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Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Schaub JA, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, García-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU. Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.18.24304401. [PMID: 38562892 PMCID: PMC10984064 DOI: 10.1101/2024.03.18.24304401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.
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Zacharias M, Thüringer A, Krause R, Kashofer K, Gorkiewicz G. The mutual value of histopathology and ITS sequencing in the diagnosis of mucormycosis. Histopathology 2024; 84:702-706. [PMID: 38192085 DOI: 10.1111/his.15131] [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: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
AIMS Mucormycosis is a fast-progressing disease with a high mortality rate. The most important factor determining survival of patients is early and accurate diagnosis. Although histopathology often recognises invasive mould infections at first, histomorphology alone is insufficient in providing an accurate diagnosis. Unbiased molecular methods to detect and identify fungi are promising, yet their role in complementing routine histopathological workflows has not been studied sufficiently. METHODS AND RESULTS We performed a retrospective single-centre study examining the clinical value of complementing histopathology with internal transcribed spacer (ITS) sequencing of fungal DNA in the routine diagnosis of mucormycosis. At our academic centre, we identified 14 consecutive mucormycosis cases diagnosed by histopathology and subsequent ITS sequencing. Using histomorphological examination, fungal hyphae could be detected in all cases; however, morphological features were unreliable regarding specifying the taxa. Subsequent ITS sequencing identified a remarkable phylogenetic diversity among Mucorales: the most common species was Rhizopus microsporus (six of 14; 42.9%), followed by Lichtheimia corymbifera (three of 14, 21.4%) and single detections of Rhizopus oryzae, Actinomucor elegans, Mucor circinelloides, Rhizomucor pusillus and Rhizomucor miehei (one of 14; 7.1%, respectively). In one case, we additionally detected Pneumocystis jirovecii in the same lung tissue specimen, suggesting a clinically relevant co-infection. Fungal culture was performed in 10 cases but yielded positive results in only two of 10 (20%), revealing its limited value in the diagnosis of mucormycosis. CONCLUSIONS Our study demonstrates that a combination of histopathology and ITS sequencing is a practically feasible approach that outperforms fungal culture in detecting Mucorales in tissue-associated infections. Therefore, pathologists might adapt diagnostic workflows accordingly when mucormycosis is suspected.
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Affiliation(s)
- Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andrea Thüringer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Robert Krause
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
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3
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Wang L, Cao JB, Xia BB, Li YJ, Zhang X, Mo GX, Wang RJ, Guo SQ, Zhang YQ, Xiao K, Zhu GF, Liu PF, Song LC, Ma XH, Xiang PC, Wang J, Liu YH, Xie F, Zhang XD, Li XX, Sun WL, Cao Y, Wang KF, Zhang WH, Zhao WC, Yan P, Chen JC, Yang YW, Yu ZK, Tang JS, Xiao L, Zhou JM, Xie LX, Wang J. Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients. Signal Transduct Target Ther 2023; 8:432. [PMID: 37949875 PMCID: PMC10638395 DOI: 10.1038/s41392-023-01684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/21/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023] Open
Abstract
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.
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Affiliation(s)
- Lin Wang
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jia-Bao Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin-Bin Xia
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue-Juan Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, 014030, China
| | - Guo-Xin Mo
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Rui-Juan Wang
- Department of Respiratory Medicine, PLA Strategic Support Force Medical Center, Beijing, 100101, China
| | - Si-Qi Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu-Qing Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Xiao
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Guang-Fa Zhu
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Peng-Fei Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Li-Cheng Song
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Xi-Hui Ma
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Ping-Chao Xiang
- Shougang hospital of Peking University, Beijing, 100144, China
| | - Jiang Wang
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Yu-Hong Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Fei Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Xu-Dong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Xin Li
- Department of Respiratory Medicine, Beijing Changping Hospital, Beijing, 102200, China
| | - Wan-Lu Sun
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yan Cao
- Pulmonary research institute, Senior Department of Respiratory and Critical Care Medicine, the 8th medical center of Chinese PLA general hospital, Beijing, 100091, China
| | - Kai-Fei Wang
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853, China
| | - Wen-Hui Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Chao Zhao
- Department of Respiratory Medicine, PLA Strategic Support Force Medical Center, Beijing, 100101, China
| | - Peng Yan
- China Aerospace Science & Industry Corporation 731 hospital, Beijing, 100074, China
| | - Ji-Chao Chen
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Beijing, 100049, China
| | - Yu-Wei Yang
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Zhong-Kuo Yu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jing-Si Tang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Xiao
- Respiratory Research Institute, Department of Pulmonary & Critical Care Medicine, Beijing Key Laboratory of OTIR, the 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China
| | - Jie-Min Zhou
- Vision Medicals Center for Infectious Diseases, Guangzhou, 510700, China
| | - Li-Xin Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, 100091, China.
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Noack P, Grosse C, Bodingbauer J, Almeder M, Lohfink-Schumm S, Salzer HJF, Meier J, Lamprecht B, Schmitt CA, Langer R. Minimally invasive autopsies for the investigation of pulmonary pathology of COVID-19-experiences of a longitudinal series of 92 patients. Virchows Arch 2023; 483:611-619. [PMID: 37653260 PMCID: PMC10673967 DOI: 10.1007/s00428-023-03622-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
Minimally invasive autopsies (MIAs) allow the collection of tissue samples for diagnostic and research purposes in special situations, e.g., when there is a high risk of infection which is the case in the context of COVID-19 or restrictions due to legal or personal reasons. We performed MIA to analyze lung tissue from 92 COVID-19 patients (mean age 78 years; range 48-98; 35 women, 57 men), representing 44% of all patients who died from the disease between October 2020 and April 2021. An intercostal approach was used with removal of a 5-cm rib section followed by manual collection of four lung tissue samples (5-8 cm in size). Diffuse alveolar damage (DAD) was found in 89 (97%) patients at various stages. Exudative DAD (eDAD) predominated in 18 (20%) patients, proliferative DAD (pDAD) in 43 (47%) patients, and mixed DAD (mDAD) in 31 (34%) patients. There were no significant differences in the predominant DAD pattern between tissue samples from the same patient. Additional purulent components were present in 46 (50%) cases. Fungi were detected in 11 (12%) patients. The pDAD pattern was associated with longer hospital stay including intensive care unit (p=0.026 and p<0.001) and younger age (p=0.019). Positive bronchoalveolar lavage and blood cultures were observed more frequently in pDAD patterns (p<0.001; p=0.018). In contrast, there was no significant association between intravital positive microbiological results and superimposed bronchopneumonia or fungal infection at autopsy. Having demonstrated the characteristic lung changes in a large longitudinal autopsy series, we conclude that the presented MIA approach can be considered a reliable and safe method for performing post mortem lung diagnostics in COVID-19 and other high-risk situations. The lack of correlation between histological changes indicative of bacterial or fungal superinfection and microbiology could have clinical implications for disease and treatment surveillance.
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Affiliation(s)
- Petar Noack
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Claudia Grosse
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
| | - Jacob Bodingbauer
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Marion Almeder
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Sylvia Lohfink-Schumm
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Helmut J F Salzer
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Division of Infectious Diseases and Tropical Medicine, Department of Pulmonary Medicine, Kepler University Hospital, Linz, Austria
- Ignaz-Semmelweis-Institute, Interuniversity Institute for Infection Research, Vienna, Austria
| | - Jens Meier
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Anesthesiology and Intensive Care Medicine, Kepler University Hospital, Linz, Austria
| | - Bernd Lamprecht
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Pulmonary Medicine, Kepler University Hospital, Linz, Austria
| | - Clemens A Schmitt
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Hematology and Medical Oncology, Kepler University Hospital, Linz, Austria
| | - Rupert Langer
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria.
- Medical Faculty, Johannes Kepler University, Linz, Austria.
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5
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Tana C, Moffa L, Falasca K, Vecchiet J, Tana M, Mantini C, Ricci F, Ticinesi A, Meschi T, Cipollone F, Giamberardino MA. Approach to COVID-19 in older adults and indications for improving the outcomes. Ann Med 2023; 55:2265298. [PMID: 37839411 PMCID: PMC10578089 DOI: 10.1080/07853890.2023.2265298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Background: COVID-19 continues to present challenges in the care of older adults with frailty and/or comorbidities and very old patients, who can be hospitalized with severe COVID-19 despite full vaccination. Frailty is a heterogeneous syndrome characterized by an increased aging-related vulnerability due to a reduced physiological reserve and function of systemic organs, and is associated with an impairment of activities of daily living. Frail older adults remain at elevated risk of mortality from COVID-19 compared to older adults without frailty, and some pre-existing risk factors such as malnutrition, prolonged bed rest, and the association with comorbidities can aggravate the SARS-CoV-2 infection. Furthermore, the severity of COVID-19 can impact on long-term functioning of older patients surviving from the infection. Persistent symptoms are another emerging problem of the post-vaccination phase of pandemic, as most patients suffer from chronic symptoms which can become debilitating and affect the daily routine. Aim of this review: In this complex relationship, the evaluation of COVID-19 in vulnerable categories is still a matter of high interest and personalized care plans based on a comprehensive geriatric assessment, tailored interventions; specific therapeutic algorithms among older adults are thus recommended in order to improve the outcomes.
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Affiliation(s)
- Claudio Tana
- Geriatrics Clinic, SS Annunziata Hospital of Chieti, Chieti, Italy
| | - Livia Moffa
- Infectious Disease Department and COVID-19 Unit, University Hospital of Chieti, Chieti, Italy
| | - Katia Falasca
- Infectious Disease Department and COVID-19 Unit, University Hospital of Chieti, Chieti, Italy
| | - Jacopo Vecchiet
- Infectious Disease Department and COVID-19 Unit, University Hospital of Chieti, Chieti, Italy
| | - Marco Tana
- Internal Medicine Unit, SS. Annunziata Hospital of Chieti, Chieti, Italy
| | - Cesare Mantini
- Department of Neuroscience, Imaging and Clinical Sciences, "G. D’Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Fabrizio Ricci
- Department of Neuroscience, Imaging and Clinical Sciences, "G. D’Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Italy and Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Italy and Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Francesco Cipollone
- Medical Clinic, SS. Annunziata Hospital of Chieti, Department of Medicine and Science of Aging, "G. D’Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Maria Adele Giamberardino
- Geriatrics Clinic, SS Annunziata Hospital of Chieti, Chieti, Italy
- Department of Medicine and Science of Aging, “G. D’Annunzio” University of Chieti, Chieti, Italy
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6
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Autsch A, Ihle H, Kleemann S, Sanft J, Hahnemann M, Hubig M, Philipp M, Bauer M, Deinhardt-Emmer S, Gaßler N, Mall G, Wittschieber D. SARS-CoV-2-assoziierte Todesfälle innerhalb des ersten Jahres der COVID-19-Pandemie: eine Autopsiestudie. Rechtsmedizin (Berl) 2023; 33:262-268. [DOI: 10.1007/s00194-023-00636-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2023] [Indexed: 10/09/2023]
Abstract
Abstract
Background
COVID-19 now exists for more than 3 years and has caused almost 7 million deaths worldwide. At the beginning of this study only little was known on the patients’ characteristics and comparative autopsy studies are still rare.
Material and methods
Between 11 March 2020 and 10 March 2021, 55 consecutive and complete autopsies of individuals who died in association with SARS-CoV‑2 infections were performed shortly after death (median PMI 6.8 h) by the same team. Clinical data were available in 45 of 55 cases. 1st vs. 2nd infection wave cases and male vs. female cases were compared.
Results
Thirty-five patients were male (63.6%) 20 were female (36.4%), average age 72.4 years. Seventeen cases (30.9%) could be assigned to the 1st and 38 cases (69.1%) to the 2nd infection wave. Forty-two of the decedents (76.4%) died due to COVID-19. Arterial hypertension, obesity, and cardiac hypertrophy were the most frequent detected comorbidities.
Discussion
The present study corroborates previous research data but also reveals new approaches for further comparative studies. Patient-specific personal and general ICU-related risk factors for the development of thromboembolisms oppose the effects of changes in anticoagulant medication.
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7
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Shaw JA, Meiring M, Snyders C, Everson F, Sigwadhi LN, Ngah V, Tromp G, Allwood B, Koegelenberg CFN, Irusen EM, Lalla U, Baines N, Zemlin AE, Erasmus RT, Chapanduka ZC, Matsha TE, Walzl G, Strijdom H, du Plessis N, Zumla A, Chegou N, Malherbe ST, Nyasulu PS. Immunologic and vascular biomarkers of mortality in critical COVID-19 in a South African cohort. Front Immunol 2023; 14:1219097. [PMID: 37465683 PMCID: PMC10351604 DOI: 10.3389/fimmu.2023.1219097] [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: 05/08/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction Biomarkers predicting mortality among critical Coronavirus disease 2019 (COVID-19) patients provide insight into the underlying pathophysiology of fatal disease and assist with triaging of cases in overburdened settings. However, data describing these biomarkers in Sub-Saharan African populations are sparse. Methods We collected serum samples and corresponding clinical data from 87 patients with critical COVID-19 on day 1 of admission to the intensive care unit (ICU) of a tertiary hospital in Cape Town, South Africa, during the second wave of the COVID-19 pandemic. A second sample from the same patients was collected on day 7 of ICU admission. Patients were followed up until in-hospital death or hospital discharge. A custom-designed 52 biomarker panel was performed on the Luminex® platform. Data were analyzed for any association between biomarkers and mortality based on pre-determined functional groups, and individual analytes. Results Of 87 patients, 55 (63.2%) died and 32 (36.8%) survived. We found a dysregulated cytokine response in patients who died, with elevated levels of type-1 and type-2 cytokines, chemokines, and acute phase reactants, as well as reduced levels of regulatory T cell cytokines. Interleukin (IL)-15 and IL-18 were elevated in those who died, and levels reduced over time in those who survived. Procalcitonin (PCT), C-reactive protein, Endothelin-1 and vascular cell adhesion molecule-1 were elevated in those who died. Discussion These results show the pattern of dysregulation in critical COVID-19 in a Sub-Saharan African cohort. They suggest that fatal COVID-19 involved excessive activation of cytotoxic cells and the NLRP3 (nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3) inflammasome. Furthermore, superinfection and endothelial dysfunction with thrombosis might have contributed to mortality. HIV infection did not affect the outcome. A clinically relevant biosignature including PCT, pH and lymphocyte percentage on differential count, had an 84.8% sensitivity for mortality, and outperformed the Luminex-derived biosignature.
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Affiliation(s)
- Jane Alexandra Shaw
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Maynard Meiring
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Candice Snyders
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Frans Everson
- Centre for Cardiometabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Lovemore Nyasha Sigwadhi
- Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Veranyay Ngah
- Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerard Tromp
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Brian Allwood
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Coenraad F. N. Koegelenberg
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Elvis M. Irusen
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Usha Lalla
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Nicola Baines
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Annalise E. Zemlin
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Rajiv T. Erasmus
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Zivanai C. Chapanduka
- Division of Haematological Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service (NHLS) Tygerberg Hospital, Cape Town, South Africa
| | - Tandi E. Matsha
- Sefako Makgatho University of Health Sciences, Ga-Rankuwa, South Africa
| | - Gerhard Walzl
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Hans Strijdom
- Centre for Cardiometabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nelita du Plessis
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
- National Institute for Health Care Research (NIHR) Biomedical Research Centre, University College London (UCL) Hospitals National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Novel Chegou
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanus T. Malherbe
- Department of Science and Technology/National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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8
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Jandl K, Berg JL, Birnhuber A, Fliesser E, Borek I, Seeliger B, David S, Schmidt JJ, Gorkiewicz G, Zacharias M, Welte T, Olschewski H, Heinemann A, Wygrecka M, Kwapiszewska G. Basement membrane product, endostatin, as a link between inflammation, coagulation and vascular permeability in COVID-19 and non-COVID-19 acute respiratory distress syndrome. Front Immunol 2023; 14:1188079. [PMID: 37283766 PMCID: PMC10241244 DOI: 10.3389/fimmu.2023.1188079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Background Immune cell recruitment, endothelial cell barrier disruption, and platelet activation are hallmarks of lung injuries caused by COVID-19 or other insults which can result in acute respiratory distress syndrome (ARDS). Basement membrane (BM) disruption is commonly observed in ARDS, however, the role of newly generated bioactive BM fragments is mostly unknown. Here, we investigate the role of endostatin, a fragment of the BM protein collagen XVIIIα1, on ARDS associated cellular functions such as neutrophil recruitment, endothelial cell barrier integrity, and platelet aggregation in vitro. Methods In our study we analyzed endostatin in plasma and post-mortem lung specimens of patients with COVID-19 and non-COVID-19 ARDS. Functionally, we investigated the effect of endostatin on neutrophil activation and migration, platelet aggregation, and endothelial barrier function in vitro. Additionally, we performed correlation analysis for endostatin and other critical plasma parameters. Results We observed increased plasma levels of endostatin in our COVID-19 and non-COVID-19 ARDS cohort. Immunohistochemical staining of ARDS lung sections depicted BM disruption, alongside immunoreactivity for endostatin in proximity to immune cells, endothelial cells, and fibrinous clots. Functionally, endostatin enhanced the activity of neutrophils, and platelets, and the thrombin-induced microvascular barrier disruption. Finally, we showed a positive correlation of endostatin with soluble disease markers VE-Cadherin, c-reactive protein (CRP), fibrinogen, and interleukin (IL)-6 in our COVID-19 cohort. Conclusion The cumulative effects of endostatin on propagating neutrophil chemotaxis, platelet aggregation, and endothelial cell barrier disruption may suggest endostatin as a link between those cellular events in ARDS pathology.
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Affiliation(s)
- Katharina Jandl
- Otto Loewi Research Center, Division of Pharmacology, Medical University of Graz, Graz, Austria
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - Johannes Lorenz Berg
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
- Otto Loewi Research Center, Division of Physiology and Pathophysiology, Medical University of Graz, Graz, Austria
| | - Anna Birnhuber
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
- Otto Loewi Research Center, Division of Physiology and Pathophysiology, Medical University of Graz, Graz, Austria
| | | | - Izabela Borek
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - Benjamin Seeliger
- Department of Respiratory Medicine/Infectious Diseases, Hannover Medical School, Member of the German Lung Center (DZL), Hannover, Germany
| | - Sascha David
- Institute of Intensive Care, University Hospital Zurich, Zurich, Switzerland
| | - Julius J. Schmidt
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria
| | - Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria
| | - Tobias Welte
- Department of Respiratory Medicine/Infectious Diseases, Hannover Medical School, Member of the German Lung Center (DZL), Hannover, Germany
| | - Horst Olschewski
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
- Division of Pulmonology, Medical University of Graz, Graz, Austria
| | - Akos Heinemann
- Otto Loewi Research Center, Division of Pharmacology, Medical University of Graz, Graz, Austria
| | - Malgorzata Wygrecka
- Center for Infection and Genomics of the Lung, Universities of Giessen and Marburg Lung Center, Member of the German Lung Center (DZL), Giessen, Germany
- Institute for Lung Health, Member of the German Lung Center (DZL), Giessen, Germany
| | - Grazyna Kwapiszewska
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
- Otto Loewi Research Center, Division of Physiology and Pathophysiology, Medical University of Graz, Graz, Austria
- Institute for Lung Health, Member of the German Lung Center (DZL), Giessen, Germany
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9
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Gindlhuber J, Tomin T, Wiesenhofer F, Zacharias M, Liesinger L, Demichev V, Kratochwill K, Gorkiewicz G, Schittmayer M, Birner-Gruenberger R. Proteomic profiling of end-stage COVID-19 lung biopsies. Clin Proteomics 2022; 19:46. [PMID: 36526981 PMCID: PMC9758034 DOI: 10.1186/s12014-022-09386-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The outbreak of a novel coronavirus (SARS-CoV-2) in 2019 led to a worldwide pandemic, which remains an integral part of our lives to this day. Coronavirus disease (COVID-19) is a flu like condition, often accompanied by high fever and respiratory distress. In some cases, conjointly with other co-morbidities, COVID-19 can become severe, leading to lung arrest and even death. Although well-known from a clinical standpoint, the mechanistic understanding of lethal COVID-19 is still rudimentary. Studying the pathology and changes on a molecular level associated with the resulting COVID-19 disease is impeded by the highly infectious nature of the virus and the concomitant sampling challenges. We were able to procure COVID-19 post-mortem lung tissue specimens by our collaboration with the BSL-3 laboratory of the Biobanking and BioMolecular resources Research Infrastructure Austria which we subjected to state-of-the-art quantitative proteomic analysis to better understand the pulmonary manifestations of lethal COVID-19. Lung tissue samples from age-matched non-COVID-19 patients who died within the same period were used as controls. Samples were subjected to parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) on a timsTOF Pro and obtained raw data was processed using DIA-NN software. Here we report that terminal COVID-19 patients display an increase in inflammation, acute immune response and blood clot formation (with concomitant triggering of fibrinolysis). Furthermore, we describe that COVID-19 diseased lungs undergo severe extracellular matrix restructuring, which was corroborated on the histopathological level. However, although undergoing an injury, diseased lungs seem to have impaired proliferative and tissue repair signalling, with several key kinase-mediated signalling pathways being less active. This might provide a mechanistic link to post-acute sequelae of COVID-19 (PASC; "Long COVID"). Overall, we emphasize the importance of histopathological patient stratification when interpreting molecular COVID-19 data.
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Affiliation(s)
- Juergen Gindlhuber
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria
| | - Florian Wiesenhofer
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Vadim Demichev
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Klaus Kratochwill
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria.
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria.
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria.
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