Thymic macrophages consist of two populations with distinct localization and origin

Abstract
Data availability
Article and author information
Metrics

Abstract

Tissue-resident macrophages are essential to protect from pathogen invasion and maintain organ homeostasis. The ability of thymic macrophages to engulf apoptotic thymocytes is well appreciated, but little is known about their ontogeny, maintenance, and diversity. Here, we characterized the surface phenotype and transcriptional profile of these cells and defined their expression signature. Thymic macrophages were most closely related to spleen red pulp macrophages and Kupffer cells and shared the expression of the transcription factor SpiC with these cells. Single-cell RNA sequencing showed that the macrophages in the adult thymus are composed of two populations distinguished by the expression of Timd4 and Cx3cr1. Remarkably, Timd4⁺ cells were located in the cortex, while Cx3cr1⁺ macrophages were restricted to the medulla and the cortico-medullary junction. Using shield chimeras, transplantation of embryonic thymuses, and genetic fate mapping, we found that the two populations have distinct origins. Timd4⁺ thymic macrophages are of embryonic origin, while Cx3cr1⁺ macrophages are derived from adult hematopoietic stem cells. Aging has a profound effect on the macrophages in the thymus. Timd4⁺ cells underwent gradual attrition, while Cx3cr1⁺ cells slowly accumulated with age and, in older mice, were the dominant macrophage population in the thymus. Altogether, our work defines the phenotype, origin, and diversity of thymic macrophages.

Data availability

The RNA Sequencing data of thymic macrophages and thymic dendritic cells are available at NCBI Gene Expression Omnibus (GEO) as part of GSE122108 and at www.immgen.org. The single cell RNA sequencing data is deposited at NCBI GEO under accession number GSE185460. The source data underlying Fig. 1G and H, Fig. 3B, D, and G, Fig. 5C, F, and I, Fig. 6B, E, G, and I, Fig. 7B, C, D, and G, Fig. 8B, D, E, and F, Fig. 1S4, Fig. 2S1, Fig. 2S2, Fig. 2S3, Fig. 5S1, and Fig. 5S2 are provided in the Source Data files. All other data supporting the findings of this study are available within the article.

The following data sets were generated

1. Zhou TA
2. Dzhagalov IL
(2021) Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice
NCBI Gene Expression Omnibus, GSE185460.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185460

The following previously published data sets were used

1. Immunological Genome Project Consortium
(2018) OpenSource Mononuclear Phagocytes Project
NCBI Gene Expression Omnibus, GSE122108.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122108

Article and author information

Author details

Tyng-An Zhou

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4031-4947
Hsuan-Po Hsu

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Yueh-Hua Tu

Institute of Information Science, Academia Sinica, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Hui-Kuei Cheng

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Chih-Yu Lin

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Nien-Jung Chen

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Jin-Wu Tsai

Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Ellen A Robey

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3630-5266
Hsuan-Cheng Huang

Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Chia-Lin Hsu

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

Competing interests
The authors declare that no competing interests exist.
Ivan L Dzhagalov

Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan

For correspondence
ivan.dzhagalov@nycu.edu.tw

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9209-4582

Funding

Ministry of Science and Technology, Taiwan (107-2320-B-010 -016 -MY3)

Ivan L Dzhagalov

Ministry of Science and Technology, Taiwan (110-2320-B-A49A-521 -)

Ivan L Dzhagalov

Ministry of Science and Technology, Taiwan (111-2320-B-A49 -031 -MY3)

Ivan L Dzhagalov

Yen Tjing Ling Medical Foundation (CI-111-6)

Ivan L Dzhagalov

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All experimental procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) of National Yang Ming Chiao Tung University (animal protocols #1070506, and 1090301). All surgery was performed under Ketamine + Xylazine anesthesia, and every effort was made to minimize suffering.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.