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Chen H, Deng C, Gao J, Wang J, Fu F, Wang Y, Wang Q, Zhang M, Zhang S, Fan F, Liu K, Yang B, He Q, Zheng Q, Shen X, Wang J, Hu T, Zhu C, Yang F, He Y, Hu H, Wang J, Li Y, Zhang Y, Cao Z. Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer. Cancer Cell 2025; 43:519-536.e5. [PMID: 39983726 DOI: 10.1016/j.ccell.2025.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 11/12/2024] [Accepted: 01/29/2025] [Indexed: 02/23/2025]
Abstract
Recent advances have shed light on the molecular heterogeneity of small cell lung cancer (SCLC), yet the spatial organizations and cellular interactions in tumor immune microenvironment remain to be elucidated. Here, we employ co-detection by indexing (CODEX) and multi-omics profiling to delineate the spatial landscape for 165 SCLC patients, generating 267 high-dimensional images encompassing over 9.3 million cells. Integrating CODEX and genomic data reveals a multi-positive tumor cell neighborhood within ASCL1+ (SCLC-A) subtype, characterized by high SLFN11 expression and associated with poor prognosis. We further develop a cell colony detection algorithm (ColonyMap) and reveal a spatially assembled immune niche consisting of antitumoral macrophages, CD8+ T cells and natural killer T cells (MT2) which highly correlates with superior survival and predicts improving immunotherapy response in an independent cohort. This study serves as a valuable resource to study SCLC spatial heterogeneity and offers insights into potential patient stratification and personalized treatments.
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Affiliation(s)
- Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Jian Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jun Wang
- School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yue Wang
- Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Qiming Wang
- School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Mou Zhang
- School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Shiyue Zhang
- School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Fanfan Fan
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Kun Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bo Yang
- Department of Life and Health, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Qiming He
- Department of Life and Health, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Qiang Zheng
- Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xuxia Shen
- Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jin Wang
- Department of Translational Medicine, Amoy Diagnostics Co., Ltd, Xiamen 361000, China
| | - Tao Hu
- Department of Translational Medicine, Amoy Diagnostics Co., Ltd, Xiamen 361000, China
| | - Changbin Zhu
- Department of Translational Medicine, Amoy Diagnostics Co., Ltd, Xiamen 361000, China
| | - Fei Yang
- Janssen China Research & Development, Shanghai 200233, China
| | - Yonghong He
- Department of Life and Health, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jialei Wang
- Department of Thoracic Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Yuan Li
- Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai 200032, China.
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Lee KJ, Soyer HP, Stark MS. The Skin Molecular Ecosystem Holds the Key to Nevogenesis and Melanomagenesis. J Invest Dermatol 2024; 144:456-465. [PMID: 37921715 DOI: 10.1016/j.jid.2023.09.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Early detection of melanoma is critical to good patient outcomes, but we still know little about the mechanisms of early melanoma development. Normal epidermis has many of the sequence variants and genetic architecture disruptions found in both benign nevi, melanomas, and other skin cancers, yet continues to behave more or less normally. One hypothesis is that many melanocytes in this context are "tumor competent" but are regulated by the microenvironment provided by the surrounding keratinocytes to inhibit progress to nevi or melanoma. There is evidence of accumulating disorder in several measures of the genomic and epigenomic landscape from normal skin through nevi to melanoma that may be key to promoting nevogenesis and melanomagenesis.
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Affiliation(s)
- Katie J Lee
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia.
| | - H Peter Soyer
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia; Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Mitchell S Stark
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia
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Jayasinghe D, Betz-Stablein B, Stark MS, Soyer HP, Janda M. Spatial Randomness in the Distribution of Acquired Melanocytic Nevi of the Back in a Population-Based Sample. J Invest Dermatol 2022; 143:1108-1111.e3. [PMID: 36525993 DOI: 10.1016/j.jid.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Dilki Jayasinghe
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Brigid Betz-Stablein
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
| | - Mitchell S Stark
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
| | - H Peter Soyer
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia; Dermatology Department, Princess Alexandra Hospital, Brisbane, Australia
| | - Monika Janda
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
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