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1. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

Author

Al Ozonoff, Joanna Schaenman, Naresh Doni Jayavelu, Carly E. Milliren, Carolyn S. Calfee, Charles B. Cairns, Monica Kraft, Lindsey R. Baden, Albert C. Shaw, Florian Krammer, Harm van Bakel, Denise A. Esserman, Shanshan Liu, Ana Fernandez Sesma, Viviana Simon, David A. Hafler, Ruth R. Montgomery, Steven H. Kleinstein, Ofer Levy, Christian Bime, Elias K. Haddad, David J. Erle, Bali Pulendran, Kari C. Nadeau, Mark M. Davis, Catherine L. Hough, William B. Messer, Nelson I. Agudelo Higuita, Jordan P. Metcalf, Mark A. Atkinson, Scott C. Brakenridge, David Corry, Farrah Kheradmand, Lauren I.R. Ehrlich, Esther Melamed, Grace A. McComsey, Rafick Sekaly, Joann Diray-Arce, Bjoern Peters, Alison D. Augustine, Elaine F. Reed, Matthew C. Altman, Patrice M. Becker, Nadine Rouphael, Chris Bime, Mark M Davis, Kerry McEnaney, Brenda Barton, Claudia Lentucci, Mehmet Saluvan, Ana C. Chang, Annmarie Hoch, Marisa Albert, Tanzia Shaheen, Alvin T. Kho, Sanya Thomas, Jing Chen, Maimouna D. Murphy, Mitchell Cooney, Scott Presnell, Gabriela K. Fragiadakis, Ravi Patel, Leying Guan, Jeremy Gygi, Shrikant Pawar, Anderson Brito, Zain Khalil, Cole Maguire, Slim Fourati, James A. Overton, Randi Vita, Kerstin Westendorf, Ramin Salehi-Rad, Aleksandra Leligdowicz, Michael A. Matthay, Jonathan P. Singer, Kirsten N. Kangelaris, Carolyn M. Hendrickson, Matthew F. Krummel, Charles R. Langelier, Prescott G. Woodruff, Debra L. Powell, James N. Kim, Brent Simmons, I. Michael Goonewardene, Cecilia M. Smith, Mark Martens, Jarrod Mosier, Hiroki Kimura, Amy C. Sherman, Stephen R. Walsh, Nicolas C. Issa, Charles Dela Cruz, Shelli Farhadian, Akiko Iwasaki, Albert I. Ko, Sharon Chinthrajah, Neera Ahuja, Angela J. Rogers, Maja Artandi, Sarah A.R. Siegel, Zhengchun Lu, Douglas A. Drevets, Brent R. Brown, Matthew L. Anderson, Faheem W. Guirgis, Rama V. Thyagarajan, Justin F. Rousseau, Dennis Wylie, Johanna Busch, Saurin Gandhi, Todd A. Triplett, George Yendewa, Olivia Giddings, Evan J. Anderson, Aneesh K. Mehta, Jonathan E. Sevransky, Bernard Khor, Adeeb Rahman, Daniel Stadlbauer, Jayeeta Dutta, Hui Xie, Seunghee Kim-Schulze, Ana Silvia Gonzalez-Reiche, Adriana van de Guchte, Keith Farrugia, Zenab Khan, Holden T. Maecker, David Elashoff, Jenny Brook, Estefania Ramires-Sanchez, Megan Llamas, Adreanne Rivera, Claudia Perdomo, Dawn C. Ward, Clara E. Magyar, Jennifer A. Fulcher, Yumiko Abe-Jones, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Sidney A. Carrillo, Suzanna Chak, Rajani Ghale, Ana Gonzalez, Alejandra Jauregui, Norman Jones, Tasha Lea, Deanna Lee, Raphael Lota, Jeff Milush, Viet Nguyen, Logan Pierce, Priya A. Prasad, Arjun Rao, Bushra Samad, Cole Shaw, Austin Sigman, Pratik Sinha, Alyssa Ward, Andrew Willmore, Jenny Zhan, Sadeed Rashid, Nicklaus Rodriguez, Kevin Tang, Luz Torres Altamirano, Legna Betancourt, Cindy Curiel, Nicole Sutter, Maria Tercero Paz, Gayelan Tietje-Ulrich, Carolyn Leroux, Jennifer Connors, Mariana Bernui, Michel A. Kutzler, Carolyn Edwards, Edward Lee, Edward Lin, Brett Croen, Nicholas C. Semenza, Brandon Rogowski, Nataliya Melnyk, Kyra Woloszczuk, Gina Cusimano, Mathew R. Bell, Sara Furukawa, Renee McLin, Pamela Marrero, Julie Sheidy, George P. Tegos, Crystal Nagle, Nathan Mege, Kristen Ulring, Vicki Seyfert-Margolis, Michelle Conway, Dave Francisco, Allyson Molzahn, Heidi Erickson, Connie Cathleen Wilson, Ron Schunk, Bianca Sierra, Trina Hughes, Kinga Smolen, Michael Desjardins, Simon van Haren, Xhoi Mitre, Jessica Cauley, Xiaofang Li, Alexandra Tong, Bethany Evans, Christina Montesano, Jose Humberto Licona, Jonathan Krauss, Jun Bai Park Chang, Natalie Izaguirre, Omkar Chaudhary, Andreas Coppi, John Fournier, Subhasis Mohanty, M. Catherine Muenker, Allison Nelson, Khadir Raddassi, Michael Rainone, William E. Ruff, Syim Salahuddin, Wade L. Schulz, Pavithra Vijayakumar, Haowei Wang, Elsio Wunder Jr., H. Patrick Young, Yujiao Zhao, Miti Saksena, Deena Altman, Erna Kojic, Komal Srivastava, Lily Q. Eaker, Maria C. Bermúdez-González, Katherine F. Beach, Levy A. Sominsky, Arman R. Azad, Juan Manuel Carreño, Gagandeep Singh, Ariel Raskin, Johnstone Tcheou, Dominika Bielak, Hisaaki Kawabata, Lubbertus CF Mulder, Giulio Kleiner, Alexandra S. Lee, Evan Do Do, Andrea Fernandes, Monali Manohar, Thomas Hagan, Catherine A. Blish, Hena Naz Din, Jonasel Roque, Samuel Yang, Amanda Brunton, Peter E. Sullivan, Matthew Strnad, Zoe L. Lyski, Felicity J. Coulter, J. Leland Booth, Lauren A. Sinko, Lyle L. Moldawer, Brittany Borresen, Brittney Roth-Manning, Li-Zhen Song, Ebony Nelson, Megan Lewis-Smith, Jacob Smith, Pablo Guaman Tipan, Nadia Siles, Sam Bazzi, Janelle Geltman, Kerin Hurley, Gio Gabriele, Scott Sieg, Tatyana Vaysman, Laurel Bristow, Laila Hussaini, Kieffer Hellmeister, Hady Samaha, Andrew Cheng, Christine Spainhour, Erin M. Scherer, Brandi Johnson, Amer Bechnak, Caroline R. Ciric, Lauren Hewitt, Erin Carter, Nina Mcnair, Bernadine Panganiban, Christopher Huerta, Jacob Usher, and Susan Pereira Ribeiro

Subjects
Male, IMPACC study group members, Clinical Sciences, Severity of Illness Index, General Biochemistry, Genetics and Molecular Biology, Post-Acute COVID-19 Syndrome, Clinical Research, Humans, Viral load, Viral, Prospective Studies, Lung, Antibody, SARS-CoV-2, Prevention, COVID-19, General Medicine, Troponin, Hospitalization, Infectious Diseases, Good Health and Well Being, Phenotype, Creatinine, Public Health and Health Services, RNA, RNA, Viral, Female
Abstract

BackgroundBetter understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management.MethodsImmunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed.FindingsThe median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC.InterpretationIntegration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19.FundingNIH.

Published
2022

2. Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients

Author

Cassandra E. Burnett, Trine Line Hauge Okholm, Iliana Tenvooren, Diana M. Marquez, Stanley Tamaki, Priscila Munoz Sandoval, Andrew Willmore, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Charles R. Langelier, Matthew F. Krummel, Prescott G. Woodruff, Carolyn S. Calfee, David J. Erle, K. Mark Ansel, Matthew H. Spitzer, Ravi Patel, Yumiko Abe-Jones, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Cathy Cai, Maria Calvo, Sidney A. Carrillo, Suzanna Chak, Zachary Collins, Spyros Darmanis, Gabriela K. Fragiadakis, Rajani Ghale, Jeremy Giberson, Pat Glenn, Ana Gonzalez, Kamir Hiam-Galvez, Alejandra Jauregui, Serena Ke, Tasha Lea, Deanna Lee, Raphael Lota, Leonard Lupin-Jimenez, Viet Nguyen, Nishita Nigam, Logan Pierce, Priya Prasad, Arjun Rao, Sadeed Rashid, Nicklaus Rodriguez, Bushra Samad, Cole Shaw, Austin Sigman, Pratik Sinha, Kevin Tang, Luz Torres Altamirano, Erden Tumurbaatar, Vaibhav Upadhyay, Alyssa Ward, Kristine Wong, Chun Jimmie Ye, Kimberly Yee, and Mingyue Zhou

Subjects
Infectious Diseases, SARS-CoV-2, Immunology, Disease Progression, COVID-19, Humans, Immunology and Allergy, Pneumonia
Abstract

While studies have elucidated many pathophysiological elements of COVID-19, little is known about immunological changes during COVID-19 resolution. We analyzed immune cells and phosphorylated signaling states at single-cell resolution from longitudinal blood samples of patients hospitalized with COVID-19, pneumonia and/or sepsis, and healthy individuals by mass cytometry. COVID-19 patients showed distinct immune compositions and an early, coordinated, and elevated immune cell signaling profile associated with early hospital discharge. Intra-patient longitudinal analysis revealed changes in myeloid and T cell frequencies and a reduction in immune cell signaling across cell types that accompanied disease resolution and discharge. These changes, together with increases in regulatory T cells and reduced signaling in basophils, also accompanied recovery from respiratory failure and were associated with better outcomes at time of admission. Therefore, although patients have heterogeneous immunological baselines and highly variable disease courses, a core immunological trajectory exists that defines recovery from severe SARS-CoV-2 infection.

Published
2022
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3. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

Author

Austin Hsu, Agnieszka P. Looney, Valerie Fong, Atul J. Butte, Paul J. Wolters, Esther Wu, Leqian Liu, Ram P. Naikawadi, Adam R. Abate, Dvir Aran, Mallar Bhattacharya, and Suzanna Chak

Subjects
Male, Transcriptome, Idiopathic pulmonary fibrosis, Mice, 0302 clinical medicine, Fibrosis, Gene expression, Immunology and Allergy, Macrophage, 2.1 Biological and endogenous factors, Aetiology, Lung, Cells, Cultured, 0303 health sciences, Cultured, Up-Regulation, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Differentiation, Respiratory, Female, Single-Cell Analysis, Sequence Analysis, Mesenchyme, Cells, Immunology, CX3C Chemokine Receptor 1, Antigens, Differentiation, Myelomonocytic, Biology, Alveolar, Article, 03 medical and health sciences, Bleomycin, Downregulation and upregulation, Macrophages, Alveolar, medicine, Genetics, Animals, Humans, Antigens, 030304 developmental biology, Sialic Acid Binding Immunoglobulin-like Lectins, Sequence Analysis, RNA, Animal, Macrophages, Gene Expression Profiling, Myelomonocytic, Macrophage Activation, medicine.disease, Idiopathic Pulmonary Fibrosis, Disease Models, Animal, Good Health and Well Being, Disease Models, Cancer research, RNA
Abstract

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologues of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury.

Published
2019

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