1
|
Ysasi AB, Engler AE, Bawa PS, Wang F, Conrad RD, Yeung AK, Rock JR, Beane-Ebel J, Mazzilli SA, Franklin RA, Mizgerd JP, Murphy GJ. A specialized population of monocyte-derived tracheal macrophages promote airway epithelial regeneration through a CCR2-dependent mechanism. iScience 2024; 27:110169. [PMID: 38993668 PMCID: PMC11238131 DOI: 10.1016/j.isci.2024.110169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 03/05/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Macrophages are critical for maintenance and repair of mucosal tissues. While functionally distinct subtypes of macrophage are known to have important roles in injury response and repair in the lungs, little is known about macrophages in the proximal conducting airways. Single-cell RNA sequencing and flow cytometry demonstrated murine tracheal macrophages are largely monocyte-derived and are phenotypically distinct from lung macrophages at homeostasis. Following sterile airway injury, monocyte-derived macrophages are recruited to the trachea and activate a pro-regenerative phenotype associated with wound healing. Animals lacking the chemokine receptor CCR2 have reduced numbers of circulating monocytes and tracheal macrophages, deficient pro-regenerative macrophage activation and defective epithelial repair. Together, these studies indicate that recruitment and activation of monocyte-derived tracheal macrophages is CCR2-dependent and is required for normal airway epithelial regeneration.
Collapse
Affiliation(s)
- Alexandra B Ysasi
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Anna E Engler
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pushpinder Singh Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Regan D Conrad
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Anthony K Yeung
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jason R Rock
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jennifer Beane-Ebel
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Sarah A Mazzilli
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Ruth A Franklin
- Department of Stem Cell and Regenerative Biology, Harvard University, Boston, MA 02115, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph P Mizgerd
- Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - George J Murphy
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| |
Collapse
|
2
|
Pan L, Mou T, Huang Y, Hong W, Yu M, Li X. Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis. Mol Biol Evol 2023; 40:msad267. [PMID: 38091963 PMCID: PMC10752348 DOI: 10.1093/molbev/msad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 11/03/2023] [Indexed: 12/28/2023] Open
Abstract
The burgeoning amount of single-cell data has been accompanied by revolutionary changes to computational methods to map, quantify, and analyze the outputs of these cutting-edge technologies. Many are still unable to reap the benefits of these advancements due to the lack of bioinformatics expertise. To address this issue, we present Ursa, an automated single-cell multiomics R package containing 6 automated single-cell omics and spatial transcriptomics workflows. Ursa allows scientists to carry out post-quantification single or multiomics analyses in genomics, transcriptomics, epigenetics, proteomics, and immunomics at the single-cell level. It serves as a 1-stop analytic solution by providing users with outcomes to quality control assessments, multidimensional analyses such as dimension reduction and clustering, and extended analyses such as pseudotime trajectory and gene-set enrichment analyses. Ursa aims bridge the gap between those with bioinformatics expertise and those without by providing an easy-to-use bioinformatics package for scientists in hoping to accelerate their research potential. Ursa is freely available at https://github.com/singlecellomics/ursa.
Collapse
Affiliation(s)
- Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, Solna 171 65, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna 171 65, Sweden
| | - Tian Mou
- School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yue Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna 171 65, Sweden
| | - Weifeng Hong
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Min Yu
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xuexin Li
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna 171 65, Sweden
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang 110032, China
| |
Collapse
|