{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:59:09Z","timestamp":1785430749297,"version":"3.56.0"},"reference-count":43,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62173117"],"award-info":[{"award-number":["62173117"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62461046"],"award-info":[{"award-number":["62461046"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["62173117"],"award-info":[{"award-number":["62173117"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"award":["62461046"],"award-info":[{"award-number":["62461046"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Non-small cell lung cancer (NSCLC) is the most prevalent type of lung cancer and remains a major global health burden. Comprehensive characterization of tumor microenvironment (TME) heterogeneity is critical for understanding tumor progression and clinical outcomes in NSCLC. In this study, we identified 34 transcriptionally defined cell states and 6 multicellular ecotypes using the EcoTyper framework, thereby systematically delineating the TME landscape of NSCLC. These cell states and ecotypes were further validated across 11 independent bulk transcriptomic cohorts, one single-cell RNA sequencing cohort, and one spatial transcriptomics cohort, demonstrating strong reproducibility and robustness. Prognostic analyses revealed that several cell states and ecotypes were significantly associated with patient survival outcomes in NSCLC. Transcriptional regulatory analysis further identified SP8, MAZ, and FOS as potential regulators involved in shaping NSCLC ecotypes. Collectively, this study provides a comprehensive atlas of TME-associated cell states and ecotypes in NSCLC, offering new insights into tumor heterogeneity and potential opportunities for personalized prognostic assessment and therapeutic intervention.<\/jats:p>","DOI":"10.3390\/ijms27156718","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T07:55:41Z","timestamp":1785225341000},"page":"6718","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Landscape of Cell States and Multicellular Ecotypes in Non-Small Cell Lung Cancer"],"prefix":"10.3390","volume":"27","author":[{"given":"Honghao","family":"Li","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengchun","family":"Huo","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaokang","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumeng","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qilemuge","family":"Xi","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1133-9099","authenticated-orcid":false,"given":"Lei","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"ref_1","first-page":"e70043","article-title":"Cancer statistics, 2026","volume":"76","author":"Siegel","year":"2026","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"10435","DOI":"10.1038\/s41467-025-65421-8","article-title":"Single-cell and spatial transcriptomics implicate a prognostic function of tertiary lymphoid structures in gastric cancer","volume":"16","author":"Wang","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_3","first-page":"229","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_4","first-page":"209","article-title":"Global Cancer Statistics 2020: GLOBOCAN estimates of Incidence and mortality worldwide for 36 cancers in 185 countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41572-024-00551-9","article-title":"Non-small-cell lung cancer","volume":"10","author":"Hendriks","year":"2024","journal-title":"Nat. Rev. Dis. Prim."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e32899","DOI":"10.1097\/MD.0000000000032899","article-title":"Non-small cell lung cancer (NSCLC): A review of risk factors, diagnosis, and treatment","volume":"102","author":"Alduais","year":"2023","journal-title":"Medicine"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1038\/s41591-021-01450-2","article-title":"Toward personalized treatment approaches for non-small-cell lung cancer","volume":"27","author":"Wang","year":"2021","journal-title":"Nat. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1097\/JTO.0000000000000146","article-title":"Cisplatin versus Carboplatin-Based Regimens for the Treatment of Patients with Metastatic Lung Cancer. An Analysis of Veterans Health Administration Data","volume":"9","author":"Szabo","year":"2014","journal-title":"J. Thorac. Oncol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"104633","DOI":"10.1016\/j.ebiom.2023.104633","article-title":"Immunoscore immune checkpoint using spatial quantitative analysis of CD8 and PD-L1 markers is predictive of the efficacy of anti- PD1\/PD-L1 immunotherapy in non-small cell lung cancer","volume":"92","author":"Ghiringhelli","year":"2023","journal-title":"eBioMedicine"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1097\/JTO.0000000000000074","article-title":"Incorporating Immune-Checkpoint Inhibitors into Systemic Therapy of NSCLC","volume":"9","author":"Champiat","year":"2014","journal-title":"J. Thorac. Oncol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.ccell.2023.02.016","article-title":"The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth","volume":"41","author":"Joyce","year":"2023","journal-title":"Cancer Cell"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"R921","DOI":"10.1016\/j.cub.2020.06.081","article-title":"The tumor microenvironment","volume":"30","author":"Anderson","year":"2020","journal-title":"Curr. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41698-022-00272-w","article-title":"Tumor microenvironment heterogeneity an important mediator of prostate cancer progression and therapeutic resistance","volume":"6","author":"Ge","year":"2022","journal-title":"npj Precis. Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1038\/s41586-026-10452-4","article-title":"Non-invasive profiling of the tumour microenvironment with spatial ecotypes","volume":"654","author":"Zhang","year":"2026","journal-title":"Nature"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5482","DOI":"10.1016\/j.cell.2021.09.014","article-title":"Atlas of clinically distinct cell states and ecosystems across human solid tumors","volume":"184","author":"Luca","year":"2021","journal-title":"Cell"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1016\/j.ccell.2021.08.011","article-title":"The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma","volume":"39","author":"Steen","year":"2021","journal-title":"Cancer Cell"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1158\/2159-8290.CD-24-0605","article-title":"Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution","volume":"15","author":"Ma","year":"2025","journal-title":"Cancer Discov."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1186\/s12967-025-06521-3","article-title":"Multi-dimensional characterization of cellular states reveals clinically relevant immunological subtypes and therapeutic vulnerabilities in ovarian cancer","volume":"23","author":"Zhang","year":"2025","journal-title":"J. Transl. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"9968","DOI":"10.1038\/s41467-025-65016-3","article-title":"Multicellular immune ecotypes within solid tumors predict real-world therapeutic benefits with immune checkpoint inhibitors","volume":"16","author":"Wang","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"101489","DOI":"10.1016\/j.xcrm.2024.101489","article-title":"Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity toward advanced stages","volume":"5","author":"Deng","year":"2024","journal-title":"Cell Rep. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s42003-023-05117-1","article-title":"Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer","volume":"6","author":"Li","year":"2023","journal-title":"Commun. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41586-026-10469-9","article-title":"Ecotypes of triple-negative breast cancer in response to chemotherapy","volume":"654","author":"Yan","year":"2026","journal-title":"Nature"},{"key":"ref_23","first-page":"1843","article-title":"Expression Profile of Genes in Non-Small Cell Lung Carcinomas from Long-Term Surviving Patients","volume":"8","author":"Volm","year":"2002","journal-title":"Clin. Cancer Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3619","DOI":"10.1038\/s41388-024-03194-y","article-title":"MAZ promotes tumor proliferation and immune evasion in lung adenocarcinoma","volume":"43","author":"Chen","year":"2024","journal-title":"Oncogene"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1038\/s41467-023-36560-7","article-title":"Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis","volume":"14","author":"Xun","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.semradonc.2010.01.003","article-title":"The Tumor Microenvironment in Non\u2013Small-Cell Lung Cancer","volume":"20","author":"Graves","year":"2010","journal-title":"Semin. Radiat. Oncol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/s12032-025-02765-7","article-title":"The role of the tumour microenvironment in lung cancer and its therapeutic implications","volume":"42","author":"Edirisinghe","year":"2025","journal-title":"Med. Oncol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1007\/s12539-025-00699-2","article-title":"Deep Clustering-Based Metabolic Stratification of Non-Small Cell Lung Cancer Patients Through Integration of Somatic Mutation Profile and Network Propagation Algorithm","volume":"17","author":"Luo","year":"2025","journal-title":"Interdiscip. Sci. Comput. Life Sci."},{"key":"ref_29","first-page":"1","article-title":"Tumor microenvironment evolution in lung cancer: Spatio-temporal dynamics and clinical implications","volume":"123\u2013124","author":"Timofeev","year":"2026","journal-title":"Semin. Cancer Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1111\/imcb.70114","article-title":"Defining the tumor microenvironment of non-small cell lung cancer","volume":"104","author":"Embaye","year":"2026","journal-title":"Immunol. Cell Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1038\/s41467-025-56546-x","article-title":"Spatially mapping the tumour immune microenvironments of non-small cell lung cancer","volume":"16","author":"Desharnais","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"eadu2151","DOI":"10.1126\/sciadv.adu2151","article-title":"Single-cell multimodal analysis reveals tumor microenvironment predictive of treatment response in non\u2013small cell lung cancer","volume":"11","author":"Zheng","year":"2025","journal-title":"Sci. Adv."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"De Lucia, A., Mazzotti, L., Gaimari, A., Zurlo, M., Maltoni, R., Cerchione, C., Bravaccini, S., Delmonte, A., Crin\u00f2, L., and Borges de Souza, P. (2025). Non-small cell lung cancer and the tumor microenvironment: Making headway from targeted therapies to advanced immunotherapy. Front. Immunol., 16.","DOI":"10.3389\/fimmu.2025.1515748"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","article-title":"affy-analysis of Affymetrix GeneChip data at the probe level","volume":"20","author":"Gautier","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","article-title":"The sva package for removing batch effects and other unwanted variation in high-throughput experiments","volume":"28","author":"Leek","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"4388","DOI":"10.1038\/s41467-024-48700-8","article-title":"Single-cell and spatial transcriptomics analysis of non-small cell lung cancer","volume":"15","author":"Xue","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1038\/s41467-020-16164-1","article-title":"Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma","volume":"11","author":"Kim","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","article-title":"Determining cell type abundance and expression from bulk tissues with digital cytometry","volume":"37","author":"Newman","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_40","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The molecular signatures database hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"180015","DOI":"10.1038\/sdata.2018.15","article-title":"ImmPort, toward repurposing of open access immunological assay data for translational and clinical research","volume":"5","author":"Bhattacharya","year":"2018","journal-title":"Sci. Data"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"bbab260","DOI":"10.1093\/bib\/bbab260","article-title":"oncoPredict: An R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data","volume":"22","author":"Maeser","year":"2021","journal-title":"Brief. Bioinform."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6718\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T04:25:10Z","timestamp":1785385510000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6718"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,28]]},"references-count":43,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27156718"],"URL":"https:\/\/doi.org\/10.3390\/ijms27156718","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,28]]}}}