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Yoon H, Dean LS, Jiyarom B, Khadka VS, Deng Y, Nerurkar VR, Chow DC, Shikuma CM, Devendra G, Koh Y, Park J. Single-cell RNA sequencing reveals characteristics of myeloid cells in post-acute sequelae of SARS-CoV-2 patients with persistent respiratory symptoms. Front Immunol 2024; 14:1268510. [PMID: 38259488 PMCID: PMC10800799 DOI: 10.3389/fimmu.2023.1268510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Although our understanding of the immunopathology and subsequent risk and severity of COVID-19 disease is evolving, a detailed account of immune responses that contribute to the long-term consequences of pulmonary complications in COVID-19 infection remains unclear. Few studies have detailed the immune and cytokine profiles associated with post-acute sequelae of SARS-CoV-2 infection (PASC) with persistent pulmonary symptoms. The dysregulation of the immune system that drives pulmonary sequelae in COVID-19 survivors and PASC sufferers remains largely unknown. Results To characterize the immunological features of pulmonary PASC (PPASC), we performed droplet-based single-cell RNA sequencing (scRNA-seq) to study the transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) from a participant naïve to SARS-CoV-2 (Control) (n=1) and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC) (n=2). After integrating scRNA-seq data with a naïve participant from a published dataset, 11 distinct cell populations were identified based on the expression of canonical markers. The proportion of myeloid-lineage cells ([MLCs]; CD14+/CD16+monocytes, and dendritic cells) was increased in PPASC (n=2) compared to controls (n=2). MLCs from PPASC displayed up-regulation of genes associated with pulmonary symptoms/fibrosis, while glycolysis metabolism-related genes were downregulated. Similarly, pathway analysis showed that fibrosis-related (VEGF, WNT, and SMAD) and cell death pathways were up-regulated, but immune pathways were down-regulated in PPASC. Further comparison of PPASC with scRNA-seq data with Severe COVID-19 (n=4) data demonstrated enrichment of fibrotic transcriptional signatures. In PPASC, we observed interactive VEGF ligand-receptor pairs among MLCs, and network modules in CD14+ (cluster 4) and CD16+ (Cluster 5) monocytes displayed a significant enrichment for biological pathways linked to adverse COVID-19 outcomes, fibrosis, and angiogenesis. Further analysis revealed a distinct metabolic alteration in MLCs with a down-regulation of glycolysis/gluconeogenesis in PPASC compared to SARS-CoV-2 naïve samples. Conclusion Analysis of a small scRNA-seq dataset demonstrated alterations in the immune response and cellular landscape in PPASC. The presence of elevated MLC levels and their corresponding gene signatures associated with fibrosis, immune response suppression, and altered metabolic states suggests a potential role in PPASC development.
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Affiliation(s)
- Hyundong Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Logan S. Dean
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Boonyanudh Jiyarom
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI, United States
| | - Vivek R. Nerurkar
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Dominic C. Chow
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Gehan Devendra
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Pulmonary and Critical Care, Queen’s Medical Center, Honolulu, HI, United States
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Juwon Park
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
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