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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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Zeng W, Thatayatikom A, Winn N, Lovelace TC, Bhattacharyya I, Schrepfer T, Shah A, Gonik R, Benos PV, Cha S. The Florida Scoring System for stratifying children with suspected Sjögren's disease: a cross-sectional machine learning study. Lancet Rheumatol 2024; 6:e279-e290. [PMID: 38658114 DOI: 10.1016/s2665-9913(24)00059-6] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Childhood Sjögren's disease is a rare, underdiagnosed, and poorly-understood condition. By integrating machine learning models on a paediatric cohort in the USA, we aimed to develop a novel system (the Florida Scoring System) for stratifying symptomatic paediatric patients with suspected Sjögren's disease. METHODS This cross-sectional study was done in symptomatic patients who visited the Department of Pediatric Rheumatology at the University of Florida, FL, USA. Eligible patients were younger than 18 years or had symptom onset before 18 years of age. Patients with confirmed diagnosis of another autoimmune condition or infection with a clear aetiological microorganism were excluded. Eligible patients underwent comprehensive examinations to rule out or diagnose childhood Sjögren's disease. We used latent class analysis with clinical and laboratory variables to detect heterogeneous patient classes. Machine learning models, including random forest, gradient-boosted decision tree, partial least square discriminatory analysis, least absolute shrinkage and selection operator-penalised ordinal regression, artificial neural network, and super learner were used to predict patient classes and rank the importance of variables. Causal graph learning selected key features to build the final Florida Scoring System. The predictors for all models were the clinical and laboratory variables and the outcome was the definition of patient classes. FINDINGS Between Jan 16, 2018, and April 28, 2022, we screened 448 patients for inclusion. After excluding 205 patients due to symptom onset later than 18 years of age, we recruited 243 patients into our cohort. 26 patients were excluded because of confirmed diagnosis of a disorder other than Sjögren's disease, and 217 patients were included in the final analysis. Median age at diagnosis was 15 years (IQR 11-17). 155 (72%) of 216 patients were female and 61 (28%) were male, 167 (79%) of 212 were White, and 20 (9%) of 213 were Hispanic, Latino, or Spanish. The latent class analysis identified three distinct patient classes: class I (dryness dominant with positive tests, n=27), class II (high symptoms with negative tests, n=98), and class III (low symptoms with negative tests, n=92). Machine learning models accurately predicted patient class and ranked variable importance consistently. The causal graphical model discovered key features for constructing the Florida Scoring System. INTERPRETATION The Florida Scoring System is a paediatrician-friendly tool that can be used to assist classification and long-term monitoring of suspected childhood Sjögren's disease. The resulting stratification has important implications for clinical management, trial design, and pathobiological research. We found a highly symptomatic patient group with negative serology and diagnostic profiles, which warrants clinical attention. We further revealed that salivary gland ultrasonography can be a non-invasive alternative to minor salivary gland biopsy in children. The Florida Scoring System requires validation in larger prospective paediatric cohorts. FUNDING National Institute of Dental and Craniofacial Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Heart, Lung, and Blood Institute, and Sjögren's Foundation.
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Affiliation(s)
- Wenjie Zeng
- Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, FL, USA
| | - Akaluck Thatayatikom
- Pediatric Rheumatology, AdventHealth for Children, AdventHealth Medical Group, Orlando, FL, USA
| | - Nicole Winn
- Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, FL, USA; Oral Medicine, Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Tyler C Lovelace
- Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Indraneel Bhattacharyya
- Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, FL, USA; Oral Pathology, Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Thomas Schrepfer
- Pediatric Otolaryngology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ankit Shah
- Ophthalmology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Renato Gonik
- Pediatric Neurology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Panayiotis V Benos
- Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, FL, USA
| | - Seunghee Cha
- Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, FL, USA; Oral Medicine, Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL, USA.
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Walton NA, Nagarajan R, Wang C, Sincan M, Freimuth RR, Everman DB, Walton DC, McGrath SP, Lemas DJ, Benos PV, Alekseyenko AV, Song Q, Gamsiz Uzun E, Taylor CO, Uzun A, Person TN, Rappoport N, Zhao Z, Williams MS. Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J Am Med Inform Assoc 2024; 31:536-541. [PMID: 38037121 PMCID: PMC10797281 DOI: 10.1093/jamia/ocad211] [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: 02/11/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
OBJECTIVE Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space. PROCESS A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members. CONCLUSIONS Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.
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Affiliation(s)
- Nephi A Walton
- Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 ,United States
| | - Radha Nagarajan
- Enterprise Information Services, Cedars-Sinai Medical Center, Los Angeles, CA 90025, United States
- Information Services Department, Children’s Hospital of Orange County, Orange, CA 92868, United States
| | - Chen Wang
- Division of Computational Biology, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Murat Sincan
- Flatiron Health, New York, NY 10013, United States
- Department of Internal Medicine, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57107, United States
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - David B Everman
- EverMed Genetics and Genomics Consulting LLC, Greenville, SC 29607, United States
| | | | - Scott P McGrath
- CITRIS Health, CITRIS and Banatao Institute, University of California Berkeley, Berkeley, CA 94720, United States
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32610, United States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, United States
| | - Alexander V Alekseyenko
- Department of Public Health Sciences, Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC 29403, United States
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32610, United States
| | - Ece Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Providence, RI 02915, United States
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02915, United States
| | - Casey Overby Taylor
- Departments of Medicine and Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Alper Uzun
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02915, United States
- Legorreta Cancer Center, Brown University, Providence, RI 02915, United States
| | - Thomas Nate Person
- Department of Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Penn State University, Bloomsburg, PA 16802, United States
| | - Nadav Rappoport
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, United States
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Gregg RW, Benos PV. CellularPotts.jl: simulating multiscale cellular models in Julia. Bioinformatics 2024; 40:btad773. [PMID: 38134421 PMCID: PMC10781660 DOI: 10.1093/bioinformatics/btad773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023] Open
Abstract
SUMMARY CellularPotts.jl is a software package written in Julia to simulate biological cellular processes such as division, adhesion, and signaling. Accurately modeling and predicting these simple processes is crucial because they facilitate more complex biological phenomena related to important disease states like tumor growth, wound healing, and infection. Here we take advantage of Cellular Potts Modeling to simulate cellular interactions and combine them with differential equations to model dynamic cell signaling patterns. These models are advantageous over other approaches because they retain spatial information about each cell while remaining computationally efficient at larger scales. Users of this package define three key inputs to create valid model definitions: a 2- or 3-dimensional space, a table describing the cells to be positioned in that space, and a list of model penalties that dictate cell behaviors. Models can then be evolved over time to collect statistics, simulated repeatedly to investigate how changing a specific property impacts cellular behavior, and visualized using any of the available plotting libraries in Julia. AVAILABILITY AND IMPLEMENTATION The CellularPotts.jl package is released under the MIT license and is available at https://github.com/RobertGregg/CellularPotts.jl. An archived version of the code (v0.3.2) at time of submission can also be found at https://doi.org/10.5281/zenodo.10407783.
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Affiliation(s)
- Robert W Gregg
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
- Department of Epidemiology, University of Florida, Gainesville, FL 32603, United States
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
- Department of Epidemiology, University of Florida, Gainesville, FL 32603, United States
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Regan EA, Lowe ME, Make BJ, Curtis JL, Chen Q(G, Crooks JL, Wilson C, Oates GR, Gregg RW, Baldomero AK, Bhatt SP, Diaz AA, Benos PV, O’Brien JK, Young KA, Kinney GL, Conrad DJ, Lowe KE, DeMeo DL, Non A, Cho MH, Kallet J, Foreman MG, Westney GE, Hoth K, MacIntyre NR, Hanania NA, Wolfe A, Amaza H, Han M, Beaty TH, Hansel NN, McCormack MC, Balasubramanian A, Crapo JD, Silverman EK, Casaburi R, Wise RA. Early Evidence of Chronic Obstructive Pulmonary Disease Obscured by Race-Specific Prediction Equations. Am J Respir Crit Care Med 2024; 209:59-69. [PMID: 37611073 PMCID: PMC10870894 DOI: 10.1164/rccm.202303-0444oc] [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: 03/13/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023] Open
Abstract
Rationale: The identification of early chronic obstructive pulmonary disease (COPD) is essential to appropriately counsel patients regarding smoking cessation, provide symptomatic treatment, and eventually develop disease-modifying treatments. Disease severity in COPD is defined using race-specific spirometry equations. These may disadvantage non-White individuals in diagnosis and care. Objectives: Determine the impact of race-specific equations on African American (AA) versus non-Hispanic White individuals. Methods: Cross-sectional analyses of the COPDGene (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease) cohort were conducted, comparing non-Hispanic White (n = 6,766) and AA (n = 3,366) participants for COPD manifestations. Measurements and Main Results: Spirometric classifications using race-specific, multiethnic, and "race-reversed" prediction equations (NHANES [National Health and Nutrition Examination Survey] and Global Lung Function Initiative "Other" and "Global") were compared, as were respiratory symptoms, 6-minute-walk distance, computed tomography imaging, respiratory exacerbations, and St. George's Respiratory Questionnaire. Application of different prediction equations to the cohort resulted in different classifications by stage, with NHANES and Global Lung Function Initiative race-specific equations being minimally different, but race-reversed equations moving AA participants to more severe stages and especially between the Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 0 and preserved ratio impaired spirometry groups. Classification using the established NHANES race-specific equations demonstrated that for each of GOLD stages 1-4, AA participants were younger, had fewer pack-years and more current smoking, but had more exacerbations, shorter 6-minute-walk distance, greater dyspnea, and worse BODE (body mass index, airway obstruction, dyspnea, and exercise capacity) scores and St. George's Respiratory Questionnaire scores. Differences were greatest in GOLD stages 1 and 2. Race-reversed equations reclassified 774 AA participants (43%) from GOLD stage 0 to preserved ratio impaired spirometry. Conclusions: Race-specific equations underestimated disease severity among AA participants. These effects were particularly evident in early disease and may result in late detection of COPD.
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Affiliation(s)
| | - Melissa E. Lowe
- Biostatistics, Duke Cancer Center, Duke University Medical Center, Durham, North Carolina
| | - Barry J. Make
- Division of Pulmonary, Critical Care and Sleep Medicine
| | - Jeffrey L. Curtis
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Medical Service, Veterans Affairs Medical Center, Ann Arbor, Michigan
| | | | - James L. Crooks
- Division of Biostatistics and Bioinformatics
- Department of Immunology and Genomic Medicine, and
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
| | - Carla Wilson
- Research Informatics Services, National Jewish Health, Denver, Colorado
| | | | - Robert W. Gregg
- Department of Epidemiology, University of Florida, Gainesville, Florida
| | - Arianne K. Baldomero
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Surya P. Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | | | - Kendra A. Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
| | - Gregory L. Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
| | | | - Katherine E. Lowe
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve School of Medicine, Cleveland, Ohio
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amy Non
- Department of Anthropology, University of California, San Diego, La Jolla, California
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Marilyn G. Foreman
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Morehouse College, Atlanta, Georgia
| | - Gloria E. Westney
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Morehouse College, Atlanta, Georgia
| | - Karin Hoth
- Department of Psychiatry and
- Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa
| | - Neil R. MacIntyre
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University, Durham, North Carolina
| | - Nicola A. Hanania
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, Baylor University, Houston, Texas
| | - Amy Wolfe
- Section of Pulmonology and Critical Care, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | | | - MeiLan Han
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, and
| | - Nadia N. Hansel
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | - Meredith C. McCormack
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | - Aparna Balasubramanian
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Richard Casaburi
- Rehabilitation Clinical Trials Center, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Robert A. Wise
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland; and
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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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Barak O, Lovelace T, Chu T, Cao Z, Sadovsky E, Mouillet JF, Ouyang Y, Benos PV, Sadovsky Y. Defining trophoblast injury patterns in the transcriptomes of dysfunctional placentas. Placenta 2023; 143:87-90. [PMID: 37866321 PMCID: PMC10842313 DOI: 10.1016/j.placenta.2023.10.010] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Trophoblast injury is central to clinically relevant placenta dysfunction. We hypothesized that the mRNA of primary human trophoblasts, exposed to distinct injuries in vitro, capture transcriptome patterns of placental biopsies obtained from common obstetrical syndromes. We deployed a CIBERSORTx deconvolution method to correlate trophoblastic RNAseq-based expression matrices with the transcriptome of omics-defined placental dysfunction patterns in vivo. We found distinct trophoblast injury patterns in placental biopsies from women with fetal growth restriction and a hypertensive disorder, or in biopsies clustered by their omics analysis. Our RNAseq data are useful for defining the contribution of trophoblast injuries to placental dysfunction syndromes.
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Affiliation(s)
- Oren Barak
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tyler Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhishen Cao
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | | | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA; Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Jia M, Agudelo Garcia PA, Ovando‐Ricardez JA, Tabib T, Bittar HT, Lafyatis RA, Mora AL, Benos PV, Rojas M. Transcriptional changes of the aging lung. Aging Cell 2023; 22:e13969. [PMID: 37706427 PMCID: PMC10577555 DOI: 10.1111/acel.13969] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/09/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023] Open
Abstract
Aging is a natural process associated with declined organ function and higher susceptibility to developing chronic diseases. A systemic single-cell type-based study provides a unique opportunity to understand the mechanisms behind age-related pathologies. Here, we use single-cell gene expression analysis comparing healthy young and aged human lungs from nonsmoker donors to investigate age-related transcriptional changes. Our data suggest that aging has a heterogenous effect on lung cells, as some populations are more transcriptionally dynamic while others remain stable in aged individuals. We found that monocytes and alveolar macrophages were the most transcriptionally affected populations. These changes were related to inflammation and regulation of the immune response. Additionally, we calculated the LungAge score, which reveals the diversity of lung cell types during aging. Changes in DNA damage repair, fatty acid metabolism, and inflammation are essential for age prediction. Finally, we quantified the senescence score in aged lungs and found that the more biased cells toward senescence are immune and progenitor cells. Our study provides a comprehensive and systemic analysis of the molecular signatures of lung aging. Our LungAge signature can be used to predict molecular signatures of physiological aging and to detect common signatures of age-related lung diseases.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Joint Carnegie Mellon ‐ University of Pittsburgh Computational Biology Ph.D. ProgramPittsburghPennsylvaniaUSA
| | | | | | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Humberto T. Bittar
- Division of Rheumatology and Clinical Immunology, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Robert A. Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Ana L. Mora
- Department of Internal MedicineOhio State UniversityColumbusOhioUSA
| | - Panayiotis V. Benos
- Department of Computational and Systems BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Joint Carnegie Mellon ‐ University of Pittsburgh Computational Biology Ph.D. ProgramPittsburghPennsylvaniaUSA
- Department of EpidemiologyUniversity of FloridaGainesvilleFloridaUSA
| | - Mauricio Rojas
- Department of Internal MedicineOhio State UniversityColumbusOhioUSA
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10
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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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11
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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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12
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Shan F, Cillo AR, Cardello C, Yuan DY, Kunning SR, Cui J, Lampenfeld C, Williams AM, McDonough AP, Pennathur A, Luketich JD, Kirkwood JM, Ferris RL, Bruno TC, Workman CJ, Benos PV, Vignali DAA. Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells. Sci Immunol 2023; 8:eadf6717. [PMID: 37713508 PMCID: PMC11045170 DOI: 10.1126/sciimmunol.adf6717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Human regulatory T cells (Tregs) are crucial regulators of tissue repair, autoimmune diseases, and cancer. However, it is challenging to inhibit the suppressive function of Tregs for cancer therapy without affecting immune homeostasis. Identifying pathways that may distinguish tumor-restricted Tregs is important, yet the transcriptional programs that control intratumoral Treg gene expression, and that are distinct from Tregs in healthy tissues, remain largely unknown. We profiled single-cell transcriptomes of CD4+ T cells in tumors and peripheral blood from patients with head and neck squamous cell carcinomas (HNSCC) and those in nontumor tonsil tissues and peripheral blood from healthy donors. We identified a subpopulation of activated Tregs expressing multiple tumor necrosis factor receptor (TNFR) genes (TNFR+ Tregs) that is highly enriched in the tumor microenvironment (TME) compared with nontumor tissue and the periphery. TNFR+ Tregs are associated with worse prognosis in HNSCC and across multiple solid tumor types. Mechanistically, the transcription factor BATF is a central component of a gene regulatory network that governs key aspects of TNFR+ Tregs. CRISPR-Cas9-mediated BATF knockout in human activated Tregs in conjunction with bulk RNA sequencing, immunophenotyping, and in vitro functional assays corroborated the central role of BATF in limiting excessive activation and promoting the survival of human activated Tregs. Last, we identified a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral Tregs in patients with HNSCC. These findings uncover a primary transcriptional regulator of highly suppressive intratumoral Tregs, highlighting potential opportunities for therapeutic intervention in cancer without affecting immune homeostasis.
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Affiliation(s)
- Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R. Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Daniel Y. Yuan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sheryl R. Kunning
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Caleb Lampenfeld
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Asia M. Williams
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Alexandra P. McDonough
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Arjun Pennathur
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John M. Kirkwood
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert L. Ferris
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tullia C. Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Creg J. Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Dario A. A. Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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13
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Barak O, Lovelace T, Piekos S, Chu T, Cao Z, Sadovsky E, Mouillet JF, Ouyang Y, Parks WT, Hood L, Price ND, Benos PV, Sadovsky Y. Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes. BMC Med 2023; 21:349. [PMID: 37679695 PMCID: PMC10485945 DOI: 10.1186/s12916-023-03054-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Placental dysfunction, a root cause of common syndromes affecting human pregnancy, such as preeclampsia (PE), fetal growth restriction (FGR), and spontaneous preterm delivery (sPTD), remains poorly defined. These common, yet clinically disparate obstetrical syndromes share similar placental histopathologic patterns, while individuals within each syndrome present distinct molecular changes, challenging our understanding and hindering our ability to prevent and treat these syndromes. METHODS Using our extensive biobank, we identified women with severe PE (n = 75), FGR (n = 40), FGR with a hypertensive disorder (FGR + HDP; n = 33), sPTD (n = 72), and two uncomplicated control groups, term (n = 113), and preterm without PE, FGR, or sPTD (n = 16). We used placental biopsies for transcriptomics, proteomics, metabolomics data, and histological evaluation. After conventional pairwise comparison, we deployed an unbiased, AI-based similarity network fusion (SNF) to integrate the datatypes and identify omics-defined placental clusters. We used Bayesian model selection to compare the association between the histopathological features and disease conditions vs SNF clusters. RESULTS Pairwise, disease-based comparisons exhibited relatively few differences, likely reflecting the heterogeneity of the clinical syndromes. Therefore, we deployed the unbiased, omics-based SNF method. Our analysis resulted in four distinct clusters, which were mostly dominated by a specific syndrome. Notably, the cluster dominated by early-onset PE exhibited strong placental dysfunction patterns, with weaker injury patterns in the cluster dominated by sPTD. The SNF-defined clusters exhibited better correlation with the histopathology than the predefined disease groups. CONCLUSIONS Our results demonstrate that integrated omics-based SNF distinctively reclassifies placental dysfunction patterns underlying the common obstetrical syndromes, improves our understanding of the pathological processes, and could promote a search for more personalized interventions.
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Affiliation(s)
- Oren Barak
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Tyler Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Joint CMU-Pitt PhD Program in Computational Biology, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
| | - Samantha Piekos
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Zhishen Cao
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Elena Sadovsky
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - W Tony Parks
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Simcoe Hall, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Leroy Hood
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
| | - Nathan D Price
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
- Thorne HealthTech, 152 West 57th Street, New York, NY, 10019, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Joint CMU-Pitt PhD Program in Computational Biology, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
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14
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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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15
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Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M. An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinformatics 2023; 39:i413-i422. [PMID: 37387140 PMCID: PMC10311317 DOI: 10.1093/bioinformatics/btad271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post hoc analyses, and even then, one can often not explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called totally interpretable sequence-to-function model (tiSFM). tiSFM improves upon the performance of standard multilayer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multilayer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. RESULTS We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state-of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context-specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM's model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. AVAILABILITY AND IMPLEMENTATION The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv, implemented in Python.
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Affiliation(s)
- Ali Tuğrul Balcı
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Mark Maher Ebeid
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, United States
| | - Dennis Kostka
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Maria Chikina
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
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16
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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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17
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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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18
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Britton N, Yang H, Fitch A, Li K, Seyed K, Guo R, Qin S, Zhang Y, Bain W, Shah F, Biswas P, Choi W, Finkelman M, Zhang Y, Haggerty CL, Benos PV, Brooks MM, McVerry BJ, Methe B, Kitsios GD, Morris A. Respiratory Fungal Communities are Associated with Systemic Inflammation and Predict Survival in Patients with Acute Respiratory Failure. medRxiv 2023:2023.05.11.23289861. [PMID: 37292915 PMCID: PMC10246035 DOI: 10.1101/2023.05.11.23289861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rationale Disruption of respiratory bacterial communities predicts poor clinical outcomes in critical illness; however, the role of respiratory fungal communities (mycobiome) is poorly understood. Objectives We investigated whether mycobiota variation in the respiratory tract is associated with host-response and clinical outcomes in critically ill patients. Methods To characterize the upper and lower respiratory tract mycobiota, we performed rRNA gene sequencing (internal transcribed spacer) of oral swabs and endotracheal aspirates (ETA) from 316 mechanically-ventilated patients. We examined associations of mycobiome profiles (diversity and composition) with clinical variables, host-response biomarkers, and outcomes. Measurements and Main Results ETA samples with >50% relative abundance for C. albicans (51%) were associated with elevated plasma IL-8 and pentraxin-3 (p=0.05), longer time-to-liberation from mechanical ventilation (p=0.04) and worse 30-day survival (adjusted hazards ratio (adjHR): 1.96 [1.04-3.81], p=0.05). Using unsupervised clustering, we derived two clusters in ETA samples, with Cluster 2 (39%) showing lower alpha diversity (p<0.001) and higher abundance of C. albicans (p<0.001). Cluster 2 was significantly associated with the prognostically adverse hyperinflammatory subphenotype (odds ratio 2.07 [1.03-4.18], p=0.04) and predicted worse survival (adjHR: 1.81 [1.03-3.19], p=0.03). C. albicans abundance in oral swabs was also associated with the hyperinflammatory subphenotype and mortality. Conclusions Variation in respiratory mycobiota was significantly associated with systemic inflammation and clinical outcomes. C. albicans abundance emerged as a negative predictor in both the upper and lower respiratory tract. The lung mycobiome may play an important role in the biological and clinical heterogeneity among critically ill patients and represent a potential therapeutic target for lung injury in critical illness.
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Affiliation(s)
- Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Adam Fitch
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Khaled Seyed
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Rui Guo
- Department of Critical Care Medicine, First Affiliated Hospital of Chongqing Medical University, China
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Partha Biswas
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Wonseok Choi
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Yonglong Zhang
- Associates of Cape Cod Inc., East Falmouth, Massachusetts, USA
| | - Catherine L. Haggerty
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Maria M. Brooks
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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19
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Jia M, Rosas L, Kapetanaki MG, Tabib T, Sebrat J, Cruz T, Bondonese A, Mora AL, Lafyatis R, Rojas M, Benos PV. Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis. Respir Res 2023; 24:116. [PMID: 37085855 PMCID: PMC10122312 DOI: 10.1186/s12931-023-02419-0] [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: 09/24/2022] [Accepted: 04/12/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is an age-associated progressive lung disease with accumulation of scar tissue impairing gas exchange. Previous high-throughput studies elucidated the role of cellular heterogeneity and molecular pathways in advanced disease. However, critical pathogenic pathways occurring in the transition of fibroblasts from normal to profibrotic have been largely overlooked. METHODS We used single cell transcriptomics (scRNA-seq) from lungs of healthy controls and IPF patients (lower and upper lobes). We identified fibroblast subclusters, genes and pathways associated with early disease. Immunofluorescence assays validated the role of MOXD1 early in fibrosis. RESULTS We identified four distinct fibroblast subgroups, including one marking the normal-to-profibrotic state transition. Our results show for the first time that global downregulation of ribosomal proteins and significant upregulation of the majority of copper-binding proteins, including MOXD1, mark the IPF transition. We find no significant differences in gene expression in IPF upper and lower lobe samples, which were selected to have low and high degree of fibrosis, respectively. CONCLUSIONS Early events during IPF onset in fibroblasts include dysregulation of ribosomal and copper-binding proteins. Fibroblasts in early stage IPF may have already acquired a profibrotic phenotype while hallmarks of advanced disease, including fibroblast foci and honeycomb formation, are still not evident. The new transitional fibroblasts we discover could prove very important for studying the role of fibroblast plasticity in disease progression and help develop early diagnosis tools and therapeutic interventions targeting earlier disease states.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
| | - Lorena Rosas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Maria G. Kapetanaki
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - John Sebrat
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Tamara Cruz
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Anna Bondonese
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Ana L. Mora
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
- Department of Epidemiology, University of Florida, 2004 Mowry Rd, Gainesville, FL 32610 USA
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20
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Yuan DY, McKeague ML, Dracz MT, Finn OJ, Benos PV. Abstract 6537: Single cell transcriptomics uncovers cellular and molecular differences in PBMCs of responders and non-responders to the MUC1 cancer vaccine given in the preventative setting. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial (NCT02134925) were conducted in patients with newly diagnosed advanced colonic adenomas to test the safety and immunogenicity of the MUC1 antigen vaccine and its potential to prevent new adenoma formation. These are the first trials of a non-viral cancer vaccine administered in the absence of cancer. In both trials, the vaccine was safe and strongly immunogenic in 43% and 25% of participants (Responders), respectively. The lack of robust response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to regulatory influences that, in the case of the vaccine, determine who does and who does not respond. We hypothesized that there could be molecular and cellular differences in the immune competence between vaccine responders and non-responders, and that they could be identified by studying their pre-vaccination peripheral blood mononuclear cells (PBMCs).
Methods: The two MUC1 vaccine trials are described in https://doi.org/10.1101/2022.10.05.22280474 and https://doi.org/10.1158%2F1940-6207.CAPR-12-0275. We performed single cell RNA-sequencing (scRNAseq) on banked pre-vaccination PBMCs from 16 Responders and 16 Non-Responders, determined by anti-MUC1 IgG response. Using differential gene expression (DGE), pathway enrichment, and network estimation analyses, we identified specific cell types, genes, and pathways that differ between responders and non-responders.
Results: Pre-vaccination PBMCs from Responders contained a significantly higher percentage of CD4+ naive T cells, while Non-Responders showed significantly higher percentage of CD8+ T effector memory (TEM) cells and a higher percentage of CD16+ monocytes. DGE and gene interaction network analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in the CD4+ naive T cells in Responders. Further network analysis showed that these genes were directly connected to response. We also found pre-vaccination specific gene ontology (GO) pathways for translational and transcriptional activity enriched in all cell types in Responders compared to Non-Responders.
Conclusion: Our analyses identified candidate biomarkers that are predictive of a preventative cancer vaccine response. Thus, our results can be used for patient selection for vaccine administration. Furthermore, we identified cell type differences and transcriptional pathways that provide information of possible mechanisms of vaccine response.
Citation Format: Daniel Y. Yuan, Michelle L. McKeague, Matthew T. Dracz, Olivera J. Finn, Panayiotis V. Benos. Single cell transcriptomics uncovers cellular and molecular differences in PBMCs of responders and non-responders to the MUC1 cancer vaccine given in the preventative setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6537.
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21
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Zuppo DA, Missinato MA, Santana-Santos L, Li G, Benos PV, Tsang M. Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury. Development 2023; 150:dev201163. [PMID: 36846912 PMCID: PMC10108034 DOI: 10.1242/dev.201163] [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: 07/26/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
The regenerative capacity of the mammalian heart is poor, with one potential reason being that adult cardiomyocytes cannot proliferate at sufficient levels to replace lost tissue. During development and neonatal stages, cardiomyocytes can successfully divide under injury conditions; however, as these cells mature their ability to proliferate is lost. Therefore, understanding the regulatory programs that can induce post-mitotic cardiomyocytes into a proliferative state is essential to enhance cardiac regeneration. Here, we report that the forkhead transcription factor Foxm1 is required for cardiomyocyte proliferation after injury through transcriptional regulation of cell cycle genes. Transcriptomic analysis of injured zebrafish hearts revealed that foxm1 expression is increased in border zone cardiomyocytes. Decreased cardiomyocyte proliferation and expression of cell cycle genes in foxm1 mutant hearts was observed, suggesting it is required for cell cycle checkpoints. Subsequent analysis of a candidate Foxm1 target gene, cenpf, revealed that this microtubule and kinetochore binding protein is also required for cardiac regeneration. Moreover, cenpf mutants show increased cardiomyocyte binucleation. Thus, foxm1 and cenpf are required for cardiomyocytes to complete mitosis during zebrafish cardiac regeneration.
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Affiliation(s)
- Daniel A. Zuppo
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Maria A. Missinato
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
- Avidity Biosciences, 10578 Science Center Dr. Suite 125, San Diego, CA 92121, USA
| | - Lucas Santana-Santos
- Department of Computational and Systems Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Guang Li
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
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22
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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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23
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Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M. An intrinsically interpretable neural network architecture for sequence to function learning. bioRxiv 2023:2023.01.25.525572. [PMID: 36747873 PMCID: PMC9900791 DOI: 10.1101/2023.01.25.525572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Motivation Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post-hoc analyses, and even then, we often cannot explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called tiSFM (totally interpretable sequence to function model). tiSFM improves upon the performance of standard multi-layer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multi-layer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. Results tiSFM's model architecture makes use of convolutions with a fixed set of kernel weights representing known transcription factor (TF) binding site motifs. We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state- of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM's model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. Availability and implementation The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv , implemented in Python. Contact atb44@pitt.edu.
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Affiliation(s)
- Ali Tuğrul Balcı
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States
| | - Mark Maher Ebeid
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, 32610, Unites States
| | - Dennis Kostka
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States, (D.K.) and (M.C.)
| | - Maria Chikina
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States, (D.K.) and (M.C.)
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24
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Buschur KL, Riley C, Saferali A, Castaldi P, Zhang G, Aguet F, Ardlie KG, Durda P, Craig Johnson W, Kasela S, Liu Y, Manichaikul A, Rich SS, Rotter JI, Smith J, Taylor KD, Tracy RP, Lappalainen T, Graham Barr R, Sciurba F, Hersh CP, Benos PV. Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis. Respir Res 2023; 24:30. [PMID: 36698131 PMCID: PMC9875487 DOI: 10.1186/s12931-023-02316-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) varies significantly in symptomatic and physiologic presentation. Identifying disease subtypes from molecular data, collected from easily accessible blood samples, can help stratify patients and guide disease management and treatment. METHODS Blood gene expression measured by RNA-sequencing in the COPDGene Study was analyzed using a network perturbation analysis method. Each COPD sample was compared against a learned reference gene network to determine the part that is deregulated. Gene deregulation values were used to cluster the disease samples. RESULTS The discovery set included 617 former smokers from COPDGene. Four distinct gene network subtypes are identified with significant differences in symptoms, exercise capacity and mortality. These clusters do not necessarily correspond with the levels of lung function impairment and are independently validated in two external cohorts: 769 former smokers from COPDGene and 431 former smokers in the Multi-Ethnic Study of Atherosclerosis (MESA). Additionally, we identify several genes that are significantly deregulated across these subtypes, including DSP and GSTM1, which have been previously associated with COPD through genome-wide association study (GWAS). CONCLUSIONS The identified subtypes differ in mortality and in their clinical and functional characteristics, underlining the need for multi-dimensional assessment potentially supplemented by selected markers of gene expression. The subtypes were consistent across cohorts and could be used for new patient stratification and disease prognosis.
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Affiliation(s)
- Kristina L Buschur
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
- Division of General Medicine, Columbia University Medical Center, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Craig Riley
- Division of Pulmonary Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Grace Zhang
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Josh Smith
- Northwest Genome Center, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - R Graham Barr
- Division of General Medicine, Columbia University Medical Center, New York, NY, USA
| | - Frank Sciurba
- Division of Pulmonary Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA.
- Department of Epidemiology, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32603, USA.
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25
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Fan Z, Kernan KF, Sriram A, Benos PV, Canna SW, Carcillo JA, Kim S, Park HJ. Deep neural networks with knockoff features identify nonlinear causal relations and estimate effect sizes in complex biological systems. Gigascience 2022; 12:giad044. [PMID: 37395630 PMCID: PMC10316696 DOI: 10.1093/gigascience/giad044] [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: 09/15/2022] [Revised: 01/31/2023] [Accepted: 05/29/2023] [Indexed: 07/04/2023] Open
Abstract
BACKGROUND Learning the causal structure helps identify risk factors, disease mechanisms, and candidate therapeutics for complex diseases. However, although complex biological systems are characterized by nonlinear associations, existing bioinformatic methods of causal inference cannot identify the nonlinear relationships and estimate their effect size. RESULTS To overcome these limitations, we developed the first computational method that explicitly learns nonlinear causal relations and estimates the effect size using a deep neural network approach coupled with the knockoff framework, named causal directed acyclic graphs using deep learning variable selection (DAG-deepVASE). Using simulation data of diverse scenarios and identifying known and novel causal relations in molecular and clinical data of various diseases, we demonstrated that DAG-deepVASE consistently outperforms existing methods in identifying true and known causal relations. In the analyses, we also illustrate how identifying nonlinear causal relations and estimating their effect size help understand the complex disease pathobiology, which is not possible using other methods. CONCLUSIONS With these advantages, the application of DAG-deepVASE can help identify driver genes and therapeutic agents in biomedical studies and clinical trials.
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Affiliation(s)
- Zhenjiang Fan
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kate F Kernan
- Division of Pediatric Critical Care Medicine, Department of Critical Care Medicine, Children's Hospital of Pittsburgh, Center for Critical Care Nephrology and Clinical Research Investigation and Systems Modeling of Acute Illness Center, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - Aditya Sriram
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, USA
| | - Scott W Canna
- Pediatric Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Joseph A Carcillo
- Division of Pediatric Critical Care Medicine, Department of Critical Care Medicine, Children's Hospital of Pittsburgh, Center for Critical Care Nephrology and Clinical Research Investigation and Systems Modeling of Acute Illness Center, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - Soyeon Kim
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
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26
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Wu J, Cyr A, Gruen DS, Lovelace TC, Benos PV, Das J, Kar UK, Chen T, Guyette FX, Yazer MH, Daley BJ, Miller RS, Harbrecht BG, Claridge JA, Phelan HA, Zuckerbraun BS, Neal MD, Johansson PI, Stensballe J, Namas RA, Vodovotz Y, Sperry JL, Billiar TR. Lipidomic signatures align with inflammatory patterns and outcomes in critical illness. Nat Commun 2022; 13:6789. [PMID: 36357394 PMCID: PMC9647252 DOI: 10.1038/s41467-022-34420-4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Alterations in lipid metabolism have the potential to be markers as well as drivers of pathobiology of acute critical illness. Here, we took advantage of the temporal precision offered by trauma as a common cause of critical illness to identify the dynamic patterns in the circulating lipidome in critically ill humans. The major findings include an early loss of all classes of circulating lipids followed by a delayed and selective lipogenesis in patients destined to remain critically ill. The previously reported survival benefit of early thawed plasma administration was associated with preserved lipid levels that related to favorable changes in coagulation and inflammation biomarkers in causal modelling. Phosphatidylethanolamines (PE) were elevated in patients with persistent critical illness and PE levels were prognostic for worse outcomes not only in trauma but also severe COVID-19 patients. Here we show selective rise in systemic PE as a common prognostic feature of critical illness.
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Affiliation(s)
- Junru Wu
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
- Department of Cardiology, The 3rd Xiangya Hospital, Central South University, Changsha, China
- Eight-year program of medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Anthony Cyr
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Danielle S Gruen
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Tyler C Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Upendra K Kar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Cellular and Molecular Pathology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Francis X Guyette
- Department of Emergency Medicine, Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark H Yazer
- The Institute for Transfusion Medicine, Pittsburgh, PA, USA
| | - Brian J Daley
- Department of Surgery, University of Tennessee Health Science Center, Knoxville, TN, USA
| | - Richard S Miller
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian G Harbrecht
- Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Jeffrey A Claridge
- Metro Health Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Herb A Phelan
- Department of Surgery, University of Texas Southwestern, Dallas, TX, USA
| | - Brian S Zuckerbraun
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Matthew D Neal
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Pär I Johansson
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jakob Stensballe
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Anesthesia and Trauma Center, Centre of Head and Orthopaedics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Emergency Medical Services, The Capital Region of Denmark, Hillerød, Denmark
| | - Rami A Namas
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA
| | - Jason L Sperry
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA.
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, PA, USA.
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27
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Jia M, Yuan DY, Lovelace TC, Hu M, Benos PV. Causal Discovery in High-dimensional, Multicollinear Datasets. Front Epidemiol 2022; 2:899655. [PMID: 36778756 PMCID: PMC9910507 DOI: 10.3389/fepid.2022.899655] [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] [Received: 03/19/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022]
Abstract
As the cost of high-throughput genomic sequencing technology declines, its application in clinical research becomes increasingly popular. The collected datasets often contain tens or hundreds of thousands of biological features that need to be mined to extract meaningful information. One area of particular interest is discovering underlying causal mechanisms of disease outcomes. Over the past few decades, causal discovery algorithms have been developed and expanded to infer such relationships. However, these algorithms suffer from the curse of dimensionality and multicollinearity. A recently introduced, non-orthogonal, general empirical Bayes approach to matrix factorization has been demonstrated to successfully infer latent factors with interpretable structures from observed variables. We hypothesize that applying this strategy to causal discovery algorithms can solve both the high dimensionality and collinearity problems, inherent to most biomedical datasets. We evaluate this strategy on simulated data and apply it to two real-world datasets. In a breast cancer dataset, we identified important survival-associated latent factors and biologically meaningful enriched pathways within factors related to important clinical features. In a SARS-CoV-2 dataset, we were able to predict whether a patient (1) had Covid-19 and (2) would enter the ICU. Furthermore, we were able to associate factors with known Covid-19 related biological pathways.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, Pittsburgh, PA, United States
| | - Daniel Y. Yuan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, Pittsburgh, PA, United States
| | - Tyler C. Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, Pittsburgh, PA, United States
| | - Mengying Hu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, Pittsburgh, PA, United States
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, Pittsburgh, PA, United States
- Department of Epidemiology, University of Florida, Gainesville, FL, United States
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28
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Bing X, Lovelace T, Bunea F, Wegkamp M, Kasturi SP, Singh H, Benos PV, Das J. Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets. Patterns (N Y) 2022; 3:100473. [PMID: 35607614 PMCID: PMC9122954 DOI: 10.1016/j.patter.2022.100473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 03/01/2022] [Indexed: 01/19/2023]
Abstract
High-dimensional cellular and molecular profiling of biological samples highlights the need for analytical approaches that can integrate multi-omic datasets to generate prioritized causal inferences. Current methods are limited by high dimensionality of the combined datasets, the differences in their data distributions, and their integration to infer causal relationships. Here, we present Essential Regression (ER), a novel latent-factor-regression-based interpretable machine-learning approach that addresses these problems by identifying latent factors and their likely cause-effect relationships with system-wide outcomes/properties of interest. ER can integrate many multi-omic datasets without structural or distributional assumptions regarding the data. It outperforms a range of state-of-the-art methods in terms of prediction. ER can be coupled with probabilistic graphical modeling, thereby strengthening the causal inferences. The utility of ER is demonstrated using multi-omic system immunology datasets to generate and validate novel cellular and molecular inferences in a wide range of contexts including immunosenescence and immune dysregulation.
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Affiliation(s)
- Xin Bing
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Tyler Lovelace
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Carnegie Mellon – University of Pittsburgh, Pittsburgh, PA, USA
| | - Florentina Bunea
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Marten Wegkamp
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
- Department of Mathematics, Cornell University, Ithaca, NY, USA
| | - Sudhir Pai Kasturi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Harinder Singh
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V. Benos
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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29
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Bebis G, Levy D, Rockne R, Lima EABDF, Benos PV. Editorial: Advances in Mathematical and Computational Oncology. Front Physiol 2022; 13:889198. [PMID: 35464082 PMCID: PMC9021698 DOI: 10.3389/fphys.2022.889198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- George Bebis
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, United States
- *Correspondence: George Bebis,
| | - Doron Levy
- Department of Mathematics, University of Maryland, College Park, MD, United States
| | - Russell Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Pasadena, CA, United States
| | - Ernesto Augusto Bueno Da Fonseca Lima
- Center for Computational Oncology, Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, United States
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
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30
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Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Ruffin AT, Kunning S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews LP, Duprex WP, Joglekar AV, Benos PV, Ray P, Ray A, McVerry BJ, Zhang Y, Lee JS, Das J, Singh H, Morris A, Bruno TC, Vignali DAA. People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden. Cell Rep Med 2021; 2:100476. [PMID: 34873589 PMCID: PMC8636386 DOI: 10.1016/j.xcrm.2021.100476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/26/2021] [Revised: 07/27/2021] [Accepted: 11/23/2021] [Indexed: 01/08/2023]
Abstract
Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in people critically ill with COVID-19. Here, we present high-dimensional profiling of blood and respiratory samples from people with severe COVID-19 to examine the association between cell-linked molecular features and mortality outcomes. Peripheral transcriptional profiles by single-cell RNA sequencing (RNA-seq)-based deconvolution of immune states are associated with COVID-19 mortality. Further, persistently high levels of an interferon signaling module in monocytes over time lead to subsequent concerted upregulation of inflammatory cytokines. SARS-CoV-2-infected myeloid cells in the lower respiratory tract upregulate CXCL10, leading to a higher risk of death. Our analysis suggests a pivotal role for viral-infected myeloid cells and protracted interferon signaling in severe COVID-19.
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Affiliation(s)
- Anthony R Cillo
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Ashwin Somasundaram
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Feng Shan
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Integrative Systems Biology (ISB) Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carly Cardello
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Creg J Workman
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ayana T Ruffin
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sheryl Kunning
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Caleb Lampenfeld
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Sayali Onkar
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Stephanie Grebinoski
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Gaurav Deshmukh
- Meso Scale Discovery, A division of Meso Scale Diagnostics, LLC, 1601 Research Boulevard, Rockville, MD 20850-3173, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Chang Liu
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence P Andrews
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Panayiotis V Benos
- Department of Computer Science, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, PA 15260, USA.,Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anuradha Ray
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Harinder Singh
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alison Morris
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Tullia C Bruno
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Dario A A Vignali
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
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Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. Eur Respir J 2021; 58:2002950. [PMID: 34083402 PMCID: PMC9759791 DOI: 10.1183/13993003.02950-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. METHODS RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50). RESULTS Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg. CONCLUSION Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada
- Equally contributing authors
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Dept of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Equally contributing authors
| | - Kevin F Gibson
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Mridu Gulati
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Buqu Hu
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Antun Mihaljinec
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tony N Woolard
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Heather Lynn
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- University of Arizona Health Sciences, Tucson, AZ, USA
| | - Nkiruka Emeagwali
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Erica L Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Alison Morris
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Joseph K Leader
- Dept of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | | | | | | | | | - Michael J Becich
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Harry Hochheiser
- Dept of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven R Wisniewski
- Dept of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, US
| | - Panayiotis V Benos
- Dept of Computational and Systems Biology and Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Antje Prasse
- Hannover Medical School (MHH), Hannover, Germany
- Fraunhofer ITEM, Hannover, Germany
| | - Laura L Koth
- University of California San Francisco, San Francisco, CA, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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32
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Raghu VK, Horvat CM, Kochanek PM, Fink EL, Clark RSB, Benos PV, Au AK. Neurological Complications Acquired During Pediatric Critical Illness: Exploratory "Mixed Graphical Modeling" Analysis Using Serum Biomarker Levels. Pediatr Crit Care Med 2021; 22:906-914. [PMID: 34054117 PMCID: PMC8490289 DOI: 10.1097/pcc.0000000000002776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Neurologic complications, consisting of the acute development of a neurologic disorder, that is, not present at admission but develops during the course of illness, can be difficult to detect in the PICU due to sedation, neuromuscular blockade, and young age. We evaluated the direct relationships of serum biomarkers and clinical variables to the development of neurologic complications. Analysis was performed using mixed graphical models, a machine learning approach that allows inference of cause-effect associations from continuous and discrete data. DESIGN Secondary analysis of a previous prospective observational study. SETTING PICU, single quaternary-care center. PATIENTS Individuals admitted to the PICU, younger than18 years old, with intravascular access via an indwelling catheter. INTERVENTIONS None. MEASUREMENTS About 101 patients were included in this analysis. Serum (days 1-7) was analyzed for glial fibrillary acidic protein, ubiquitin C-terminal hydrolase-L1, and alpha-II spectrin breakdown product 150 utilizing enzyme-linked immunosorbent assays. Serum levels of neuron-specific enolase, myelin basic protein, and S100 calcium binding protein B used in these models were reported previously. Demographic data, use of selected clinical therapies, lengths of stay, and ancillary neurologic testing (head CT, brain MRI, and electroencephalogram) results were recorded. The Mixed Graphical Model-Fast-Causal Inference-Maximum algorithm was applied to the dataset. MAIN RESULTS About 13 of 101 patients developed a neurologic complication during their critical illness. The mixed graphical model identified peak levels of the neuronal biomarker neuron-specific enolase and ubiquitin C-terminal hydrolase-L1, and the astrocyte biomarker glial fibrillary acidic protein to be the direct causal determinants for the development of a neurologic complication; in contrast, clinical variables including age, sex, length of stay, and primary neurologic diagnosis were not direct causal determinants. CONCLUSIONS Graphical models that include biomarkers in addition to clinical data are promising methods to evaluate direct relationships in the development of neurologic complications in critically ill children. Future work is required to validate and refine these models further, to determine if they can be used to predict which patients are at risk for/or with early neurologic complications.
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Affiliation(s)
- Vineet K. Raghu
- Department of Computer Science, University of Pittsburgh,
Pittsburgh, PA
| | - Christopher M. Horvat
- Department of Critical Care Medicine, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Department of Pediatrics, University
of Pittsburgh School of Medicine, Pittsburgh, PA
- Safar Center for Resuscitation Research, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Brain Care Institute, UPMC
Children’s Hospital of Pittsburgh, PA
| | - Patrick M. Kochanek
- Department of Critical Care Medicine, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Department of Pediatrics, University
of Pittsburgh School of Medicine, Pittsburgh, PA
- Safar Center for Resuscitation Research, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Brain Care Institute, UPMC
Children’s Hospital of Pittsburgh, PA
| | - Ericka L. Fink
- Department of Critical Care Medicine, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Department of Pediatrics, University
of Pittsburgh School of Medicine, Pittsburgh, PA
- Safar Center for Resuscitation Research, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Brain Care Institute, UPMC
Children’s Hospital of Pittsburgh, PA
| | - Robert S. B. Clark
- Department of Critical Care Medicine, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Department of Pediatrics, University
of Pittsburgh School of Medicine, Pittsburgh, PA
- Safar Center for Resuscitation Research, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Brain Care Institute, UPMC
Children’s Hospital of Pittsburgh, PA
| | - Panayiotis V. Benos
- Department of Computer Science, University of Pittsburgh,
Pittsburgh, PA
- Department of Computational and Systems Biology, University
of Pittsburgh, Pittsburgh PA
| | - Alicia K. Au
- Department of Critical Care Medicine, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Department of Pediatrics, University
of Pittsburgh School of Medicine, Pittsburgh, PA
- Safar Center for Resuscitation Research, University of
Pittsburgh School of Medicine, Pittsburgh, PA; Brain Care Institute, UPMC
Children’s Hospital of Pittsburgh, PA
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33
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Kitsios GD, Kotok D, Yang H, Finkelman MA, Zhang Y, Britton N, Li X, Levochkina MS, Wagner AK, Schaefer C, Villandre JJ, Guo R, Evankovich JW, Bain W, Shah F, Zhang Y, Methé BA, Benos PV, McVerry BJ, Morris A. Plasma 1,3-β-d-glucan levels predict adverse clinical outcomes in critical illness. JCI Insight 2021; 6:e141277. [PMID: 34128840 PMCID: PMC8410081 DOI: 10.1172/jci.insight.141277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/09/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUNDThe fungal cell wall constituent 1,3-β-d-glucan (BDG) is a pathogen-associated molecular pattern that can stimulate innate immunity. We hypothesized that BDG from colonizing fungi in critically ill patients may translocate into the systemic circulation and be associated with host inflammation and outcomes.METHODSWe enrolled 453 mechanically ventilated patients with acute respiratory failure (ARF) without invasive fungal infection and measured BDG, innate immunity, and epithelial permeability biomarkers in serially collected plasma samples.RESULTSCompared with healthy controls, patients with ARF had significantly higher BDG levels (median [IQR], 26 pg/mL [15-49 pg/mL], P < 0.001), whereas patients with ARF with high BDG levels (≥40 pg/mL, 31%) had higher odds for assignment to the prognostically adverse hyperinflammatory subphenotype (OR [CI], 2.88 [1.83-4.54], P < 0.001). Baseline BDG levels were predictive of fewer ventilator-free days and worse 30-day survival (adjusted P < 0.05). Integrative analyses of fungal colonization and epithelial barrier disruption suggested that BDG may translocate from either the lung or gut compartment. We validated the associations between plasma BDG and host inflammatory responses in 97 hospitalized patients with COVID-19.CONCLUSIONBDG measurements offered prognostic information in critically ill patients without fungal infections. Further research in the mechanisms of translocation and innate immunity recognition and stimulation may offer new therapeutic opportunities in critical illness.FUNDINGUniversity of Pittsburgh Clinical and Translational Science Institute, COVID-19 Pilot Award and NIH grants (K23 HL139987, U01 HL098962, P01 HL114453, R01 HL097376, K24 HL123342, U01 HL137159, R01 LM012087, K08HK144820, F32 HL142172, K23 GM122069).
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Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome and.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel Kotok
- Department of Pulmonary and Critical Care Medicine, Cleveland Clinic Florida, Weston Hospital, Weston, Florida, USA
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,School of Medicine, Tsinghua University, Beijing, China.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Yonglong Zhang
- Associates of Cape Cod Inc., East Falmouth, Massachusetts, USA
| | - Noel Britton
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome and
| | - Xiaoyun Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Marina S Levochkina
- Department of Infectious Diseases and Microbiology and.,Departments of Physical Medicine and Rehabilitation, Neuroscience, and Clinical and Translational Science, Center for Neuroscience, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amy K Wagner
- Departments of Physical Medicine and Rehabilitation, Neuroscience, and Clinical and Translational Science, Center for Neuroscience, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John J Villandre
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Rui Guo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Department of Emergency and Critical Care Medicine, First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - John W Evankovich
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Barbara A Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome and
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome and.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome and.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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34
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Tabib T, Huang M, Morse N, Papazoglou A, Behera R, Jia M, Bulik M, Monier DE, Benos PV, Chen W, Domsic R, Lafyatis R. Myofibroblast transcriptome indicates SFRP2 hi fibroblast progenitors in systemic sclerosis skin. Nat Commun 2021; 12:4384. [PMID: 34282151 PMCID: PMC8289865 DOI: 10.1038/s41467-021-24607-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Skin and lung fibrosis in systemic sclerosis (SSc) is driven by myofibroblasts, alpha-smooth muscle actin expressing cells. The number of myofibroblasts in SSc skin correlates with the modified Rodnan skin score, the most widely used clinical measure of skin disease severity. Murine fibrosis models indicate that myofibroblasts can arise from a variety of different cell types, but their origin in SSc skin has remained uncertain. Utilizing single cell RNA-sequencing, we define different dermal fibroblast populations and transcriptome changes, comparing SSc to healthy dermal fibroblasts. Here, we show that SSc dermal myofibroblasts arise in two steps from an SFRP2hi/DPP4-expressing progenitor fibroblast population. In the first step, SSc fibroblasts show globally upregulated expression of transcriptome markers, such as PRSS23 and THBS1. A subset of these cells shows markers indicating that they are proliferating. Only a fraction of SFRP2hi SSc fibroblasts differentiate into myofibroblasts, as shown by expression of additional markers, SFRP4 and FNDC1. Bioinformatics analysis of the SSc fibroblast transcriptomes implicated upstream transcription factors, including FOSL2, RUNX1, STAT1, FOXP1, IRF7 and CREB3L1, as well as SMAD3, driving SSc myofibroblast differentiation. Myofibroblasts drive fibrosis in systemic sclerosis (SSc), but the cellular progenitors are unknown. Utilizing single cell RNA-sequencing, the authors show that SSc dermal myofibroblasts arise in a two-step process from SFRP2/DPP4-expressing progenitors and implicate upstream transcription factors.
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Affiliation(s)
- Tracy Tabib
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Nina Morse
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Anna Papazoglou
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Rithika Behera
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Minxue Jia
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Melissa Bulik
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Daisy E Monier
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robyn Domsic
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA.
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35
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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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Raghu VK, Ge X, Balajiee A, Shirer DJ, Das I, Benos PV, Chrysanthis PK. A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:811-822. [PMID: 32841121 PMCID: PMC8237279 DOI: 10.1109/tcbb.2020.3019237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Genome sequencing technologies have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level. However, to truly understand mechanisms of disease and predict the effects of medical interventions, high-throughput data must be integrated with demographic, phenotypic, environmental, and behavioral data from individuals. Further, effective knowledge discovery methods must infer relationships between these data types. We recently proposed a pipeline (CausalMGM) to achieve this. CausalMGM uses probabilistic graphical models to infer the relationships between variables in the data; however, CausalMGM's graphical structure learning algorithm can only handle small datasets efficiently. We propose a new methodology (piPref-Div) that selects the most informative variables for CausalMGM, enabling it to scale. We validate the efficacy of piPref-Div against other feature selection methods and demonstrate how the use of the full pipeline improves breast cancer outcome prediction and provides biologically interpretable views of gene expression data.
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Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Ruffin A, Kunning S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews L, Duprex WP, Joglekar AV, Benos PV, Ray P, Ray A, McVerry BJ, Zhang Y, Lee JS, Das J, Singh H, Morris A, Bruno TC, Vignali DAA. Bifurcated monocyte states are predictive of mortality in severe COVID-19. bioRxiv 2021:2021.02.10.430499. [PMID: 33594364 PMCID: PMC7885916 DOI: 10.1101/2021.02.10.430499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection presents with varied clinical manifestations1, ranging from mild symptoms to acute respiratory distress syndrome (ARDS) with high mortality2,3. Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in severe COVID-19. We performed high-dimensional cellular and molecular profiling of blood and respiratory samples from critically ill COVID-19 patients to define immune cell genomic states that are predictive of outcome in severe COVID-19 disease. Critically ill patients admitted to the intensive care unit (ICU) manifested increased frequencies of inflammatory monocytes and plasmablasts that were also associated with ARDS not due to COVID-19. Single-cell RNAseq (scRNAseq)-based deconvolution of genomic states of peripheral immune cells revealed distinct gene modules that were associated with COVID-19 outcome. Notably, monocytes exhibited bifurcated genomic states, with expression of a cytokine gene module exemplified by CCL4 (MIP-1β) associated with survival and an interferon signaling module associated with death. These gene modules were correlated with higher levels of MIP-1β and CXCL10 levels in plasma, respectively. Monocytes expressing genes reflective of these divergent modules were also detectable in endotracheal aspirates. Machine learning algorithms identified the distinctive monocyte modules as part of a multivariate peripheral immune system state that was predictive of COVID-19 mortality. Follow-up analysis of the monocyte modules on ICU day 5 was consistent with bifurcated states that correlated with distinct inflammatory cytokines. Our data suggests a pivotal role for monocytes and their specific inflammatory genomic states in contributing to mortality in life-threatening COVID-19 disease and may facilitate discovery of new diagnostics and therapeutics.
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Affiliation(s)
- Anthony R Cillo
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Ashwin Somasundaram
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Feng Shan
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Integrative Systems Biology (ISB) Graduate Program, University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Carly Cardello
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Creg J Workman
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Ayana Ruffin
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Sheryl Kunning
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Caleb Lampenfeld
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Sayali Onkar
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Stephanie Grebinoski
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Gaurav Deshmukh
- Meso Scale Discovery, A division of Meso Scale Diagnostics, LLC, 1601 Research Boulevard, Rockville, MD 20850-3173, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Chang Liu
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence Andrews
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Panayiotis V Benos
- Department of Computer Science, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anuradha Ray
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Harinder Singh
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Alison Morris
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Tullia C Bruno
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Dario A A Vignali
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
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38
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Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang XH, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A, McVerry BJ. Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients. Am J Respir Crit Care Med 2021; 202:1666-1677. [PMID: 32717152 DOI: 10.1164/rccm.201912-2441oc] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: Host inflammatory responses have been strongly associated with adverse outcomes in critically ill patients, but the biologic underpinnings of such heterogeneous responses have not been defined.Objectives: We examined whether respiratory tract microbiome profiles are associated with host inflammation and clinical outcomes of acute respiratory failure.Methods: We collected oral swabs, endotracheal aspirates (ETAs), and plasma samples from mechanically ventilated patients. We performed 16S ribosomal RNA gene sequencing to characterize upper and lower respiratory tract microbiota and classified patients into host-response subphenotypes on the basis of clinical variables and plasma biomarkers of innate immunity and inflammation. We derived diversity metrics and composition clusters with Dirichlet multinomial models and examined our data for associations with subphenotypes and clinical outcomes.Measurements and Main Results: Oral and ETA microbial communities from 301 mechanically ventilated subjects had substantial heterogeneity in α and β diversity. Dirichlet multinomial models revealed a cluster with low α diversity and enrichment for pathogens (e.g., high Staphylococcus or Pseudomonadaceae relative abundance) in 35% of ETA samples, associated with a hyperinflammatory subphenotype, worse 30-day survival, and longer time to liberation from mechanical ventilation (adjusted P < 0.05), compared with patients with higher α diversity and relative abundance of typical oral microbiota. Patients with evidence of dysbiosis (low α diversity and low relative abundance of "protective" oral-origin commensal bacteria) in both oral and ETA samples (17%, combined dysbiosis) had significantly worse 30-day survival and longer time to liberation from mechanical ventilation than patients without dysbiosis (55%; adjusted P < 0.05).Conclusions: Respiratory tract dysbiosis may represent an important, modifiable contributor to patient-level heterogeneity in systemic inflammatory responses and clinical outcomes.
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Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Department of Computational and Systems Biology, and.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Libing Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | | | - Xiao-Hong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - Katherine Fair
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - John Evankovich
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,School of Medicine, Tsinghua University, Beijing, China; and
| | - Kelvin Li
- Center for Medicine and the Microbiome
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
| | | | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome.,Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine and University of Pittsburgh Medical Center.,Center for Medicine and the Microbiome
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Cárdenes N, Sembrat J, Noda K, Lovelace T, Álvarez D, Bittar HET, Philips BJ, Nouraie M, Benos PV, Sánchez PG, Rojas M. Human ex vivo lung perfusion: a novel model to study human lung diseases. Sci Rep 2021; 11:490. [PMID: 33436736 PMCID: PMC7804395 DOI: 10.1038/s41598-020-79434-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022] Open
Abstract
Experimental animal models to predict physiological responses to injury and stress in humans have inherent limitations. Therefore, the development of preclinical human models is of paramount importance. Ex vivo lung perfusion (EVLP) has typically been used to recondition donor lungs before transplantation. However, this technique has recently advanced into a model to emulate lung mechanics and physiology during injury. In the present study, we propose that the EVLP of diseased human lungs is a well-suited preclinical model for translational research on chronic lung diseases. Throughout this paper, we demonstrate this technique's feasibility in pulmonary arterial hypertension (PAH), idiopathic pulmonary fibrosis (IPF), emphysema, and non-disease donor lungs not suitable for transplantation. In this study, we aimed to perfuse the lungs for 6 h with the EVLP system. This facilitated a robust and continuous assessment of airway mechanics, pulmonary hemodynamics, gas exchange, and biochemical parameters. We then collected at different time points tissue biopsies of lung parenchyma to isolate RNA and DNA to identify each disease's unique gene expression. Thus, demonstrating that EVLP could successfully serve as a clinically relevant experimental model to derive essential insights into pulmonary pathophysiology and various human lung diseases.
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Affiliation(s)
- Nayra Cárdenes
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, W1244 BST Tower, 200 Lothrop Street, Pittsburgh, PA, 15261, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Sembrat
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, W1244 BST Tower, 200 Lothrop Street, Pittsburgh, PA, 15261, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kentaro Noda
- Division of Lung Transplant and Lung Failure, Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tyler Lovelace
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
| | - Diana Álvarez
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Humberto E Trejo Bittar
- Department of Pathology, Thoracic and Autopsy Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Brian J Philips
- Division of Lung Transplant and Lung Failure, Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mehdi Nouraie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, W1244 BST Tower, 200 Lothrop Street, Pittsburgh, PA, 15261, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt Ph.D. Program in Computational Biology, Pittsburgh, PA, USA
| | - Pablo G Sánchez
- Division of Lung Transplant and Lung Failure, Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, W1244 BST Tower, 200 Lothrop Street, Pittsburgh, PA, 15261, USA. .,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
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40
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Wu J, Cyr A, Gruen DS, Lovelace TC, Benos PV, Chen T, Guyette FX, Yazer MH, Daley BJ, Miller RS, Harbrecht BG, Claridge JA, Phelan HA, Zuckerbraun BS, Neal MD, Johansson PI, Stensballe J, Namas RA, Vodovotz Y, Sperry JL, Billiar TR. Lipidomic Signatures Align with Inflammatory Patterns and Outcomes in Critical Illness. Res Sq 2021:rs.3.rs-106579. [PMID: 33442677 PMCID: PMC7805459 DOI: 10.21203/rs.3.rs-106579/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Alterations in lipid metabolism have the potential to be markers as well as drivers of the pathobiology of acute critical illness. Here, we took advantage of the temporal precision offered by trauma as a common cause of critical illness to identify the dynamic patterns in the circulating lipidome in critically ill humans. The major findings include an early loss of all classes of circulating lipids followed by a delayed and selective lipogenesis in patients destined to remain critically ill. Early in the clinical course, Fresh Frozen Plasma administration led to improved survival in association with preserved lipid levels that related to favorable changes in coagulation and inflammation biomarkers. Late over-representation of phosphatidylethanolamines with critical illness led to the validation of a Lipid Reprogramming Score that was prognostic not only in trauma but also severe COVID-19 patients. Our lipidomic findings provide a new paradigm for the lipid response underlying critical illness.
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Affiliation(s)
- Junru Wu
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
- Department of Cardiology, The 3rd Xiangya Hospital, Central South University, Changsha, China
- Eight-year program of medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Anthony Cyr
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Danielle S. Gruen
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Tyler C. Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, Pennsylvania, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, Pennsylvania, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Cellular and Molecular Pathology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Francis X. Guyette
- Department of Emergency Medicine, Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark H. Yazer
- The Institute for Transfusion Medicine, Pittsburgh, Pennsylvania, USA
| | - Brian J. Daley
- Department of Surgery, University of Tennessee Health Science Center, Knoxville, Tennessee, USA
| | - Richard S. Miller
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Brian G. Harbrecht
- Department of Surgery, University of Louisville, Louisville, Kentucky, USA
| | - Jeffrey A. Claridge
- Metro Health Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Herb A. Phelan
- Department of Surgery, University of Texas Southwestern, Dallas, Texas, USA
| | - Brian S. Zuckerbraun
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Matthew D. Neal
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Pär I. Johansson
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jakob Stensballe
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Anesthesia and Trauma Center, Centre of Head and Orthopaedics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Emergency Medical Services, The Capital Region of Denmark, Denmark
| | - Rami A. Namas
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Jason L. Sperry
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Trauma Research Center, Division of Trauma and Acute Care Surgery, Pittsburgh, Pennsylvania, US
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Valenzi E, Yang H, Sembrat JC, Yang L, Winters S, Nettles R, Kass DJ, Qin S, Wang X, Myerburg MM, Methé B, Fitch A, Alder JK, Benos PV, McVerry BJ, Rojas M, Morris A, Kitsios GD. Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study. Thorax 2020; 76:239-247. [PMID: 33268457 DOI: 10.1136/thoraxjnl-2020-214770] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lung microbiota profiles in patients with early idiopathic pulmonary fibrosis (IPF) have been associated with disease progression; however, the topographic heterogeneity of lung microbiota and their roles in advanced IPF are unknown. METHODS We performed a retrospective, case-control study of explanted lung tissue obtained at the time of lung transplantation or rapid autopsy from patients with IPF and other chronic lung diseases (connective tissue disease-associated interstitial lung disease (CTD-ILD), cystic fibrosis (CF), COPD and donor lungs unsuitable for transplant from Center for Organ Recovery and Education (CORE)). We sampled subpleural tissue and airway-based specimens (bronchial washings and airway tissue) and quantified bacterial load and profiled communities by amplification and sequencing of the 16S rRNA gene. FINDINGS Explants from 62 patients with IPF, 15 patients with CTD-ILD, 20 patients with CF, 20 patients with COPD and 20 CORE patients were included. Airway-based samples had higher bacterial load compared with distal parenchymal tissue. IPF basilar tissue had much lower bacterial load compared with CF and CORE lungs (p<0.001). No microbial community differences were found between parenchymal tissue samples from different IPF lobes. Dirichlet multinomial models revealed an IPF cluster (29%) with distinct composition, high bacterial load and low alpha diversity, exhibiting higher odds for acute exacerbation or death. INTERPRETATION IPF explants had low biomass in the distal parenchyma of all three lobes with higher bacterial load in the airways. The discovery of a distinct subgroup of patients with IPF with higher bacterial load and worse clinical outcomes supports investigation of personalised medicine approaches for microbiome-targeted interventions.
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Affiliation(s)
- Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Haopu Yang
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - John C Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Libing Yang
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - Spencer Winters
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Bronson Adult Critical Care, Kalamazoo, Michigan, USA
| | - Rachel Nettles
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel J Kass
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael M Myerburg
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam Fitch
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jonathan K Alder
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mauricio Rojas
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA .,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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42
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Bertolazzi G, Cipollina C, Benos PV, Tumminello M, Coronnello C. miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA. Front Cell Infect Microbiol 2020; 10:586592. [PMID: 33194826 PMCID: PMC7658538 DOI: 10.3389/fcimb.2020.586592] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
The present study focuses on the role of human miRNAs in SARS-CoV-2 infection. An extensive analysis of human miRNA binding sites on the viral genome led to the identification of miR-1207-5p as potential regulator of the viral Spike protein. It is known that exogenous RNA can compete for miRNA targets of endogenous mRNAs leading to their overexpression. Our results suggest that SARS-CoV-2 virus can act as an exogenous competing RNA, facilitating the over-expression of its endogenous targets. Transcriptomic analysis of human alveolar and bronchial epithelial cells confirmed that the CSF1 gene, a known target of miR-1207-5p, is over-expressed following SARS-CoV-2 infection. CSF1 enhances macrophage recruitment and activation and its overexpression may contribute to the acute inflammatory response observed in severe COVID-19. In summary, our results indicate that dysregulation of miR-1207-5p-target genes during SARS-CoV-2 infection may contribute to uncontrolled inflammation in most severe COVID-19 cases.
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Affiliation(s)
- Giorgio Bertolazzi
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
- Fondazione Ri.MED, Palermo, Italy
| | - Chiara Cipollina
- Fondazione Ri.MED, Palermo, Italy
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Michele Tumminello
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
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Buschur KL, Chikina M, Benos PV. Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinformatics 2020; 36:2515-2521. [PMID: 31873725 PMCID: PMC7178399 DOI: 10.1093/bioinformatics/btz949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/22/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Complex diseases involve perturbation in multiple pathways and a major challenge in clinical genomics is characterizing pathway perturbations in individual samples. This can lead to patient-specific identification of the underlying mechanism of disease thereby improving diagnosis and personalizing treatment. Existing methods rely on external databases to quantify pathway activity scores. This ignores the data dependencies and that pathways are incomplete or condition-specific. RESULTS ssNPA is a new approach for subtyping samples based on deregulation of their gene networks. ssNPA learns a causal graph directly from control data. Sample-specific network neighborhood deregulation is quantified via the error incurred in predicting the expression of each gene from its Markov blanket. We evaluate the performance of ssNPA on liver development single-cell RNA-seq data, where the correct cell timing is recovered; and two TCGA datasets, where ssNPA patient clusters have significant survival differences. In all analyses ssNPA consistently outperforms alternative methods, highlighting the advantage of network-based approaches. AVAILABILITY AND IMPLEMENTATION http://www.benoslab.pitt.edu/Software/ssnpa/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kristina L Buschur
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA 15260, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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44
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Bertolazzi G, Benos PV, Tumminello M, Coronnello C. An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinformatics 2020; 21:201. [PMID: 32938407 PMCID: PMC7493982 DOI: 10.1186/s12859-020-3519-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 02/04/2023] Open
Abstract
MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs. MicroRNA regulation activity depends on the recognition of binding sites located on mRNA molecules. ComiR is a web tool realized to predict the targets of a set of microRNAs, starting from their expression profile. ComiR was trained with the information regarding binding sites in the 3’utr region, by using a reliable dataset containing the targets of endogenously expressed microRNA in D. melanogaster S2 cells. This dataset was obtained by comparing the results from two different experimental approaches, i.e., inhibition, and immunoprecipitation of the AGO1 protein--a component of the microRNA induced silencing complex. In this work, we tested whether including coding region binding sites in ComiR algorithm improves the performance of the tool in predicting microRNA targets. We focused the analysis on the D. melanogaster species and updated the ComiR underlying database with the currently available releases of mRNA and microRNA sequences. As a result, we find that ComiR algorithm trained with the information related to the coding regions is more efficient in predicting the microRNA targets, with respect to the algorithm trained with 3’utr information. On the other hand, we show that 3’utr based predictions can be seen as complementary to the coding region based predictions, which suggests that both predictions, from 3’utr and coding regions, should be considered in comprehensive analysis. Furthermore, we observed that the lists of targets obtained by analyzing data from one experimental approach only, that is, inhibition or immunoprecipitation of AGO1, are not reliable enough to test the performance of our microRNA target prediction algorithm. Further analysis will be conducted to investigate the effectiveness of the tool with data from other species, provided that validated datasets, as obtained from the comparison of RISC proteins inhibition and immunoprecipitation experiments, will be available for the same samples. Finally, we propose to upgrade the existing ComiR web-tool by including the coding region based trained model, available together with the 3’utr based one.
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Affiliation(s)
- Giorgio Bertolazzi
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy.,Advanced Data Analysis Group, Fondazione Ri.MED, Palermo, Italy
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - Michele Tumminello
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
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Yang H, Benos PV, Kitsios GD. Protecting the lungs but hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS. Ann Transl Med 2020; 8:985. [PMID: 32953785 PMCID: PMC7475484 DOI: 10.21037/atm-20-2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Georgios D Kitsios
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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46
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Caparosa EM, Sedgewick AJ, Zenonos G, Zhao Y, Carlisle DL, Stefaneanu L, Jankowitz BT, Gardner P, Chang YF, Lariviere WR, LaFramboise WA, Benos PV, Friedlander RM. Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque. Neurosurgery 2020; 85:E284-E293. [PMID: 30335165 DOI: 10.1093/neuros/nyy470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Many studies have explored molecular markers of carotid plaque development and vulnerability to rupture, usually having examined whole carotid plaques. However, there are regional differences in plaque morphology and known shear-related mechanisms in areas surrounding the lipid core. OBJECTIVE To determine whether there are regional differences in protein expression along the long axis of the carotid plaque and how that might produce gaps in our understanding of the carotid plaque molecular signature. METHODS Levels of 7 inflammatory cytokines (IL-1β, IL-6, IL-8, IL-10, IL-12 p70, IFN-γ, and TNF-α) and caspase-3 were analyzed in prebifurcation, bifurcation, and postbifurcation segments of internal carotid plaques surgically removed from symptomatic and asymptomatic patients. Expression profiles of miRNAs and mRNAs were determined with microarrays for the rupture-prone postbifurcation segment for comparison with published whole plaque results. RESULTS Expression levels of all proteins examined, except IL-10, were lowest in the prebifurcation segment and significantly higher in the postbifurcation segment. Patient group differences in protein expression were observed for the prebifurcation segment; however, no significant differences were observed in the postbifurcation segment between symptomatic and asymptomatic patients. Expression profiles from postbifurcation carotid plaques identified 4 novel high priority miRNAs differentially expressed between patient groups (miR-214, miR-484, miR-942, and miR-1287) and 3 high-confidence miRNA:mRNA targets, including miR-214:APOD, miR-484:DACH1, and miR-942:GPR56. CONCLUSION The results demonstrate regional differences in protein expression for the first time and show that focus on the rupture-prone postbifurcation region leads to prioritization for further study of novel miRNA gene regulation mechanisms.
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Affiliation(s)
- Ellen M Caparosa
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew J Sedgewick
- Joint Carnegie-Mellon -University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Georgios Zenonos
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yin Zhao
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Diane L Carlisle
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lucia Stefaneanu
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian T Jankowitz
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Paul Gardner
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yue-Fang Chang
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - William R Lariviere
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Joint Carnegie-Mellon -University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania
| | - Robert M Friedlander
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
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Kotok D, Yang L, Evankovich JW, Bain W, Dunlap DG, Shah F, Zhang Y, Manatakis DV, Benos PV, Barbash IJ, Rapport SF, Lee JS, Morris A, McVerry BJ, Kitsios GD. The evolution of radiographic edema in ARDS and its association with clinical outcomes: A prospective cohort study in adult patients. J Crit Care 2020; 56:222-228. [PMID: 32028223 PMCID: PMC7136845 DOI: 10.1016/j.jcrc.2020.01.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 07/06/2019] [Revised: 12/13/2019] [Accepted: 01/12/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE To assess the longitudinal evolution of radiographic edema using chest X-rays (CXR) in patients with Acute Respiratory Distress Syndrome (ARDS) and to examine its association with prognostic biomarkers, ARDS subphenotypes and outcomes. MATERIALS AND METHODS We quantified radiographic edema on CXRs from patients with ARDS or cardiogenic pulmonary edema (controls) using the Radiographic Assessment of Lung Edema (RALE) score on day of intubation and up to 10 days after. We measured baseline plasma biomarkers and recorded clinical variables. RESULTS The RALE score had good inter-rater agreement (r = 0.83, p < 0.0001) applied on 488 CXRs from 129 patients, with higher RALE scores in patients with ARDS (n = 108) compared to controls (n = 21, p = 0.01). Baseline RALE scores were positively correlated with levels of the receptor for end-glycation end products (RAGE) in ARDS patients (p < 0.05). Baseline RALE scores were not predictive of 30- or 90-day survival. Persistently elevated RALE scores were associated with prolonged need for mechanical ventilation (p = 0.002). CONCLUSIONS The RALE score is easily implementable with high inter-rater reliability. Longitudinal RALE scoring appears to be a reproducible approach to track the evolution of radiographic edema in patients with ARDS and can potentially predict prolonged need for mechanical ventilation.
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Affiliation(s)
- Daniel Kotok
- Internal Medicine Residency Program, University of Pittsburgh Medical Center McKeesport, USA
| | - Libing Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John W Evankovich
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniel G Dunlap
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Dimitris V Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ian J Barbash
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sarah F Rapport
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, USA.
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Kitsios GD, Yang L, Manatakis DV, Nouraie M, Evankovich J, Bain W, Dunlap DD, Shah F, Barbash IJ, Rapport SF, Zhang Y, DeSensi RS, Weathington NM, Chen BB, Ray P, Mallampalli RK, Benos PV, Lee JS, Morris A, McVerry BJ. Host-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome. Crit Care Med 2019; 47:1724-1734. [PMID: 31634231 PMCID: PMC6865808 DOI: 10.1097/ccm.0000000000004018] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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] [Indexed: 01/16/2023]
Abstract
OBJECTIVES Classification of patients with acute respiratory distress syndrome into hyper- and hypoinflammatory subphenotypes using plasma biomarkers may facilitate more effective targeted therapy. We examined whether established subphenotypes are present not only in patients with acute respiratory distress syndrome but also in patients at risk for acute respiratory distress syndrome (ARFA) and then assessed the prognostic information of baseline subphenotyping on the evolution of host-response biomarkers and clinical outcomes. DESIGN Prospective, observational cohort study. SETTING Medical ICU at a tertiary academic medical center. PATIENTS Mechanically ventilated patients with acute respiratory distress syndrome or ARFA. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS We performed longitudinal measurements of 10 plasma biomarkers of host injury and inflammation. We applied unsupervised latent class analysis methods utilizing baseline clinical and biomarker variables and demonstrated that two-class models (hyper- vs hypoinflammatory subphenotypes) offered improved fit compared with one-class models in both patients with acute respiratory distress syndrome and ARFA. Baseline assignment to the hyperinflammatory subphenotype (39/104 [38%] acute respiratory distress syndrome and 30/108 [28%] ARFA patients) was associated with higher severity of illness by Sequential Organ Failure Assessment scores and incidence of acute kidney injury in patients with acute respiratory distress syndrome, as well as higher 30-day mortality and longer duration of mechanical ventilation in ARFA patients (p < 0.0001). Hyperinflammatory patients exhibited persistent elevation of biomarkers of innate immunity for up to 2 weeks postintubation. CONCLUSIONS Our results suggest that two distinct subphenotypes are present not only in patients with established acute respiratory distress syndrome but also in patients at risk for its development. Hyperinflammatory classification at baseline is associated with higher severity of illness, worse clinical outcomes, and trajectories of persistently elevated biomarkers of host injury and inflammation during acute critical illness compared with hypoinflammatory patients. Our findings provide strong rationale for examining treatment effect modifications by subphenotypes in randomized clinical trials to inform precision therapeutic approaches in critical care.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh
| | - Libing Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Dimitris V. Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John Evankovich
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniel D. Dunlap
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ian J Barbash
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sarah F. Rapport
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rebecca S. DeSensi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Nathaniel M. Weathington
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Bill B. Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rama K. Mallampalli
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Veterans Affairs Pittsburgh Healthcare System
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Janet S. Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh
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McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019; 4:131597. [PMID: 31600171 PMCID: PMC6948862 DOI: 10.1172/jci.insight.131597] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [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: 07/08/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary fibrosis (IPF) and 6 control lungs. Extent of fibrosis in each sample was assessed by microCT-measured alveolar surface density (ASD) and confirmed by histology. Regulatory gene expression networks were identified using linear mixed-effect models and dynamic regulatory events miner (DREM). Differential gene expression analysis identified a core set of genes increased or decreased before fibrosis was histologically evident that continued to change with advanced fibrosis. DREM generated a systems biology model (www.sb.cs.cmu.edu/IPFReg) that identified progressively divergent gene expression tracks with microRNAs and transcription factors that specifically regulate mild or advanced fibrosis. We confirmed model predictions by demonstrating that expression of POU2AF1, previously unassociated with lung fibrosis but proposed by the model as regulator, is increased in B lymphocytes in IPF lungs and that POU2AF1-knockout mice were protected from bleomycin-induced lung fibrosis. Our results reveal distinct regulation of gene expression changes in IPF tissue that remained structurally normal compared with moderate or advanced fibrosis and suggest distinct regulatory mechanisms for each stage.
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Affiliation(s)
- John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Siddhartha Jain
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Stijn E. Verleden
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Jose Herazo-Maya
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Milica Vukmirovic
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Argyrios Tzouvelekis
- Division of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Naoya Tanabe
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Fanny Chu
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johny Verschakelen
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven,Connecticut, USA
- Pathology and Laboratory Medicine Service, VA CT HealthCare System, West Haven, Connecticut, USA
| | - Dimitris V. Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junke Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jun Ding
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Karen Maes
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Laurens De Sadeleer
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robin Vos
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Arne Neyrinck
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ziv Bar-Joseph
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | | | - Wim A. Wuyts
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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50
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Lowe KE, Regan EA, Anzueto A, Austin E, Austin JHM, Beaty TH, Benos PV, Benway CJ, Bhatt SP, Bleecker ER, Bodduluri S, Bon J, Boriek AM, Boueiz ARE, Bowler RP, Budoff M, Casaburi R, Castaldi PJ, Charbonnier JP, Cho MH, Comellas A, Conrad D, Costa Davis C, Criner GJ, Curran-Everett D, Curtis JL, DeMeo DL, Diaz AA, Dransfield MT, Dy JG, Fawzy A, Fleming M, Flenaugh EL, Foreman MG, Fortis S, Gebrekristos H, Grant S, Grenier PA, Gu T, Gupta A, Han MK, Hanania NA, Hansel NN, Hayden LP, Hersh CP, Hobbs BD, Hoffman EA, Hogg JC, Hokanson JE, Hoth KF, Hsiao A, Humphries S, Jacobs K, Jacobson FL, Kazerooni EA, Kim V, Kim WJ, Kinney GL, Koegler H, Lutz SM, Lynch DA, MacIntye Jr. NR, Make BJ, Marchetti N, Martinez FJ, Maselli DJ, Mathews AM, McCormack MC, McDonald MLN, McEvoy CE, Moll M, Molye SS, Murray S, Nath H, Newell Jr. JD, Occhipinti M, Paoletti M, Parekh T, Pistolesi M, Pratte KA, Putcha N, Ragland M, Reinhardt JM, Rennard SI, Rosiello RA, Ross JC, Rossiter HB, Ruczinski I, San Jose Estepar R, Sciurba FC, Sieren JC, Singh H, Soler X, Steiner RM, Strand MJ, Stringer WW, Tal-Singer R, Thomashow B, Vegas Sánchez-Ferrero G, Walsh JW, Wan ES, Washko GR, Michael Wells J, Wendt CH, Westney G, Wilson A, Wise RA, Yen A, Young K, Yun J, Silverman EK, Crapo JD. COPDGene ® 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease. Chronic Obstr Pulm Dis 2019; 6:384-399. [PMID: 31710793 PMCID: PMC7020846 DOI: 10.15326/jcopdf.6.5.2019.0149] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/11/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) remains a major cause of morbidity and mortality. Present-day diagnostic criteria are largely based solely on spirometric criteria. Accumulating evidence has identified a substantial number of individuals without spirometric evidence of COPD who suffer from respiratory symptoms and/or increased morbidity and mortality. There is a clear need for an expanded definition of COPD that is linked to physiologic, structural (computed tomography [CT]) and clinical evidence of disease. Using data from the COPD Genetic Epidemiology study (COPDGene®), we hypothesized that an integrated approach that includes environmental exposure, clinical symptoms, chest CT imaging and spirometry better defines disease and captures the likelihood of progression of respiratory obstruction and mortality. METHODS Four key disease characteristics - environmental exposure (cigarette smoking), clinical symptoms (dyspnea and/or chronic bronchitis), chest CT imaging abnormalities (emphysema, gas trapping and/or airway wall thickening), and abnormal spirometry - were evaluated in a group of 8784 current and former smokers who were participants in COPDGene® Phase 1. Using these 4 disease characteristics, 8 categories of participants were identified and evaluated for odds of spirometric disease progression (FEV1 > 350 ml loss over 5 years), and the hazard ratio for all-cause mortality was examined. RESULTS Using smokers without symptoms, CT imaging abnormalities or airflow obstruction as the reference population, individuals were classified as Possible COPD, Probable COPD and Definite COPD. Current Global initiative for obstructive Lung Disease (GOLD) criteria would diagnose 4062 (46%) of the 8784 study participants with COPD. The proposed COPDGene® 2019 diagnostic criteria would add an additional 3144 participants. Under the new criteria, 82% of the 8784 study participants would be diagnosed with Possible, Probable or Definite COPD. These COPD groups showed increased risk of disease progression and mortality. Mortality increased in patients as the number of their COPD characteristics increased, with a maximum hazard ratio for all cause-mortality of 5.18 (95% confidence interval [CI]: 4.15-6.48) in those with all 4 disease characteristics. CONCLUSIONS A substantial portion of smokers with respiratory symptoms and imaging abnormalities do not manifest spirometric obstruction as defined by population normals. These individuals are at significant risk of death and spirometric disease progression. We propose to redefine the diagnosis of COPD through an integrated approach using environmental exposure, clinical symptoms, CT imaging and spirometric criteria. These expanded criteria offer the potential to stimulate both current and future interventions that could slow or halt disease progression in patients before disability or irreversible lung structural changes develop.
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Affiliation(s)
- Katherine E. Lowe
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve School of Medicine, Cleveland, Ohio
| | | | | | | | | | | | | | | | | | | | | | - Jessica Bon
- University of Pittsburgh, Pittsburgh, Pennsylvania
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | | | | | | | - Matthew Budoff
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Margaret Fleming
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts
| | | | | | | | | | - Sarah Grant
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts
| | | | - Tian Gu
- University of Michigan, Ann Arbor
| | - Abhya Gupta
- Boehringer Ingelheim, Biberach an der Riss, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Victor Kim
- Temple University, Philadelphia, Pennsylvania
| | - Woo Jin Kim
- Kangwon National University, Chuncheon, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Matthew Moll
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen I. Rennard
- AstraZeneca, Cambridge, United Kingdom
- University of Nebraska Medical Center, Omaha
| | | | | | - Harry B. Rossiter
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
- University of Leeds, Leeds, United Kingdom
| | | | | | | | | | | | - Xavier Soler
- University of California at San Diego
- GlaxoSmithKline, Research Triangle Park, North Carolina
| | | | | | - William W. Stringer
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | | | | | | | | | - Emily S. Wan
- Brigham and Women's Hospital, Boston, Massachusetts
- VA Boston Healthcare System, Jamaica Plain, Massachusetts
| | | | | | | | | | | | | | | | - Kendra Young
- University of Colorado Anschutz Medical Campus, Aurora
| | - Jeong Yun
- Brigham and Women's Hospital, Boston, Massachusetts
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