Multiomics identifies a cholesterol–TFEB–PLD3–TLR9 axis driving immunosuppressive tumor-associated macrophage polarization in esophageal squamous cell carcinoma

L Licheng Tan (College of Chemistry and Chemical Engineering/Film Energy Chemistry for Jiangxi Provincial Key Laboratory (FEC), Nanchang University, Nanchang, China.) H Hongyu Zhou (Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University) B Baifeng Zhang (Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong) D Dora Lai Wan Kwong (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) Y Yongxu Jia (Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University) J Jiayi Huang (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) K Kin To Hugo Siu (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) S Shuang Zhang J Jiao Huang (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) J Jie Luo Y Yuma Yang (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) Q Qin Liu Y Yingchen Lyu (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) L Liuxian Ban (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) Z Ziyang Qi (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) N Nanzhou Yu (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong) C Chaohui He (Department of Cardiovascular Surgery, Songshan Lake Central Hospital of Dongguan City) W Weiguang Zhang (School of Chemistry) Y Yanru Qin (Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University) B Beilei Liu (Department of Biomedical Sciences, Tung Biomedical Sciences Centre, City University of Hong Kong) X Xinyuan Guan (Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong)

Abstract

Tumor-associated macrophages (TAMs) reshape the tumor immune microenvironment and promote tumor progression, yet the underlying mechanisms remain largely unclear. Through integration of single-cell RNA (scRNA) sequencing datasets from esophageal squamous cell carcinoma (ESCC), we identified a distinct protumoral macrophage population with elevated expression of phospholipase D3 (PLD3). Multiomics investigations revealed that high infiltration of these PLD3-high macrophages was associated with poor clinical outcomes in ESCC patients. Mechanistically, tumor cells secreted cholesterol to modulate the microenvironment. Upon the uptake by TAMs, cholesterol triggered the nuclear translocation of transcription factor EB (TFEB), which directly bound to the PLD3 promoter region and activated its transcription. The overexpressed PLD3 localized to lysosomes, enzymatically degrading single-stranded nucleic acids, thereby suppressing the activation of the toll-like receptor 9 (TLR9) pathway. This cascade ultimately impaired effector T cell function and sustained an immunosuppressive tumor microenvironment (TME). Notably, therapeutic intervention using ODN2216-siPLD3 in murine models enhanced CD8 T cell infiltration and significantly inhibited tumor growth. Our findings highlight PLD3-high macrophages as a promising diagnostic biomarker and a therapeutic target for ESCC, paving the way for potential clinical translation.

Article Details

Volume / Issue Vol. 123, Issue 3
Published January 20, 2026
ISSN 0027-8424
Publisher National Academy of Sciences

Authors (21)

L

Licheng Tan

College of Chemistry and Chemical Engineering/Film Energy Chemistry for Jiangxi Provincial Key Laboratory (FEC), Nanchang University, Nanchang, China.

H

Hongyu Zhou

Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University

B

Baifeng Zhang

Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong

D

Dora Lai Wan Kwong

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

Y

Yongxu Jia

Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University

J

Jiayi Huang

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

K

Kin To Hugo Siu

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

S

Shuang Zhang

J

Jiao Huang

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

J

Jie Luo

Y

Yuma Yang

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

Q

Qin Liu

Y

Yingchen Lyu

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

L

Liuxian Ban

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

Z

Ziyang Qi

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

N

Nanzhou Yu

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong

C

Chaohui He

Department of Cardiovascular Surgery, Songshan Lake Central Hospital of Dongguan City

W

Weiguang Zhang

School of Chemistry

Y

Yanru Qin

Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University

B

Beilei Liu

Department of Biomedical Sciences, Tung Biomedical Sciences Centre, City University of Hong Kong

X

Xinyuan Guan

Department of Clinical Oncology, Centre for Cancer Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong