DNA damage in proximal tubules triggers systemic metabolic dysfunction through epigenetically altered macrophages

Erina Sugita Nishimura, Akihito Hishikawa, Ran Nakamichi, Riki Akashio, Shunsuke Chikuma, Akinori Hashiguchi, Norifumi Yoshimoto, Eriko Yoshida Hama, Tomomi Maruki, Wataru Itoh, Shintaro Yamaguchi, Jun Yoshino, Hiroshi Itoh and Kaori Hayashi ()
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Erina Sugita Nishimura: Keio University School of Medicine
Akihito Hishikawa: Keio University School of Medicine
Ran Nakamichi: Keio University School of Medicine
Riki Akashio: Keio University School of Medicine
Shunsuke Chikuma: Keio University School of Medicine
Akinori Hashiguchi: Keio University School of Medicine
Norifumi Yoshimoto: Keio University School of Medicine
Eriko Yoshida Hama: Keio University School of Medicine
Tomomi Maruki: Keio University School of Medicine
Wataru Itoh: Keio University School of Medicine
Shintaro Yamaguchi: Keio University
Jun Yoshino: Shimane University
Hiroshi Itoh: Keio University Hospital
Kaori Hayashi: Keio University School of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: Abstract DNA damage repair is a critical physiological process closely linked to aging. The accumulation of DNA damage in renal proximal tubular epithelial cells (PTEC) is related to a decline in kidney function. Here, we report that DNA double-strand breaks in PTECs lead to systemic metabolic dysfunction, including weight loss, reduced fat mass, impaired glucose tolerance with mitochondrial dysfunction, and increased inflammation in adipose tissues and the liver. Single-cell RNA sequencing analysis reveals expansion of CD11c+ Ccr2+ macrophages in the kidney cortex, liver, and adipose tissues and Ly6Chi monocytes in peripheral blood. DNA damage in PTECs is associated with hypomethylation of macrophage activation genes, including Gasdermin D, in peripheral blood cells, which is linked to reduced DNA methylation at KLF9-binding motifs. Macrophage depletion ameliorates metabolic abnormalities. These findings highlight the impact of kidney DNA damage on systemic metabolic homeostasis, revealing a kidney-blood-metabolism axis mediated by epigenetic changes in macrophages.

Date: 2025
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DOI: 10.1038/s41467-025-59297-x

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