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Peer-reviewedCC BY-NC-ND 4.0Leukemia

Multimodal spatial profiling reveals distinct myeloid-defined ENKTL subgroups and tumor-myeloid cooperativity within prognostic inflammatory niche

15 more authors
27 affiliations
  1. 1Tsinghua Medicine, Tsinghua University, Beijing, China
  2. 2Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
  3. 3Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing, China
  4. 4Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
  5. 5Department of Medicine and Surgery, Kore University of Enna, Enna, Italy
  6. 6Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
  7. 7State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
  8. 8Department of Clinical Oncology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
  9. 9Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
  10. 10Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
  11. 11Institute of Advanced Studies Hong Kong, Sun Yat-sen University, Hong Kong SAR, China
  12. 12Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
  13. 13Department of Pathology, National University Hospital, Singapore, Singapore
  14. 14Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
  15. 15Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
  16. 16Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Health System, Singapore, Singapore
  17. 17Lymphoma Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
  18. 18ONCO-ACP, Duke-NUS Medical School, Singapore, Singapore
  19. 19Center of Excellence for Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
  20. 20Director’s Office, National Cancer Centre Singapore, Singapore, Singapore
  21. 21Office of Education, Duke-NUS Medical School, Singapore, Singapore
  22. 22Centre for Biomedical Data Science and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
  23. 23Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
  24. 24Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
  25. 25NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
  26. 26Advanced Pathology Laboratory, IFOM ETS – The AIRC Institute of Molecular Oncology, Milan, Italy
  27. 27Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy

Abstract

Extranodal NK/T-cell lymphoma (ENKTL) is an aggressive Epstein–Barr virus (EBV)-associated malignancy with a heterogeneous tumor microenvironment, yet macrophage heterogeneity and tumor-macrophage crosstalk remain poorly defined. Here, we integrate spatial transcriptomic and proteomic profiling with single-cell spatial molecular imaging of ENKTL samples and identify two subgroups defined by distinct macrophage programs. Subgroup 1 is enriched for inflammatory macrophages exhibiting IFN-α/γ responses and immune-regulatory molecules including IDO1 and CD274, whereas Subgroup 2 is immune-quiescent and macrophage-sparse, with its macrophage compartment skewed towards STAB1 macrophages with scavenging features. Notably, an NF-κB-activated and EBV-associated tumor subset is specifically enriched in Subgroup 1, displaying concurrent immunostimulatory and immunoregulatory features that parallel the co-enriched myeloid states and showing reproducible sample-level associations with these myeloid states across datasets. Spatial neighborhood analysis further delineates an inflammation niche where NF-κB tumor cells physically co-localize with these inflammatory macrophages, accompanied by enhanced tumor-myeloid and myeloid-myeloid signaling, implicating a process of tumor-associated myeloid recruitment followed by CCL- and IL1-mediated myeloid self-reinforcement. Critically, higher abundance of this niche correlates with improved survival across independent cohorts, revealing contrasting spatial tumor-immune architectures with prognostic relevance. Together, our study provides a spatially resolved framework for understanding ENKTL biology and guiding immunotherapeutic strategies.

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BibTeX
@article{deng2026multimodal,
  title = {{Multimodal spatial profiling reveals distinct myeloid-defined ENKTL subgroups and tumor-myeloid cooperativity within prognostic inflammatory niche}},
  author = {Lichang Deng and Min Liu and Reagan Entigu Anak Linton and Kaijie Hu and Shruti Sridhar and Giorgio Bertolazzi and Sai Mun Leong and Ling-Wen Ding and Nicholas Syn and Shuangyi Fan and Cho Mar Myint Wai and Yi-Qi Li and Jin-Xin Bei and Jie Xiong and Wei-Li Zhao and Susan Swee-Shan Hue and Joe Poh Sheng Yeong and Li Yen Chong and Li-Mei Poon and Choon Kiat Ong and Jing Quan Lim and Soon Thye Lim and Jinmiao Chen and Hang Xu and Anand Devaprasath Jeyasekharan and Claudio Tripodo and Siok-Bian Ng},
  journal = {Leukemia},
  year = {2026},
  month = aug,
  doi = {10.1038/s41375-026-03118-7},
  url = {https://doi.org/10.1038/s41375-026-03118-7},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Multimodal spatial profiling reveals distinct myeloid-defined ENKTL subgroups and tumor-myeloid cooperativity within prognostic inflammatory niche
AU  - Lichang Deng
AU  - Min Liu
AU  - Reagan Entigu Anak Linton
AU  - Kaijie Hu
AU  - Shruti Sridhar
AU  - Giorgio Bertolazzi
AU  - Sai Mun Leong
AU  - Ling-Wen Ding
AU  - Nicholas Syn
AU  - Shuangyi Fan
AU  - Cho Mar Myint Wai
AU  - Yi-Qi Li
AU  - Jin-Xin Bei
AU  - Jie Xiong
AU  - Wei-Li Zhao
AU  - Susan Swee-Shan Hue
AU  - Joe Poh Sheng Yeong
AU  - Li Yen Chong
AU  - Li-Mei Poon
AU  - Choon Kiat Ong
AU  - Jing Quan Lim
AU  - Soon Thye Lim
AU  - Jinmiao Chen
AU  - Hang Xu
AU  - Anand Devaprasath Jeyasekharan
AU  - Claudio Tripodo
AU  - Siok-Bian Ng
PY  - 2026
DA  - 2026/08/24
JO  - Leukemia
DO  - 10.1038/s41375-026-03118-7
UR  - https://doi.org/10.1038/s41375-026-03118-7
AB  - Extranodal NK/T-cell lymphoma (ENKTL) is an aggressive Epstein–Barr virus (EBV)-associated malignancy with a heterogeneous tumor microenvironment, yet macrophage heterogeneity and tumor-macrophage crosstalk remain poorly defined. Here, we integrate spatial transcriptomic and proteomic profiling with single-cell spatial molecular imaging of ENKTL samples and identify two subgroups defined by distinct macrophage programs. Subgroup 1 is enriched for inflammatory macrophages exhibiting IFN-α/γ responses and immune-regulatory molecules including IDO1 and CD274, whereas Subgroup 2 is immune-quiescent and macrophage-sparse, with its macrophage compartment skewed towards STAB1 macrophages with scavenging features. Notably, an NF-κB-activated and EBV-associated tumor subset is specifically enriched in Subgroup 1, displaying concurrent immunostimulatory and immunoregulatory features that parallel the co-enriched myeloid states and showing reproducible sample-level associations with these myeloid states across datasets. Spatial neighborhood analysis further delineates an inflammation niche where NF-κB tumor cells physically co-localize with these inflammatory macrophages, accompanied by enhanced tumor-myeloid and myeloid-myeloid signaling, implicating a process of tumor-associated myeloid recruitment followed by CCL- and IL1-mediated myeloid self-reinforcement. Critically, higher abundance of this niche correlates with improved survival across independent cohorts, revealing contrasting spatial tumor-immune architectures with prognostic relevance. Together, our study provides a spatially resolved framework for understanding ENKTL biology and guiding immunotherapeutic strategies.
SN  - 0887-6924
SN  - 1476-5551
ER  -