1
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Shah FA, Bahudhanapati H, Jiang M, Tabary M, van der Geest R, Tolman NJ, Kochin M, Xiong Z, Al-Yousif N, Sayed K, Benos PV, Raffensperger K, Evankovich J, Neal MD, Snyder ME, Eickelberg O, Ray P, Dela Cruz C, Bon J, McVerry BJ, Straub AC, Jurczak MJ, Suber TL, Zhang Y, Chen K, Kitsios GD, Lee JS, Alder JK, Bain WG. Lung Epithelium Releases Growth Differentiation Factor 15 in Response to Pathogen-mediated Injury. Am J Respir Cell Mol Biol 2024; 70:379-391. [PMID: 38301257 DOI: 10.1165/rcmb.2023-0429oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/01/2024] [Indexed: 02/03/2024] Open
Abstract
GDF15 (growth differentiation factor 15) is a stress cytokine with several proposed roles, including support of stress erythropoiesis. Higher circulating GDF15 levels are prognostic of mortality during acute respiratory distress syndrome, but the cellular sources and downstream effects of GDF15 during pathogen-mediated lung injury are unclear. We quantified GDF15 in lower respiratory tract biospecimens and plasma from patients with acute respiratory failure. Publicly available data from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were reanalyzed. We used mouse models of hemorrhagic acute lung injury mediated by Pseudomonas aeruginosa exoproducts in wild-type mice and mice genetically deficient for Gdf15 or its putative receptor, Gfral. In critically ill humans, plasma levels of GDF15 correlated with lower respiratory tract levels and were higher in nonsurvivors. SARS-CoV-2 infection induced GDF15 expression in human lung epithelium, and lower respiratory tract GDF15 levels were higher in coronavirus disease (COVID-19) nonsurvivors. In mice, intratracheal P. aeruginosa type II secretion system exoproducts were sufficient to induce airspace and plasma release of GDF15, which was attenuated with epithelial-specific deletion of Gdf15. Mice with global Gdf15 deficiency had decreased airspace hemorrhage, an attenuated cytokine profile, and an altered lung transcriptional profile during injury induced by P. aeruginosa type II secretion system exoproducts, which was not recapitulated in mice deficient for Gfral. Airspace GDF15 reconstitution did not significantly modulate key lung cytokine levels but increased circulating erythrocyte counts. Lung epithelium releases GDF15 during pathogen injury, which is associated with plasma levels in humans and mice and can increase erythrocyte counts in mice, suggesting a novel lung-blood communication pathway.
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Affiliation(s)
- Faraaz A Shah
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | | | - Mao Jiang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | | | | | | | - Megan Kochin
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - Zeyu Xiong
- Division of Pulmonary and Critical Care Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Nameer Al-Yousif
- Division of Pulmonary, Critical Care, and Sleep Medicine, MetroHealth Medical Center, Cleveland, Ohio
| | - Khaled Sayed
- Electrical & Computer Engineering and Computer Science Department, University of New Haven, West Haven, Connecticut
- Department of Epidemiology, University of Florida, Gainesville, Florida
| | | | | | - John Evankovich
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | | | - Mark E Snyder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | | | - Prabir Ray
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Jessica Bon
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - Adam C Straub
- Department of Pharmacology and Chemical Biology and
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael J Jurczak
- Division of Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Tomeka L Suber
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - Kong Chen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | | | - Janet S Lee
- Division of Pulmonary and Critical Care Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Jonathan K Alder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
| | - William G Bain
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
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2
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Sayed K, Dolin CE, Wilkey DW, Li J, Sato T, Beier JI, Argemi J, Bataller R, Wahed AS, Merchant ML, Benos PV, Arteel GE. A plasma peptidomic signature reveals extracellular matrix remodeling and predicts prognosis in alcohol-related hepatitis. medRxiv 2023:2023.12.13.23299905. [PMID: 38168372 PMCID: PMC10760272 DOI: 10.1101/2023.12.13.23299905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Alcohol-related hepatitis (AH) is plagued with high mortality and difficulty in identifying at-risk patients. The extracellular matrix undergoes significant remodeling during inflammatory liver injury that can be detected in biological fluids and potentially used for mortality prediction. EDTA plasma samples were collected from AH patients (n= 62); Model for End-Stage Liver Disease (MELD) score defined AH severity as moderate (12-20; n=28) and severe (>20; n=34). The peptidome data was collected by high resolution, high mass accuracy UPLC-MS. Univariate and multivariate analyses identified differentially abundant peptides, which were used for Gene Ontology, parent protein matrisomal composition and protease involvement. Machine learning methods were used on patient-specific peptidome and clinical data to develop mortality predictors. Analysis of plasma peptides from AH patients and healthy controls identified over 1,600 significant peptide features corresponding to 130 proteins. These were enriched for ECM fragments in AH samples, likely related to turnover of hepatic-derived proteins. Analysis of moderate versus severe AH peptidomes showed a shift in abundance of peptides from collagen 1A1 and fibrinogen A proteins. The dominant proteases for the AH peptidome spectrum appear to be CAPN1 and MMP12. Increase in hepatic expression of these proteases was orthogonally-validated in RNA-seq data of livers from AH patients. Causal graphical modeling identified four peptides directly linked to 90-day mortality in >90% of the learned graphs. These peptides improved the accuracy of mortality prediction over MELD score and were used to create a clinically applicable mortality prediction assay. A signature based on plasma peptidome is a novel, non-invasive method for prognosis stratification in AH patients. Our results could also lead to new mechanistic and/or surrogate biomarkers to identify new AH mechanisms. Lay summary We used degraded proteins found the blood of alcohol-related hepatitis patients to identify new potential mechanisms of injury and to predict 90 day mortality.
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Jia M, Sayed K, Kapetanaki MG, Dion W, Rosas L, Irfan S, Valenzi E, Mora AL, Lafyatis RA, Rojas M, Zhu B, Benos PV. LEF1 isoforms regulate cellular senescence and aging. Aging Cell 2023; 22:e14024. [PMID: 37961030 PMCID: PMC10726832 DOI: 10.1111/acel.14024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 11/15/2023] Open
Abstract
The study of aging and its mechanisms, such as cellular senescence, has provided valuable insights into age-related pathologies, thus contributing to their prevention and treatment. The current abundance of high-throughput data combined with the surge of robust analysis algorithms has facilitated novel ways of identifying underlying pathways that may drive these pathologies. For the purpose of identifying key regulators of lung aging, we performed comparative analyses of transcriptional profiles of aged versus young human subjects and mice, focusing on the common age-related changes in the transcriptional regulation in lung macrophages, T cells, and B immune cells. Importantly, we validated our findings in cell culture assays and human lung samples. Our analysis identified lymphoid enhancer binding factor 1 (LEF1) as an important age-associated regulator of gene expression in all three cell types across different tissues and species. Follow-up experiments showed that the differential expression of long and short LEF1 isoforms is a key regulatory mechanism of cellular senescence. Further examination of lung tissue from patients with idiopathic pulmonary fibrosis, an age-related disease with strong ties to cellular senescence, revealed a stark dysregulation of LEF1. Collectively, our results suggest that LEF1 is a key factor of aging, and its differential regulation is associated with human and murine cellular senescence.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPennsylvaniaUSA
- Joint Carnegie Mellon University‐University of Pittsburgh Ph.D. Program in Computational BiologyPittsburghPennsylvaniaUSA
| | - Khaled Sayed
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPennsylvaniaUSA
- Department of Electrical & Computer Engineering and Computer ScienceUniversity of New HavenWest HavenConnecticutUSA
| | - Maria G. Kapetanaki
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPennsylvaniaUSA
- Department of EpidemiologyUniversity of FloridaGainesvilleFloridaUSA
| | - William Dion
- Aging Institute of UPMCUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Lorena Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Saad Irfan
- Aging Institute of UPMCUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Eleanor Valenzi
- Department of RheumatologyUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Ana L. Mora
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Robert A. Lafyatis
- Department of RheumatologyUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Bokai Zhu
- Aging Institute of UPMCUniversity of PittsburghPittsburghPennsylvaniaUSA
- Department of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
- Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Panayiotis V. Benos
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPennsylvaniaUSA
- Joint Carnegie Mellon University‐University of Pittsburgh Ph.D. Program in Computational BiologyPittsburghPennsylvaniaUSA
- Department of EpidemiologyUniversity of FloridaGainesvilleFloridaUSA
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4
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Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. medRxiv 2023:2023.09.25.23296086. [PMID: 37808745 PMCID: PMC10557814 DOI: 10.1101/2023.09.25.23296086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Cruz CD, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. Res Sq 2023:rs.3.rs-3338762. [PMID: 37841841 PMCID: PMC10571606 DOI: 10.21203/rs.3.rs-3338762/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
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Jia M, Sayed K, Kapetanaki MG, Dion W, Rosas L, Irfan S, Valenzi E, Mora AL, Lafyatis RA, Rojas M, Zhu B, Benos PV. LEF1 isoforms regulate cellular senescence and aging. bioRxiv 2023:2023.07.20.549883. [PMID: 37502913 PMCID: PMC10370160 DOI: 10.1101/2023.07.20.549883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background The study of aging and its mechanisms, such as cellular senescence, has provided valuable insights into age-related pathologies, thus contributing to their prevention and treatment. The current abundance of high throughput data combined with the surge of robust analysis algorithms has facilitated novel ways of identifying underlying pathways that may drive these pathologies. Methods With the focus on identifying key regulators of lung aging, we performed comparative analyses of transcriptional profiles of aged versus young human subjects and mice, focusing on the common age-related changes in the transcriptional regulation in lung macrophages, T cells, and B immune cells. Importantly, we validated our findings in cell culture assays and human lung samples. Results We identified Lymphoid Enhancer Binding Factor 1 (LEF1) as an important age-associated regulator of gene expression in all three cell types across different tissues and species. Follow-up experiments showed that the differential expression of long and short LEF1 isoforms is a key regulatory mechanism of cellular senescence. Further examination of lung tissue from patients with Idiopathic Pulmonary Fibrosis (IPF), an age-related disease with strong ties to cellular senescence, we demonstrated a stark dysregulation of LEF1. Conclusions Collectively, our results suggest that the LEF1 is a key factor of aging, and its differential regulation is associated with human and murine cellular senescence.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, USA
| | - Khaled Sayed
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Maria G. Kapetanaki
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William Dion
- Aging Institute of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lorena Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Saad Irfan
- Aging Institute of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eleanor Valenzi
- Department of Rheumatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ana L. Mora
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Robert A. Lafyatis
- Department of Rheumatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
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7
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Li J, Sato T, Hernández-Tejero M, Beier JI, Sayed K, Benos PV, Wilkey DW, Humar A, Merchant ML, Duarte-Rojo A, Arteel GE. The plasma degradome reflects later development of NASH fibrosis after liver transplant. Sci Rep 2023; 13:9965. [PMID: 37340062 PMCID: PMC10282030 DOI: 10.1038/s41598-023-36867-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
Although liver transplantation (LT) is an effective therapy for cirrhosis, the risk of post-LT NASH is alarmingly high and is associated with accelerated progression to fibrosis/cirrhosis, cardiovascular disease and decreased survival. Lack of risk stratification strategies hampers early intervention against development of post-LT NASH fibrosis. The liver undergoes significant remodeling during inflammatory injury. During such remodeling, degraded peptide fragments (i.e., 'degradome') of the ECM and other proteins increase in plasma, making it a useful diagnostic/prognostic tool in chronic liver disease. To investigate whether liver injury caused by post-LT NASH would yield a unique degradome profile that is predictive of severe post-LT NASH fibrosis, a retrospective analysis of 22 biobanked samples from the Starzl Transplantation Institute (12 with post-LT NASH after 5 years and 10 without) was performed. Total plasma peptides were isolated and analyzed by 1D-LC-MS/MS analysis using a Proxeon EASY-nLC 1000 UHPLC and nanoelectrospray ionization into an Orbitrap Elite mass spectrometer. Qualitative and quantitative peptide features data were developed from MSn datasets using PEAKS Studio X (v10). LC-MS/MS yielded ~ 2700 identifiable peptide features based on the results from Peaks Studio analysis. Several peptides were significantly altered in patients that later developed fibrosis and heatmap analysis of the top 25 most significantly changed peptides, most of which were ECM-derived, clustered the 2 patient groups well. Supervised modeling of the dataset indicated that a fraction of the total peptide signal (~ 15%) could explain the differences between the groups, indicating a strong potential for representative biomarker selection. A similar degradome profile was observed when the plasma degradome patterns were compared being obesity sensitive (C57Bl6/J) and insensitive (AJ) mouse strains. The plasma degradome profile of post-LT patients yielded stark difference based on later development of post-LT NASH fibrosis. This approach could yield new "fingerprints" that can serve as minimally-invasive biomarkers of negative outcomes post-LT.
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Affiliation(s)
- Jiang Li
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Toshifumi Sato
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - María Hernández-Tejero
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Juliane I Beier
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering and Computer Science, University of New Haven, New Haven, CT, USA
| | | | - Daniel W Wilkey
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Abhinav Humar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andres Duarte-Rojo
- Division of Gastroenterology and Hepatology, Northwestern Medicine and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Comprehensive Transplant Center, Northwestern Medicine and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gavin E Arteel
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.
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Kitsios GD, Nguyen VD, Sayed K, Al-Yousif N, Schaefer C, Shah FA, Bain W, Yang H, Fitch A, Li K, Wang X, Qin S, Gentry H, Zhang Y, Varon J, Arciniegas Rubio A, Englert JA, Baron RM, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ. The upper and lower respiratory tract microbiome in severe aspiration pneumonia. iScience 2023; 26:106832. [PMID: 37250794 PMCID: PMC10212968 DOI: 10.1016/j.isci.2023.106832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/24/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro-aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and performed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Vi D. Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- University of California Los Angeles, Department of Medicine, Internal Medicine Residency Program, Los Angeles, CA90095, USA
| | - Khaled Sayed
- University of PittsburghDepartment of Computational & Systems Biology, Pittsburgh, PA15213, USA
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Nameer Al-Yousif
- University of Pittsburgh Medical Center Mercy, Department of Medicine, Pittsburgh, PA15219, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - Haopu Yang
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Heather Gentry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Antonio Arciniegas Rubio
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Joshua A. Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH43210, USA
| | - Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO63110, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
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Li J, Sato T, Hernández-Tejero M, Beier JI, Sayed K, Benos PV, Wilkey DW, Humar A, Merchant ML, Duarte-Rojo A, Arteel GE. The plasma degradome reflects later development of NASH fibrosis after liver transplant. bioRxiv 2023:2023.01.30.526241. [PMID: 36778394 PMCID: PMC9915514 DOI: 10.1101/2023.01.30.526241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although liver transplantation (LT) is an effective therapy for cirrhosis, the risk of post-LT NASH is alarmingly high and is associated with accelerated progression to fibrosis/cirrhosis, cardiovascular disease, and decreased survival. Lack of risk stratification strategies hamper liver undergoes significant remodeling during inflammatory injury. During such remodeling, degraded peptide fragments (i.e., 'degradome') of the ECM and other proteins increase in plasma, making it a useful diagnostic/prognostic tool in chronic liver disease. To investigate whether inflammatory liver injury caused by post-LT NASH would yield a unique degradome profile, predictive of severe post-LT NASH fibrosis, we performed a retrospective analysis of 22 biobanked samples from the Starzl Transplantation Institute (12 with post-LT NASH after 5 years and 10 without). Total plasma peptides were isolated and analyzed by 1D-LC-MS/MS analysis using a Proxeon EASY-nLC 1000 UHPLC and nanoelectrospray ionization into an Orbitrap Elite mass spectrometer. Qualitative and quantitative peptide features data were developed from MSn datasets using PEAKS Studio X (v10). LC-MS/MS yielded ∼2700 identifiable peptide features based on the results from Peaks Studio analysis. Several peptides were significantly altered in patients that later developed fibrosis and heatmap analysis of the top 25 most significantly-changed peptides, most of which were ECM-derived, clustered the 2 patient groups well. Supervised modeling of the dataset indicated that a fraction of the total peptide signal (∼15%) could explain the differences between the groups, indicating a strong potential for representative biomarker selection. A similar degradome profile was observed when the plasma degradome patterns were compared being obesity sensitive (C57Bl6/J) and insensitive (AJ) mouse strains. Both The plasma degradome profile of post-LT patients yields stark difference based on later development of post-LT NASH fibrosis. This approach could yield new "fingerprints" that can serve as minimally-invasive biomarkers of negative outcomes post-LT.
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10
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Molina LM, Zhu J, Li Q, Pradhan-Sundd T, Krutsenko Y, Sayed K, Jenkins N, Vats R, Bhushan B, Ko S, Hu S, Poddar M, Singh S, Tao J, Sundd P, Singhi A, Watkins S, Ma X, Benos PV, Feranchak A, Michalopoulos G, Nejak-Bowen K, Watson A, Bell A, Monga SP. Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors. Cell Rep 2021; 36:109310. [PMID: 34233187 PMCID: PMC8280534 DOI: 10.1016/j.celrep.2021.109310] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/14/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
Yes-associated protein 1 (YAP1) regulates cell plasticity during liver injury, regeneration, and cancer, but its role in liver development is unknown. We detect YAP1 activity in biliary cells and in cells at the hepatobiliary bifurcation in single-cell RNA sequencing analysis of developing livers. Deletion of Yap1 in hepatoblasts does not impair Notch-driven SOX9+ ductal plate formation but does prevent the formation of the abutting second layer of SOX9+ ductal cells, blocking the formation of a patent intrahepatic biliary tree. Intriguingly, these mice survive for 8 months with severe cholestatic injury and without hepatocyte-to-biliary transdifferentiation. Ductular reaction in the perihilar region suggests extrahepatic biliary proliferation, likely seeking the missing intrahepatic biliary network. Long-term survival of these mice occurs through hepatocyte adaptation via reduced metabolic and synthetic function, including altered bile acid metabolism and transport. Overall, we show YAP1 as a key regulator of bile duct development while highlighting a profound adaptive capability of hepatocytes.
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Affiliation(s)
- Laura M Molina
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Junjie Zhu
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Qin Li
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Tirthadipa Pradhan-Sundd
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Yekaterina Krutsenko
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Ave, Pittsburgh, PA 15213, USA; Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Nathaniel Jenkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ravi Vats
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Department of Bioengineering, School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bharat Bhushan
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Sungjin Ko
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Shikai Hu
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Minakshi Poddar
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sucha Singh
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Junyan Tao
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Prithu Sundd
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Aatur Singhi
- Division of Anatomic Pathology, Department of Pathology, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Simon Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xiaochao Ma
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Andrew Feranchak
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - George Michalopoulos
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Kari Nejak-Bowen
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Alan Watson
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aaron Bell
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA
| | - Satdarshan P Monga
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh and UPMC, Pittsburgh, PA, USA; Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA.
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11
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Gilboy K, Sayed K, Sundaram N, Bocan KN, Miskov-Zivanov N. A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Simulator. Annu Int Conf IEEE Eng Med Biol Soc 2020; 2019:2895-2899. [PMID: 31946496 DOI: 10.1109/embc.2019.8857495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has runtimes plagued by wasted CPU cycles and unnecessary processes. Hardware emulation affords substantial speedup, but prior attempts at hardware implementation of biological simulators have been limited in scope and have suffered from inaccuracies due to poor random number generation. In this work, we propose several simulation schemes utilizing novel random update index generation techniques for step-based and round-based stochastic simulations of cellular networks. Our results show improved runtimes while maintaining simulation accuracy compared to software implementations.
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12
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Sayed K, Mohammed F, Abdel Hay R, Ezzeldin N, Rashed L, Fahim A. Elevated serum tumour necrosis factor‐like weak inducer of apoptosis in alopecia areata: a possible marker of disease severity. Clin Exp Dermatol 2019; 45:426-431. [DOI: 10.1111/ced.14118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Affiliation(s)
- K. Sayed
- Department of DermatologyFaculty of Medicine, Cairo University Cairo Egypt
| | - F. Mohammed
- Department of Dermatology and Venereology National Research Centre Giza Egypt
| | - R. Abdel Hay
- Department of DermatologyFaculty of Medicine, Cairo University Cairo Egypt
| | - N. Ezzeldin
- Department of DermatologyFaculty of Medicine, Cairo University Cairo Egypt
| | - L. Rashed
- Department of Biochemistry Faculty of Medicine, Cairo University Cairo Egypt
| | - A. Fahim
- Department of DermatologyFaculty of Medicine, Cairo University Cairo Egypt
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13
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Sayed K, Bocan KN, Miskov-Zivanov N. Automated Extension of Cell Signaling Models with Genetic Algorithm. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:5030-5033. [PMID: 30441471 DOI: 10.1109/embc.2018.8513431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The number of published results in biology and medicine is growing at an exceeding rate, and thus, extracting relevant information for building useful models is becoming very laborious. Furthermore, with the newly published information, previously built models need to be extended and updated, and with the voluminous literature, it is necessary to automate the model extension process. In this work, we introduce a methodology for extending logical models of cell signaling networks using a Genetic Algorithm (GA). The proposed procedure is developed to optimally search for a subset of biological interactions that extend logical models while preserving their desired behavior. To evaluate the effectiveness of the proposed methodology, we randomly removed a subset of elements from an existing T cell differentiation model, and mixed them with randomly created interactions to mimic the output of literature reading. We then used the GA to search for the extensions that optimally reconstructed the model. The simulation results showed that the GA was able to find a set of extensions that preserved the desired behavior of the model with fewer elements than the original model. The results demonstrate that the GA is an efficient tool for model extension, and suggest that it can be used for model reduction as well.
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14
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Sayed K, Kamel M, Alhaddad M, Malibary HM, Kadah YM. Characterization of phase space trajectories for Brain-Computer Interface. Biomed Signal Process Control 2017. [DOI: 10.1016/j.bspc.2017.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Sayed K, Kamel M, Alhaddad M, Malibary HM, Kadah YM. Extracting Phase Space Morphological Features for Electroencephalogram-Based Brain-Computer Interface. j med imaging hlth inform 2017. [DOI: 10.1166/jmihi.2017.2078771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Metwally D, Sayed K, Abdel Hay R, Rashed L. Reduction in tissue plasmin: a new mechanism of action of narrowband ultraviolet B in psoriasis. Clin Exp Dermatol 2014; 40:416-20. [PMID: 25557337 DOI: 10.1111/ced.12517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND Plasmin (PL) is a potent inflammatory cell activator, and ultraviolet (UV)B has immunomodulatory effects on cutaneous inflammatory responses. There are no previous studies comparing the effect of narrowband (NB)-UVB on tissue PL levels in psoriasis. AIM To estimate the possible role of PL in the pathogenesis of psoriasis, and to evaluate the effect of NB-UVB on tissue PL in psoriasis. METHODS This case-control study enrolled 21 patients with psoriasis and 20 clinically healthy volunteers matched for age and sex. Patients underwent 24 sessions of NB-UVB radiation. Biopsy samples using a 4 mm punch were taken from all patients before and after treatment and from the controls for estimation of tissue PL level by ELISA. RESULTS Tissue PL was significantly upregulated in psoriasis before treatment (mean ± SD 1.73 ± 1.23 ng/mg protein) compared with controls (0.21 ± 0.15 ng/mg protein) (P < 0.001). A statistically significant positive correlation (P = 0.02) was found between the tissue PL before treatment and the Psoriasis Area and Severity Index. Patients received 24 sessions of NB-UVB, with a mean cumulative dose of 23.25 ± 8.14 mJ/cm(2) . Tissue PL levels were reduced by a mean of 30.3% post-treatment compared with baseline (P < 0.001). The reduction in Pl levels was significantly correlated with the cumulative dose of NB-UVB, and with the percentage reduction in PASI (P < 0.001). CONCLUSIONS Our study highlights the possible role played by tissue PL level in the pathogenesis of psoriasis. PL level appears to reflect disease severity, and is a possible marker of therapeutic efficacy of NB-UVB on psoriatic skin.
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Affiliation(s)
- D Metwally
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - K Sayed
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - R Abdel Hay
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - L Rashed
- Department of Clinical Biochemistry, Faculty of Medicine, Cairo University, Cairo, Egypt
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17
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Amr K, Abdel-Hameed M, Sayed K, Nour-Edin F, Abdel Hay R. The Pro12Ala polymorphism of the gene for peroxisome proliferator activated receptor-gamma is associated with a lower Global Acne Grading System score in patients with acne vulgaris. Clin Exp Dermatol 2014; 39:741-5. [PMID: 24984871 DOI: 10.1111/ced.12394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2014] [Indexed: 01/31/2023]
Abstract
BACKGROUND Acne vulgaris is a multifactorial disease of the skin. Several studies have shown that sebocyte proliferation and/or lipogenesis, as well as inflammatory reactions, may be regulated by peroxisome proliferator-activated receptor (PPAR)γ-mediated pathways. AIM To investigate whether the Pro12Ala polymorphism of the PPARγ gene might be associated with the risk of acne, and to assess the effect of this polymorphism on acne severity. METHODS This case-control study enrolled 100 patients with acne and 100 apparently healthy subjects. The clinical grade of acne was assessed using the Global Acne Grading System. We used PCR to identify the presence of the Pro12Ala polymorphism in exon 2 of PPARγ. RESULTS Our results revealed a statistically significant difference (P = 0.001) in the genotype distribution between patients and controls, with higher incidence of the Pro/Ala genotype in controls (51%) than in patients (28%). A statistically significant association (P < 0.001) between disease severity and genotype distribution was found, indicating that the Pro/Ala genotype is less prevalent in patients with severe acne. CONCLUSIONS Our results suggest that that the Ala allele might be a protective factor against acne development or may attenuate acne severity.
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Affiliation(s)
- K Amr
- Molecular Genetics, National Research Centre, Cairo, Egypt
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18
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Sayed K, Taha TT, Saad M, Mohsen LA, Ibrahiem MA, Fadeel NA, Sotouhy A. Is Mini-Mental Score Examination Scoring a New Predictor of Uncontrolled Hypertension? J Clin Hypertens (Greenwich) 2014; 16:348-53. [DOI: 10.1111/jch.12319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/08/2014] [Accepted: 02/11/2014] [Indexed: 11/25/2022]
Affiliation(s)
- Khaled Sayed
- Cardiology Department; Al-Minya University Hospital; Al-Minya Egypt
| | - Tamer T.I. Taha
- Cardiology Department; Al-Minya University Hospital; Al-Minya Egypt
| | - Mohamad Saad
- Cardiology Department; Al-Minya University Hospital; Al-Minya Egypt
| | - Laila A. Mohsen
- Radiology Department; Al-Minya University Hospital; Al-Minya Egypt
| | | | | | - Amr Sotouhy
- Cardiology Department; Al-Minya University Hospital; Al-Minya Egypt
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19
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Sayed K, Ismail TT, Saad M, Mohsen LA, Ibraheim MA, Fadeel NA, Sotouhy A. Is mini-mental score examination (MMSE scoring) a new predictor of uncontrolled hypertension? Egypt Heart J 2014. [DOI: 10.1016/j.ehj.2013.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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20
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Opdal M, Arnesen M, Sayed K, Sagedal S, Gjesdal K, Müller L, Kringen M, Brørs O, Krajci P. PP204—Methadone Kinetics and Corrected QT Time During Haemodialysis in Four Methadone Maintenance Treatment Patients with End-Stage Renal Failure. Clin Ther 2013. [DOI: 10.1016/j.clinthera.2013.07.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Fitzpatrick BT, O'Grady JF, Sayed K, Bouchier-Hayes D. Acute tracheoesophageal communication: a diagnostic sign for an unusual injury. Ir Med J 1983; 76:421-2. [PMID: 6642967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Chowdhary UM, Sayed K. Comparative clinical trial of epsilon amino-caproic acid and tranexamic acid in the prevention of early recurrence of subarachnoid haemorrhage. J Neurol Neurosurg Psychiatry 1981; 44:810-3. [PMID: 7031186 PMCID: PMC491141 DOI: 10.1136/jnnp.44.9.810] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A comparative controlled clinical trial of epsilon aminocaproic acid (EACA), 36 g/day and tranexamic acid (TEA), 6 g/day, was undertaken to assess their effectiveness in reducing early recurrence of subarachnoid haemorrhage (SAH). Of 90 patients treated with EACA recurrent haemorrhage was seen in 8% of these patients and 7% of the patients developed delayed ischaemic deficit. The total pre-operative mortality in EACA-group was 11%. Of 61 patients treated with TEA, 10% had recurrent haemorrhage and delayed ischaemic deficit occurred in 5% of the patients. The total pre-operative mortality in TEA-group was 11%. No difference was found between the effectiveness and side-effects of these drugs.
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23
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Sukhova GS, Andreeva NV, Chudakov LI, Sayed K. [Bioelectrical activity and automatic properties of different parts of a two-chambered heart]. Fiziol Zh SSSR Im I M Sechenova 1977; 63:86-93. [PMID: 832754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two pacemakers localized in sinoatrial and atrioventricular valves were revealed in the tench heart. In their absence, the ventricular and sometimes the atrial myocardium are capable of initiating the automaticity. Pacemaker's cells of the sinoatrial valve are surrounded by specific area similar to sinoauricular ring in amphibia or sino-caval region in mammals. Characteristics of the action potential in different parts of the tench heart are presented.
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