a global pandemic with severe complications and high morbidity rate. Neurological symptoms in COVID-19 patients, and neurological sequelae post COVID-19 recovery have been extensively reported. Yet, neurological molecular signature and signaling pathways that are affected in the central nervous system (CNS) of COVID-19 severe patients remain still unknown and need to be identified. Plasma samples from 49 severe COVID-19 patients, 50 mild COVID-19 patients, and 40 healthy controls were subjected to Olink proteomics analysis of 184 CNS-enriched proteins. By using a multi-approach bioinformatics analysis, we identified a 34-neurological protein signature for COVID-19 severity and unveiled dysregulated neurological pathways in severe cases. Here, we identified a new neurological protein signature for severe COVID-19 that was validated in different independent cohorts using blood and postmortem brain samples and shown to correlate with neurological diseases and pharmacological drugs. This protein signature could potentially aid the development of prognostic and diagnostic tools for neurological complications in post-COVID-19 convalescent patients with long term neurological sequelae.
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Affiliation(s)
- Omar El-Agnaf
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ilham Bensmail
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Maryam A Y Al-Nesf
- Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar; Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK
| | | | | | - Nour K Majbour
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ilham Y Abdi
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Nishant N Vaikath
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Abdulaziz Farooq
- Aspetar Hospital, Orthopaedic and Sports Medicine, Hospital, FIFA Medical Centre of Excellence, Doha, Qatar
| | | | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Khalid Ouararhni
- Genomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Heba H Al-Siddiqi
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Abdelilah Arredouani
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Patrick Wijten
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Mohammed Al-Maadheed
- Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK; Anti-Doping Laboratory Qatar, Doha, Qatar
| | - Vidya Mohamed-Ali
- Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK; Anti-Doping Laboratory Qatar, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Houari B Abdesselem
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar.
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18
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Parthasarathy V, Cravero K, Xu L, Deng J, Sun Z, Engle SM, Sims JT, Okragly AJ, Kwatra SG. The blood proteomic signature of prurigo nodularis reveals distinct inflammatory and neuropathic endotypes: A cluster analysis. J Am Acad Dermatol 2023; 88:1101-1109. [PMID: 36806647 PMCID: PMC11212685 DOI: 10.1016/j.jaad.2023.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Prurigo nodularis (PN) is an extremely pruritic, chronic inflammatory skin disease. Little is known about systemic inflammation in PN. OBJECTIVE To characterize plasma inflammatory biomarkers in patients with PN and investigate the presence of disease endotypes. METHODS In this cross-sectional study, Olink proteomic analysis was performed on plasma samples from patients with PN (n = 29) and healthy controls (n = 18). RESULTS Patients with PN had increased levels of 8 circulating biomarkers compared to controls, including tumor necrosis factor, C-X-C Motif Chemokine Ligand 9, interleukin-12B, and tumor necrosis factor receptor superfamily member 9 (P < .05). Two PN clusters were identified in cluster 1 (n = 13) and cluster 2 (n = 16). Cluster 2 had higher levels of 25 inflammatory markers than cluster 1. Cluster 1 had a greater percentage of patients with a history of myelopathy and spinal disc disease compared with cluster 2 (69% vs 25%, P = .03). Patients in cluster 2 were more likely to have a history of atopy (38% in cluster 2 vs 8% in cluster 1, P = .09). LIMITATIONS Small sample size precludes robust subgroup analyses. CONCLUSION This study provides evidence of neuroimmune-biased endotypes in PN and can aid clinicians in managing patients with PN that are nonresponsive to traditional therapies.
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Affiliation(s)
- Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Karen Cravero
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lillian Xu
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Zhe Sun
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland.
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19
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Liang X, Sun R, Wang J, Zhou K, Li J, Chen S, Lyu M, Li S, Xue Z, Shi Y, Xie Y, Zhang Q, Yi X, Pan J, Wang D, Xu J, Zhu H, Zhu G, Zhu J, Zhu Y, Zheng Y, Shen B, Guo T. Proteomics Investigation of Diverse Serological Patterns in COVID-19. Mol Cell Proteomics 2023; 22:100493. [PMID: 36621767 PMCID: PMC9814280 DOI: 10.1016/j.mcpro.2023.100493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/23/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
Serum antibodies IgM and IgG are elevated during Coronavirus Disease 2019 (COVID-19) to defend against viral attacks. Atypical results such as negative and abnormally high antibody expression were frequently observed whereas the underlying molecular mechanisms are elusive. In our cohort of 144 COVID-19 patients, 3.5% were both IgM and IgG negative, whereas 29.2% remained only IgM negative. The remaining patients exhibited positive IgM and IgG expression, with 9.3% of them exhibiting over 20-fold higher titers of IgM than the others at their plateau. IgG titers in all of them were significantly boosted after vaccination in the second year. To investigate the underlying molecular mechanisms, we classed the patients into four groups with diverse serological patterns and analyzed their 2-year clinical indicators. Additionally, we collected 111 serum samples for TMTpro-based longitudinal proteomic profiling and characterized 1494 proteins in total. We found that the continuously negative IgM and IgG expression during COVID-19 were associated with mild inflammatory reactions and high T cell responses. Low levels of serum IgD, inferior complement 1 activation of complement cascades, and insufficient cellular immune responses might collectively lead to compensatory serological responses, causing overexpression of IgM. Serum CD163 was positively correlated with antibody titers during seroconversion. This study suggests that patients with negative serology still developed cellular immunity for viral defense and that high titers of IgM might not be favorable to COVID-19 recovery.
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Affiliation(s)
- Xiao Liang
- Fudan University, Shanghai, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jing Wang
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Kai Zhou
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jun Li
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Shiyong Chen
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Mengge Lyu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Sainan Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zhangzhi Xue
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yingqiu Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yuting Xie
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Qiushi Zhang
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Xiao Yi
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Juan Pan
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Donglian Wang
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jiaqin Xu
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Hongguo Zhu
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Guangjun Zhu
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jiansheng Zhu
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Yufen Zheng
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China.
| | - Bo Shen
- Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China.
| | - Tiannan Guo
- Fudan University, Shanghai, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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20
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Palma Medina LM, Babačić H, Dzidic M, Parke Å, Garcia M, Maleki KT, Unge C, Lourda M, Kvedaraite E, Chen P, Muvva JR, Cornillet M, Emgård J, Moll K, Michaëlsson J, Flodström-Tullberg M, Brighenti S, Buggert M, Mjösberg J, Malmberg KJ, Sandberg JK, Gredmark-Russ S, Rooyackers O, Svensson M, Chambers BJ, Eriksson LI, Pernemalm M, Björkström NK, Aleman S, Ljunggren HG, Klingström J, Strålin K, Norrby-Teglund A. Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia. Respir Res 2023; 24:62. [PMID: 36829233 PMCID: PMC9950694 DOI: 10.1186/s12931-023-02364-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND COVID-19 remains a major public health challenge, requiring the development of tools to improve diagnosis and inform therapeutic decisions. As dysregulated inflammation and coagulation responses have been implicated in the pathophysiology of COVID-19 and sepsis, we studied their plasma proteome profiles to delineate similarities from specific features. METHODS We measured 276 plasma proteins involved in Inflammation, organ damage, immune response and coagulation in healthy controls, COVID-19 patients during acute and convalescence phase, and sepsis patients; the latter included (i) community-acquired pneumonia (CAP) caused by Influenza, (ii) bacterial CAP, (iii) non-pneumonia sepsis, and (iv) septic shock patients. RESULTS We identified a core response to infection consisting of 42 proteins altered in both COVID-19 and sepsis, although higher levels of cytokine storm-associated proteins were evident in sepsis. Furthermore, microbiologic etiology and clinical endotypes were linked to unique signatures. Finally, through machine learning, we identified biomarkers, such as TRIM21, PTN and CASP8, that accurately differentiated COVID-19 from CAP-sepsis with higher accuracy than standard clinical markers. CONCLUSIONS This study extends the understanding of host responses underlying sepsis and COVID-19, indicating varying disease mechanisms with unique signatures. These diagnostic and severity signatures are candidates for the development of personalized management of COVID-19 and sepsis.
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Affiliation(s)
- Laura M. Palma Medina
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Haris Babačić
- grid.4714.60000 0004 1937 0626Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Majda Dzidic
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Åsa Parke
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marina Garcia
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kimia T. Maleki
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Christian Unge
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Functional Area of Emergency Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Magda Lourda
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Egle Kvedaraite
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Puran Chen
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jagadeeswara Rao Muvva
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Martin Cornillet
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Johanna Emgård
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kirsten Moll
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | | | - Jakob Michaëlsson
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Malin Flodström-Tullberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Susanna Brighenti
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Marcus Buggert
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jenny Mjösberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Karl-Johan Malmberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Johan K. Sandberg
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Sara Gredmark-Russ
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden ,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Olav Rooyackers
- grid.24381.3c0000 0000 9241 5705Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Division for Anesthesiology and Intensive Care, Department of Clinical Interventions and Technology CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Svensson
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Benedict J. Chambers
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Lars I. Eriksson
- grid.24381.3c0000 0000 9241 5705Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pernemalm
- grid.4714.60000 0004 1937 0626Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Niklas K. Björkström
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Soo Aleman
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Jonas Klingström
- grid.24381.3c0000 0000 9241 5705Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden
| | - Kristoffer Strålin
- grid.4714.60000 0004 1937 0626Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 52, Stockholm, Sweden.
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21
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Jeon K, Kim Y, Kang SK, Park U, Kim J, Park N, Koh J, Shim MS, Kim M, Rhee YJ, Jeong H, Lee S, Park D, Lim J, Kim H, Ha NY, Jo HY, Kim SC, Lee JH, Shon J, Kim H, Jeon YK, Choi YS, Kim HY, Lee WW, Choi M, Park HY, Park WY, Kim YS, Cho NH. Elevated IFNA1 and suppressed IL12p40 associated with persistent hyperinflammation in COVID-19 pneumonia. Front Immunol 2023; 14:1101808. [PMID: 36776879 PMCID: PMC9911526 DOI: 10.3389/fimmu.2023.1101808] [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: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction Despite of massive endeavors to characterize inflammation in COVID-19 patients, the core network of inflammatory mediators responsible for severe pneumonia stillremain remains elusive. Methods Here, we performed quantitative and kinetic analysis of 191 inflammatory factors in 955 plasma samples from 80 normal controls (sample n = 80) and 347 confirmed COVID-19 pneumonia patients (sample n = 875), including 8 deceased patients. Results Differential expression analysis showed that 76% of plasmaproteins (145 factors) were upregulated in severe COVID-19 patients comparedwith moderate patients, confirming overt inflammatory responses in severe COVID-19 pneumonia patients. Global correlation analysis of the plasma factorsrevealed two core inflammatory modules, core I and II, comprising mainly myeloid cell and lymphoid cell compartments, respectively, with enhanced impact in a severity-dependent manner. We observed elevated IFNA1 and suppressed IL12p40, presenting a robust inverse correlation in severe patients, which was strongly associated with persistent hyperinflammation in 8.3% of moderate pneumonia patients and 59.4% of severe patients. Discussion Aberrant persistence of pulmonary and systemic inflammation might be associated with long COVID-19 sequelae. Our comprehensive analysis of inflammatory mediators in plasmarevealed the complexity of pneumonic inflammation in COVID-19 patients anddefined critical modules responsible for severe pneumonic progression.
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Affiliation(s)
- Kyeongseok Jeon
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Shin Kwang Kang
- Department of Thoracic and Cardiovascular Surgery, Chungnam National University School of Medicine, Deajon, Republic of Korea
| | - Uni Park
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jayoun Kim
- Medical Research Collaborating Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Nanhee Park
- Medical Research Collaborating Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jaemoon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Man-Shik Shim
- Department of Thoracic and Cardiovascular Surgery, Chungnam National University School of Medicine, Deajon, Republic of Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youn Ju Rhee
- Department of Thoracic and Cardiovascular Surgery, Chungnam National University School of Medicine, Deajon, Republic of Korea
| | - Hyeongseok Jeong
- Department of Internal Medicine, Chungnam National University School of Medicine, Deajon, Republic of Korea
| | | | | | - Jinyoung Lim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyunsu Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Na-Young Ha
- Chungnam National University Hospital, Biomedical Research Institute, Deajon, Republic of Korea
| | - Hye-Yeong Jo
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Sang Cheol Kim
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Ju-Hee Lee
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jiwon Shon
- Department of Biohealth Regulatory Science, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Hoon Kim
- Department of Biohealth Regulatory Science, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do, Republic of Korea.,Biopharmaceutical Convergence Major, School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youn-Soo Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye Young Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Won-Woo Lee
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Young Park
- Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Woong-Yang Park
- Geninus Inc., Seoul, Republic of Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Yeon-Sook Kim
- Department of Internal Medicine, Chungnam National University School of Medicine, Deajon, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Republic of Korea.,Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Republic of Korea.,Wide River Institute of Immunology, Seoul National University, Hongcheon, Gangwon-do, Republic of Korea
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22
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Iosef C, Martin CM, Slessarev M, Gillio‐Meina C, Cepinskas G, Han VKM, Fraser DD. COVID-19 plasma proteome reveals novel temporal and cell-specific signatures for disease severity and high-precision disease management. J Cell Mol Med 2022; 27:141-157. [PMID: 36537107 PMCID: PMC9806290 DOI: 10.1111/jcmm.17622] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a systemic inflammatory condition with high mortality that may benefit from personalized medicine and high-precision approaches. COVID-19 patient plasma was analysed with targeted proteomics of 1161 proteins. Patients were monitored from Days 1 to 10 of their intensive care unit (ICU) stay. Age- and gender-matched COVID-19-negative sepsis ICU patients and healthy subjects were examined as controls. Proteomic data were resolved using both cell-specific annotation and deep-analysis for functional enrichment. COVID-19 caused extensive remodelling of the plasma microenvironment associated with a relative immunosuppressive milieu between ICU Days 3-7, and characterized by extensive organ damage. COVID-19 resulted in (1) reduced antigen presentation and B/T-cell function, (2) increased repurposed neutrophils and M1-type macrophages, (3) relatively immature or disrupted endothelia and fibroblasts with a defined secretome, and (4) reactive myeloid lines. Extracellular matrix changes identified in COVID-19 plasma could represent impaired immune cell homing and programmed cell death. The major functional modules disrupted in COVID-19 were exaggerated in patients with fatal outcome. Taken together, these findings provide systems-level insight into the mechanisms of COVID-19 inflammation and identify potential prognostic biomarkers. Therapeutic strategies could be tailored to the immune response of severely ill patients.
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Affiliation(s)
| | - Claudio M. Martin
- Lawson Health Research InstituteLondonOntarioCanada,Department of MedicineWestern UniversityLondonOntarioCanada
| | - Marat Slessarev
- Lawson Health Research InstituteLondonOntarioCanada,Department of MedicineWestern UniversityLondonOntarioCanada
| | | | - Gediminas Cepinskas
- Lawson Health Research InstituteLondonOntarioCanada,Department of Medical BiophysicsWestern UniversityLondonOntarioCanada
| | - Victor K. M. Han
- Children's Health research InstituteLondonOntarioCanada,Department of PediatricsWestern UniversityLondonOntarioCanada
| | - Douglas D. Fraser
- Children's Health research InstituteLondonOntarioCanada,Lawson Health Research InstituteLondonOntarioCanada,Department of PediatricsWestern UniversityLondonOntarioCanada,Department of Physiology & PharmacologyWestern UniversityLondonOntarioCanada,Department of Clinical Neurological SciencesWestern UniversityLondonOntarioCanada
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23
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Ciccosanti F, Antonioli M, Sacchi A, Notari S, Farina A, Beccacece A, Fusto M, Vergori A, D'Offizi G, Taglietti F, Antinori A, Nicastri E, Marchioni L, Palmieri F, Ippolito G, Piacentini M, Agrati C, Fimia GM. Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation. Clin Proteomics 2022; 19:38. [PMID: 36348270 PMCID: PMC9641302 DOI: 10.1186/s12014-022-09377-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Most patients infected with SARS-CoV-2 display mild symptoms with good prognosis, while 20% of patients suffer from severe viral pneumonia and up to 5% may require intensive care unit (ICU) admission due to severe acute respiratory syndrome, which could be accompanied by multiorgan failure.Plasma proteomics provide valuable and unbiased information about disease progression and therapeutic candidates. Recent proteomic studies have identified molecular changes in plasma of COVID-19 patients that implied significant dysregulation of several aspects of the inflammatory response accompanied by a general metabolic suppression. However, which of these plasma alterations are associated with disease severity remains only partly characterized.A known limitation of proteomic studies of plasma samples is the large difference in the macromolecule abundance, with concentration spanning at least 10 orders of magnitude. To improve the coverage of plasma contents, we performed a deep proteomic analysis of plasma from 10 COVID-19 patients with severe/fatal pneumonia compared to 10 COVID-19 patients with pneumonia who did not require ICU admission (non-ICU). To this aim, plasma samples were first depleted of the most abundant proteins, trypsin digested and peptides subjected to a high pH reversed-phase peptide fractionation before LC-MS analysis.These results highlighted an increase of proteins involved in neutrophil and platelet activity and acute phase response, which is significantly higher in severe/fatal COVID-19 patients when compared to non-ICU ones. Importantly, these changes are associated with a selective induction of complement cascade factors in severe/fatal COVID-19 patients. Data are available via ProteomeXchange with identifier PXD036491. Among these alterations, we confirmed by ELISA that higher levels of the neutrophil granule proteins DEFA3 and LCN2 are present in COVID-19 patients requiring ICU admission when compared to non-ICU and healthy donors.Altogether, our study provided an in-depth view of plasma proteome changes that occur in COVID-19 patients in relation to disease severity, which can be helpful to identify therapeutic strategies to improve the disease outcome.
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Affiliation(s)
- Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Manuela Antonioli
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Sacchi
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Stefania Notari
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Anna Farina
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessia Beccacece
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Marisa Fusto
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Vergori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Gianpiero D'Offizi
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Taglietti
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Andrea Antinori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Emanuele Nicastri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Luisa Marchioni
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Palmieri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Giuseppe Ippolito
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- General Directorate for Research and Health Innovation, Italian Ministry of Health, Rome, Italy
| | - Mauro Piacentini
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Agrati
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
| | - Gian Maria Fimia
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Molecular Medicine, University of Rome "Sapienza", Rome, Italy.
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24
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Captur G, Moon JC, Topriceanu CC, Joy G, Swadling L, Hallqvist J, Doykov I, Patel N, Spiewak J, Baldwin T, Hamblin M, Menacho K, Fontana M, Treibel TA, Manisty C, O'Brien B, Gibbons JM, Pade C, Brooks T, Altmann DM, Boyton RJ, McKnight Á, Maini MK, Noursadeghi M, Mills K, Heywood WE. Plasma proteomic signature predicts who will get persistent symptoms following SARS-CoV-2 infection. EBioMedicine 2022; 85:104293. [PMID: 36182629 PMCID: PMC9515404 DOI: 10.1016/j.ebiom.2022.104293] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of those infected by ancestral Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) during the UK first wave (starting March 2020) did not require hospitalisation. Most had a short-lived mild or asymptomatic infection, while others had symptoms that persisted for weeks or months. We hypothesized that the plasma proteome at the time of first infection would reflect differences in the inflammatory response that linked to symptom severity and duration. METHODS We performed a nested longitudinal case-control study and targeted analysis of the plasma proteome of 156 healthcare workers (HCW) with and without lab confirmed SARS-CoV-2 infection. Targeted proteomic multiple-reaction monitoring analysis of 91 pre-selected proteins was undertaken in uninfected healthcare workers at baseline, and in infected healthcare workers serially, from 1 week prior to 6 weeks after their first confirmed SARS-CoV-2 infection. Symptom severity and antibody responses were also tracked. Questionnaires at 6 and 12 months collected data on persistent symptoms. FINDINGS Within this cohort (median age 39 years, interquartile range 30-47 years), 54 healthcare workers (44% male) had PCR or antibody confirmed infection, with the remaining 102 (38% male) serving as uninfected controls. Following the first confirmed SARS-CoV-2 infection, perturbation of the plasma proteome persisted for up to 6 weeks, tracking symptom severity and antibody responses. Differentially abundant proteins were mostly coordinated around lipid, atherosclerosis and cholesterol metabolism pathways, complement and coagulation cascades, autophagy, and lysosomal function. The proteomic profile at the time of seroconversion associated with persistent symptoms out to 12 months. Data are available via ProteomeXchange with identifier PXD036590. INTERPRETATION Our findings show that non-severe SARS-CoV-2 infection perturbs the plasma proteome for at least 6 weeks. The plasma proteomic signature at the time of seroconversion has the potential to identify which individuals are more likely to suffer from persistent symptoms related to SARS-CoV-2 infection. FUNDING INFORMATION The COVIDsortium is supported by funding donated by individuals, charitable Trusts, and corporations including Goldman Sachs, Citadel and Citadel Securities, The Guy Foundation, GW Pharmaceuticals, Kusuma Trust, and Jagclif Charitable Trust, and enabled by Barts Charity with support from University College London Hospitals (UCLH) Charity. This work was additionally supported by the Translational Mass Spectrometry Research Group and the Biomedical Research Center (BRC) at Great Ormond Street Hospital.
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Affiliation(s)
- Gabriella Captur
- UCL MRC Unit for Lifelong Health and Ageing, 33 Bedford Place, London WC1B 5JU, UK; Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; The Royal Free Hospital, Center for Inherited Heart Muscle Conditions, Cardiology Department, Pond Street, Hampstead, London NW3 2QG, UK
| | - James C Moon
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Constantin-Cristian Topriceanu
- UCL MRC Unit for Lifelong Health and Ageing, 33 Bedford Place, London WC1B 5JU, UK; Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK
| | - George Joy
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Jenny Hallqvist
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Ivan Doykov
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Nina Patel
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Justyna Spiewak
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Tomas Baldwin
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Matt Hamblin
- Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Katia Menacho
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Marianna Fontana
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; The Royal Free Hospital, Cardiac MRI Unit, Pond Street, Hampstead, London NW3 2QG, UK
| | - Thomas A Treibel
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK; Barts Heart Center, The Cardiovascular Magnetic Resonance Imaging Unit and The Inherited Cardiovascular Diseases Unit, St Bartholomew's Hospital, West Smithfield, London EC1A 7BE, UK
| | - Ben O'Brien
- Department of Perioperative Medicine, St. Bartholomew's Hospital, Barts Health NHS Trust, West Smithfield, London EC1A 7BE, UK; Department of Cardiac Anesthesiology and Intensive Care Medicine, German Heart Center, Augustenburger Platz 1, 13353 Berlin, Germany; Department of Cardiac Anesthesiology and Intensive Care Medicine, Charité Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Outcomes Research Consortium, Department of Outcomes Research, The Cleveland Clinic, 9500 Euclid Ave P77, Cleveland, OH 44195, USA
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Corrina Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Tim Brooks
- National Infection Service, Public Health England, Porton Down, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK; Lung Division, Royal Brompton Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London SW3 6NP, UK
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Wendy E Heywood
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health and Great Ormond Street Hospital, 30 Guilford Street, London WC1N 1EH, UK.
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25
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for mining protein dysregulation in patients with COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509819. [PMID: 36203550 PMCID: PMC9536031 DOI: 10.1101/2022.09.27.509819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers. Methods We built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers. Findings We built and maintain a web server COVIDpro ( https://www.guomics.com/covidPro/ ) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80. Interpretation COVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients. Funding National Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504). Research in context Evidence before this study: Although an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the disease’s mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets.Added value of this study: We integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples.Implications of all the available evidence: COVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.
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26
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Papapavlou Lingehed G, Hellberg S, Huang J, Khademi M, Kockum I, Carlsson H, Tjernberg I, Svenvik M, Lind J, Blomberg M, Vrethem M, Mellergård J, Gustafsson M, Jenmalm MC, Olsson T, Ernerudh J. Plasma protein profiling reveals dynamic immunomodulatory changes in multiple sclerosis patients during pregnancy. Front Immunol 2022; 13:930947. [PMID: 35967338 PMCID: PMC9373039 DOI: 10.3389/fimmu.2022.930947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neuroinflammatory and neurodegenerative disorder of the central nervous system. Pregnancy represents a natural modulation of the disease course, where the relapse rate decreases, especially in the 3rd trimester, followed by a transient exacerbation after delivery. Although the exact mechanisms behind the pregnancy-induced modulation are yet to be deciphered, it is likely that the immune tolerance established during pregnancy is involved. In this study, we used the highly sensitive and specific proximity extension assay technology to perform protein profiling analysis of 92 inflammation-related proteins in MS patients (n=15) and healthy controls (n=10), longitudinally sampled before, during, and after pregnancy. Differential expression analysis was performed using linear models and p-values were adjusted for false discovery rate due to multiple comparisons. Our findings reveal gradual dynamic changes in plasma proteins that are most prominent during the 3rd trimester while reverting post-partum. Thus, this pattern reflects the disease activity of MS during pregnancy. Among the differentially expressed proteins in pregnancy, several proteins with known immunoregulatory properties were upregulated, such as PD-L1, LIF-R, TGF-β1, and CCL28. On the other hand, inflammatory chemokines such as CCL8, CCL13, and CXCL5, as well as members of the tumor necrosis factor family, TRANCE and TWEAK, were downregulated. Further in-depth studies will reveal if these proteins can serve as biomarkers in MS and whether they are mechanistically involved in the disease amelioration and worsening. A deeper understanding of the mechanisms involved may identify new treatment strategies mimicking the pregnancy milieu.
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Affiliation(s)
- Georgia Papapavlou Lingehed
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Georgia Papapavlou Lingehed,
| | - Sandra Hellberg
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Jesse Huang
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Mohsen Khademi
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Hanna Carlsson
- Department of Clinical Chemistry and Transfusion Medicine, Region Kalmar County, and Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Ivar Tjernberg
- Department of Clinical Chemistry and Transfusion Medicine, Region Kalmar County, and Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Maria Svenvik
- Department of Obstetrics and Gynecology, Region Kalmar County, Kalmar, Sweden and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jonas Lind
- Section of Neurology, Department of Internal Medicine, County Hospital Ryhov, Jönköping, Sweden and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Marie Blomberg
- Department of Obstetrics and Gynecology in Linköping, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Magnus Vrethem
- Department of Neurology, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Mellergård
- Department of Neurology, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Maria C. Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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27
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Nuñez E, Orera I, Carmona-Rodríguez L, Paño JR, Vázquez J, Corrales FJ. Mapping the Serum Proteome of COVID-19 Patients; Guidance for Severity Assessment. Biomedicines 2022; 10:biomedicines10071690. [PMID: 35884998 PMCID: PMC9313396 DOI: 10.3390/biomedicines10071690] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose outbreak in 2019 led to an ongoing pandemic with devastating consequences for the global economy and human health. According to the World Health Organization, COVID-19 has affected more than 481 million people worldwide, with 6 million confirmed deaths. The joint efforts of the scientific community have undoubtedly increased the pace of production of COVID-19 vaccines, but there is still so much uncharted ground to cover regarding the mechanisms of SARS-CoV-2 infection, replication and host response. These issues can be approached by proteomics with unprecedented capacity paving the way for the development of more efficient strategies for patient care. In this study, we present a deep proteome analysis that has been performed on a cohort of 72 COVID-19 patients aiming to identify serum proteins assessing the dynamics of the disease at different age ranges. A panel of 53 proteins that participate in several functions such as acute-phase response and inflammation, blood coagulation, cell adhesion, complement cascade, endocytosis, immune response, oxidative stress and tissue injury, have been correlated with patient severity, suggesting a molecular basis for their clinical stratification. Eighteen protein candidates were further validated by targeted proteomics in an independent cohort of 84 patients including a group of individuals that had satisfactorily resolved SARS-CoV-2 infection. Remarkably, all protein alterations were normalized 100 days after leaving the hospital, which further supports the reliability of the selected proteins as hallmarks of COVID-19 progression and grading. The optimized protein panel may prove its value for optimal severity assessment as well as in the follow up of COVID-19 patients.
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Affiliation(s)
- Estefanía Nuñez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- Cardiovascular Proteomics Laboratory, Centro Nacional de Enfermedades Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Irene Orera
- Proteomics Research Core Facility, Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain;
| | | | - José Ramón Paño
- Division of Infectious Diseases, Hospital Clínico Universitario, IIS Aragón, Ciberinfec, 50009 Zaragoza, Spain;
| | - Jesús Vázquez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- Cardiovascular Proteomics Laboratory, Centro Nacional de Enfermedades Cardiovasculares (CNIC), 28029 Madrid, Spain
- Correspondence: (J.V.); (F.J.C.)
| | - Fernando J. Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain;
- Correspondence: (J.V.); (F.J.C.)
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28
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García-Hidalgo MC, González J, Benítez ID, Carmona P, Santisteve S, Moncusí-Moix A, Gort-Paniello C, Rodríguez-Jara F, Molinero M, Perez-Pons M, Torres G, Caballero J, Barberà C, Tedim AP, Almansa R, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D. Proteomic profiling of lung diffusion impairment in the recovery stage of SARS-CoV-2-induced ARDS. Clin Transl Med 2022; 12:e838. [PMID: 35538880 PMCID: PMC9091985 DOI: 10.1002/ctm2.838] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Ana P Tedim
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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