Transcriptomic profiling of immune cells in malignant pleural effusions identifies macrophage reprogramming associated with survival

Aaditya Khatri; Huimin Wang; Zhicheng Ji; Prekshaben Patel; Smita K. Nair; Javid P. Mohammed; Beth H. Shaz; Andrew B. Nixon; Scott M. Palmer; Kamran Mahmood

doi:10.1172/jci.insight.201691

Transcriptomic profiling of immune cells in malignant pleural effusions identifies macrophage reprogramming associated with survival

Aaditya Khatri,¹ Huimin Wang,² Zhicheng Ji,² Prekshaben Patel,³ Smita K. Nair,³ Javid P. Mohammed,⁴ Beth H. Shaz,⁵ Andrew B. Nixon,⁶ Scott M. Palmer,¹ and Kamran Mahmood¹

Published September 15, 2026 - More info

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Abstract

Despite advances in treatment approaches for lung cancer, the morbidity and survival of lung cancer patients with malignant pleural effusions (MPE) remain poor. This is in part due to gaps in understanding the role of immune cells in the pleural fluid microenvironment. We performed single cell analysis with flow cytometry validation of CD45+ cells in eight malignant and five benign pleural fluid (BPE) specimens to identify changes in the transcriptomic landscape of immune cells across disease states. We found upregulation of pro-inflammatory signaling pathways, including interferon and TNF signaling, in T cells, B cells, and macrophages in benign compared to malignant pleural effusions. Pro-inflammatory HLA-DR⁺ macrophages were associated with good survival outcomes while pro-tumorigenic HLA-DR^- macrophages with upregulation of angiogenesis, TGFβ, and fibronectin signaling were associated with poor survival outcomes in patients with MPE. We also validated these findings with macrophage cell surface expression markers using flow cytometry in 14 MPE and 7 BPE specimens. Finally, we performed multiplex cytokine analysis which showed enrichment of the type 3 inflammatory cytokine, IL17A, in MPE as a putative mechanism for macrophage reprogramming. These data provide a rich resource for interrogating the immune cell types and states present across the spectrum of pleural disease. They offer not only prognostic value for patient outcomes at the time of pleural fluid collection, but also insights into novel immunotherapy targets.

Transcriptomic profiling of immune cells in malignant pleural effusions identifies macrophage reprogramming associated with survival

Aaditya Khatri,¹ Huimin Wang,² Zhicheng Ji,² Prekshaben Patel,³ Smita K. Nair,³ Javid P. Mohammed,⁴ Beth H. Shaz,⁵ Andrew B. Nixon,⁶ Scott M. Palmer,¹ and Kamran Mahmood¹

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Transcriptomic profiling of immune cells in malignant pleural effusions identifies macrophage reprogramming associated with survival

Aaditya Khatri,1 Huimin Wang,2 Zhicheng Ji,2 Prekshaben Patel,3 Smita K. Nair,3 Javid P. Mohammed,4 Beth H. Shaz,5 Andrew B. Nixon,6 Scott M. Palmer,1 and Kamran Mahmood1

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Aaditya Khatri,¹ Huimin Wang,² Zhicheng Ji,² Prekshaben Patel,³ Smita K. Nair,³ Javid P. Mohammed,⁴ Beth H. Shaz,⁵ Andrew B. Nixon,⁶ Scott M. Palmer,¹ and Kamran Mahmood¹