
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.09.09.612126
preprint
1
Article
Epigenetic adaptation drives monocyte differentiation into microglia-like cells upon engraftment into the retina
Liu Jie
Lei Fengyang http://orcid.org/0000-0002-9169-8314

Yan Bin
Cui Naiwen http://orcid.org/0000-0002-7240-822X

Sharma Jyoti
Correa Victor http://orcid.org/0000-0001-5723-7883

Roach Lara http://orcid.org/0000-0003-2534-6588

Nicolaou Savvas
Pitts Kristen http://orcid.org/0000-0001-7049-0883

Chodosh James http://orcid.org/0000-0002-7463-1599

Maidana Daniel E. http://orcid.org/0000-0002-3447-4074

Vavvas Demetrios http://orcid.org/0000-0002-8622-6478

Margeta Milica A
Zhang Huidan
Weitz David http://orcid.org/0000-0001-6678-5208

Mostoslavsky Raul
Paschalis Eleftherios I. http://orcid.org/0000-0002-4544-4452

14 9 2024
2024.09.09.612126https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://biorxiv.org/lookup/doi/10.1101/2024.09.09.612126
nihpp-2024.09.09.612126.pdf
Abstract

The identification of specific markers for microglia has been a long-standing challenge. Recently, markers such as P2ry12, TMEM119, and Fcrls have been proposed as microglia-specific and widely used to explore microglial functions within various central nervous system (CNS) contexts. The specificity of these markers was based on the assumption that circulating monocytes retain their distinct signatures even after infiltrating the CNS. However, recent findings reveal that infiltrating monocytes can adopt microglia-like characteristics while maintaining a pro-inflammatory profile upon permanent engraftment in the CNS.In this study, we utilize bone marrow chimeras, single-cell RNA sequencing, ATAC-seq, flow cytometry, and immunohistochemistry to demonstrate that engrafted monocytes acquire expression of established microglia markers—P2ry12, TMEM119, Fcrls—and the pan-myeloid marker Iba1, which has been commonly mischaracterized as microglia-specific. These changes are accompanied by alterations in chromatin accessibility and shifts in chromatin binding motifs that are indicative of microglial identity. Moreover, we show that engrafted monocytes dynamically regulate the expression of CX3CR1, CCR2, Ly6C, and transcription factors PU.1, CTCF, RUNX, AP-1, CEBP, and IRF2, all of which are crucial for shaping microglial identity. This study is the first to illustrate that engrafted monocytes in the retina undergo both epigenetic and transcriptional changes, enabling them to express microglia-like signatures. These findings highlight the need for future research to account for these changes when assessing the roles of monocytes and microglia in CNS pathology.

Significance Statement

Monocytes can express putative microglia markers P2ry12, TMEM119, and Fcrls upon engraftment into the retina. Given their involvement in neuroinflammation, it is crucial to consider this overlap when utilizing these markers for experimental analysis.
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