{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T01:08:47Z","timestamp":1793495327466,"version":"4.5.0"},"reference-count":57,"publisher":"BMJ","issue":"1","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"unspecified","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009857","name":"Regeneron","doi-asserted-by":"crossref","award":["R2810-ONC-1901"],"award-info":[{"award-number":["R2810-ONC-1901"]}],"id":[{"id":"10.13039\/100009857","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100004328","name":"Genentech","doi-asserted-by":"publisher","award":["ML42362"],"award-info":[{"award-number":["ML42362"]}],"id":[{"id":"10.13039\/100004328","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000072","name":"National Institute of Dental and Craniofacial Research","doi-asserted-by":"publisher","award":["R35DE030054"],"award-info":[{"award-number":["R35DE030054"]}],"id":[{"id":"10.13039\/100000072","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["J Immunother Cancer"],"accepted":{"date-parts":[[2026,1,16]]},"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Neoadjuvant PD-1\/PD-L1 blockade yields robust efficacy in advanced cutaneous squamous cell carcinoma (cSCC), yet many patients fail to achieve a complete or major pathologic response. The reasons why some patients experience response but others do not are unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We profiled cSCC specimens before, after 1 dose, and after 3\u20134 doses of PD-1\/PD-L1 blockade to uncover resistance mechanisms and predict therapeutic response. In total, 27 patients across three cohorts, including two phase II trials, were studied. We created 1.7\u2009mm tissue-core microarrays and performed single-cell spatial transcriptomics, including spatial clustering, gene-set enrichment, and spatial correlation analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>After profiling all samples, six distinct spatial niches emerged, each differentially enriched in responders versus non-responders. A high antigen presentation niche, B\/plasma cell enriched niche, and inflammatory keratinocyte niche were more frequent in responders, whereas proliferative keratinocyte, low antigen presentation myeloid, and fibroblast-rich epithelial\u2013mesenchymal transition niches prevailed in non-responders. Notably, spatial niche profiling on pretreatment samples outperformed PD-L1 status in predicting pathologic response. Each niche displayed unique gene coexpression modules, suggesting niche-specific resistance mechanisms. Individual tumor analyses revealed varied immune evasion strategies, including defective interferon-induced antigen presentation, immunosuppressive myeloid environments, and epithelial\u2013mesenchymal transition.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our single-cell spatial transcriptomic approach identifies six spatial niches that predict immunotherapy response better than PD-L1 status using only 1.7\u2009mm tissue cores and may inform the development of biomarkers. Our results further underscore the heterogeneity of resistance mechanisms among cSCC patients, highlighting the need for tailored therapeutic strategies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1136\/jitc-2025-014067","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T11:35:11Z","timestamp":1769772911000},"page":"e014067","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":9,"title":["Single-cell spatial transcriptomics uncovers niches that govern response to PD-1\/PD-L1 blockade in cutaneous squamous cell carcinoma"],"prefix":"10.1136","volume":"14","clinical-trial-number":[{"clinical-trial-number":"nct04154943","registry":"10.18810\/clinical-trials-gov"},{"clinical-trial-number":"nct04710498","registry":"10.18810\/clinical-trials-gov"},{"clinical-trial-number":"nct06568172","registry":"10.18810\/clinical-trials-gov"},{"clinical-trial-number":"nct04154943","registry":"10.18810\/clinical-trials-gov"},{"clinical-trial-number":"nct04710498","registry":"10.18810\/clinical-trials-gov"}],"author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7226-4855","authenticated-orcid":false,"given":"Maxwell Y","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alistaire R","family":"Sherman","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9619-1689","authenticated-orcid":false,"given":"Luis","family":"Martinez Ramirez","sequence":"additional","affiliation":[{"name":"Stanford Cancer Institute Clinical Trials Office, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mobeen","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Zdravkovic","sequence":"additional","affiliation":[{"name":"Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"June Ho","family":"Shin","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Stepanek","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander Dimitrios","family":"Colevas","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Medical Oncology, Stanford University, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8393-4196","authenticated-orcid":false,"given":"John B","family":"Sunwoo","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasu","family":"Divi","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"239","published-online":{"date-parts":[[2026,1,30]]},"reference":[{"key":"2026013003350726000_14.1.e014067.1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra2206348"},{"key":"2026013003350726000_14.1.e014067.2","doi-asserted-by":"crossref","first-page":"5017","DOI":"10.1245\/s10434-023-13306-9","article-title":"Oncological Outcome After Lymph Node Dissection for Cutaneous Squamous Cell Carcinoma","volume":"30","author":"Huis in \u2019t Veld","year":"2023","journal-title":"Ann Surg Oncol"},{"key":"2026013003350726000_14.1.e014067.3","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1001\/jamadermatol.2018.5453","article-title":"Association of Disease Recurrence With Survival Outcomes in Patients With Cutaneous Squamous Cell Carcinoma of the Head and Neck Treated With Multimodality Therapy","volume":"155","author":"Sun","year":"2019","journal-title":"JAMA Dermatol"},{"key":"2026013003350726000_14.1.e014067.4","doi-asserted-by":"crossref","first-page":"5124","DOI":"10.1245\/s10434-022-11669-z","article-title":"Benchmarking Survival Outcomes Following Surgical Management of pT3 and pT4 Cutaneous Squamous Cell Carcinoma of the Head and Neck","volume":"29","author":"Yung","year":"2022","journal-title":"Ann Surg Oncol"},{"key":"2026013003350726000_14.1.e014067.5","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2209813"},{"key":"2026013003350726000_14.1.e014067.6","doi-asserted-by":"crossref","first-page":"9507","DOI":"10.1200\/JCO.2023.41.16_suppl.9507","article-title":"Towards organ preservation and cure via 2 infusions of immunotherapy only, in patients normally undergoing extensive and mutilating curative surgery for cutaneous squamous cell carcinoma: An investigator-initiated randomized phase II trial\u2014The MATISSE trial","volume":"41","author":"Zuur","year":"2023","journal-title":"JCO"},{"key":"2026013003350726000_14.1.e014067.7","doi-asserted-by":"crossref","first-page":"9514","DOI":"10.1200\/JCO.2024.42.16_suppl.9514","article-title":"A phase 2 study of de-escalation in resectable, locally advanced cutaneous squamous cell carcinoma (cSCC) with the use of neoadjuvant pembrolizumab: De-Squamate","volume":"42","author":"Ladwa","year":"2024","journal-title":"JCO"},{"key":"2026013003350726000_14.1.e014067.8","doi-asserted-by":"crossref","first-page":"9576","DOI":"10.1200\/JCO.2023.41.16_suppl.9576","article-title":"NEO-CESQ study: Neoadjuvant plus adjuvant treatment with cemiplimab in surgically resectable, high risk stage III\/IV (M0) cutaneous squamous cell carcinoma","volume":"41","author":"Ascierto","year":"2023","journal-title":"JCO"},{"key":"2026013003350726000_14.1.e014067.9","doi-asserted-by":"crossref","first-page":"9591","DOI":"10.1200\/JCO.2024.42.16_suppl.9591","article-title":"Pathologic response rates to neoadjuvant pembrolizumab in locally advanced (LA) resectable cutaneous squamous cell carcinoma (cSCC)","volume":"42","author":"Amatore","year":"2024","journal-title":"JCO"},{"key":"2026013003350726000_14.1.e014067.10","doi-asserted-by":"crossref","unstructured":"Divi V , Aasi S , Khan SA , et al . Neoadjuvant Atezolizumab in Patients With Surgically Resectable Advanced Cutaneous Squamous Cell Carcinoma. JCO Oncology Advances 2024. doi:10.1200\/OA-24-00058","DOI":"10.1200\/OA-24-00058"},{"key":"2026013003350726000_14.1.e014067.11","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-49718-8","article-title":"Cancer cell plasticity defines response to immunotherapy in cutaneous squamous cell carcinoma","volume":"15","author":"Lorenzo-Sanz","year":"2024","journal-title":"Nat Commun"},{"key":"2026013003350726000_14.1.e014067.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2016.10.018"},{"key":"2026013003350726000_14.1.e014067.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.aao4572"},{"key":"2026013003350726000_14.1.e014067.14","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1604958"},{"key":"2026013003350726000_14.1.e014067.15","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan6733"},{"key":"2026013003350726000_14.1.e014067.16","doi-asserted-by":"publisher","DOI":"10.1038\/nri2506"},{"key":"2026013003350726000_14.1.e014067.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2014.06.010"},{"key":"2026013003350726000_14.1.e014067.18","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/nature25501","article-title":"TGF\u03b2 attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells","volume":"554","author":"Mariathasan","year":"2018","journal-title":"Nature New Biol"},{"key":"2026013003350726000_14.1.e014067.19","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/s40257-018-0389-y","article-title":"Mechanisms of Resistance to Immune Checkpoint Blockade","volume":"20","author":"Liu","year":"2019","journal-title":"Am J Clin Dermatol"},{"key":"2026013003350726000_14.1.e014067.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41568-023-00583-5"},{"key":"2026013003350726000_14.1.e014067.21","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-023-40822-9","article-title":"Driver gene combinations dictate cutaneous squamous cell carcinoma disease continuum progression","volume":"14","author":"Bailey","year":"2023","journal-title":"Nat Commun"},{"key":"2026013003350726000_14.1.e014067.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.05.039"},{"key":"2026013003350726000_14.1.e014067.23","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1016\/S1470-2045(23)00459-X","article-title":"Neoadjuvant cemiplimab and surgery for stage II-IV cutaneous squamous-cell carcinoma: follow-up and survival outcomes of a single-arm, multicentre, phase 2 study","volume":"24","author":"Gross","year":"2023","journal-title":"Lancet Oncol"},{"key":"2026013003350726000_14.1.e014067.24","doi-asserted-by":"crossref","DOI":"10.1186\/s40246-021-00374-9","article-title":"Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders","volume":"16","author":"Ho","year":"2022","journal-title":"Hum Genomics"},{"key":"2026013003350726000_14.1.e014067.25","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02235-4"},{"key":"2026013003350726000_14.1.e014067.26","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst"},{"key":"2026013003350726000_14.1.e014067.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-022-01315-x"},{"key":"2026013003350726000_14.1.e014067.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.07.019"},{"key":"2026013003350726000_14.1.e014067.29","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2020-001111","article-title":"Antigen processing and presentation in cancer immunotherapy","volume":"8","author":"Lee","year":"2020","journal-title":"J Immunother Cancer"},{"key":"2026013003350726000_14.1.e014067.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.cytogfr.2019.06.003"},{"key":"2026013003350726000_14.1.e014067.31","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a021857","article-title":"CSF-1 receptor signaling in myeloid cells","volume":"6","author":"Stanley","year":"2014","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2026013003350726000_14.1.e014067.32","doi-asserted-by":"publisher","DOI":"10.1038\/nrc1877"},{"key":"2026013003350726000_14.1.e014067.33","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/s41580-018-0080-4","article-title":"New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer","volume":"20","author":"Dongre","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026013003350726000_14.1.e014067.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2022.01.003"},{"key":"2026013003350726000_14.1.e014067.35","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.ebiom.2016.06.011","article-title":"A Mouse Model of Hyperproliferative Human Epithelium Validated by Keratin Profiling Shows an Aberrant Cytoskeletal Response to Injury","volume":"9","author":"Zhussupbekova","year":"2016","journal-title":"EBioMedicine"},{"key":"2026013003350726000_14.1.e014067.36","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms11914","article-title":"KRT14 marks a subpopulation of bladder basal cells with pivotal role in regeneration and tumorigenesis","volume":"7","author":"Papafotiou","year":"2016","journal-title":"Nat Commun"},{"key":"2026013003350726000_14.1.e014067.37","doi-asserted-by":"crossref","unstructured":"Danaher P , McGuire D , Patrick M , et al . InSituCor: a toolkit for discovering non-trivial spatial correlations in spatial transcriptomics. Bioinformatics 2023. doi:10.1101\/2023.09.19.558514","DOI":"10.1101\/2023.09.19.558514"},{"key":"2026013003350726000_14.1.e014067.38","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/s41586-025-09370-8","article-title":"Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy","volume":"646","author":"Baruch","year":"2025","journal-title":"Nature New Biol"},{"key":"2026013003350726000_14.1.e014067.39","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(19)32591-7"},{"key":"2026013003350726000_14.1.e014067.40","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1606774"},{"key":"2026013003350726000_14.1.e014067.41","doi-asserted-by":"publisher","DOI":"10.1016\/J.CCELL.2019.01.003"},{"key":"2026013003350726000_14.1.e014067.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.028"},{"key":"2026013003350726000_14.1.e014067.43","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2022.08.004"},{"key":"2026013003350726000_14.1.e014067.44","unstructured":"Zheng Y , Pizurica M , Carrillo-Perez F , et al . Digital profiling of cancer transcriptomes from histology images with grouped vision attention. Bioinformatics [Preprint] 2023. doi:10.1101\/2023.09.28.560068 Available: https:\/\/www.biorxiv.org\/content\/10.1101\/2023.09.28.560068v2"},{"key":"2026013003350726000_14.1.e014067.45","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1038\/s43018-024-00793-2","article-title":"A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics","volume":"5","author":"Hoang","year":"2024","journal-title":"Nat Cancer"},{"key":"2026013003350726000_14.1.e014067.46","doi-asserted-by":"publisher","DOI":"10.1038\/s41571-023-00789-4"},{"key":"2026013003350726000_14.1.e014067.47","doi-asserted-by":"crossref","DOI":"10.1126\/science.adj4857","article-title":"A blueprint for tumor-infiltrating B cells across human cancers","volume":"384","author":"Ma","year":"2024","journal-title":"Science"},{"key":"2026013003350726000_14.1.e014067.48","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1922-8"},{"key":"2026013003350726000_14.1.e014067.49","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-23355-x","article-title":"B cell signatures and tertiary lymphoid structures contribute to outcome in head and neck squamous cell carcinoma","volume":"12","author":"Ruffin","year":"2021","journal-title":"Nat Commun"},{"key":"2026013003350726000_14.1.e014067.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41573-018-0007-y"},{"key":"2026013003350726000_14.1.e014067.51","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1038\/s43018-020-0038-2","article-title":"Bystander IFN-\u03b3 activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment","volume":"1","author":"Thibaut","year":"2020","journal-title":"Nat Cancer"},{"key":"2026013003350726000_14.1.e014067.52","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2020-002128","article-title":"Chimeric antigen receptor engineered NK cellular immunotherapy overcomes the selection of T-cell escape variant cancer cells","volume":"9","author":"Lee","year":"2021","journal-title":"J Immunother Cancer"},{"key":"2026013003350726000_14.1.e014067.53","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abb0152","article-title":"Uncoupling interferon signaling and antigen presentation to overcome immunotherapy resistance due to JAK1 loss in melanoma","volume":"12","author":"Kalbasi","year":"2020","journal-title":"Sci Transl Med"},{"key":"2026013003350726000_14.1.e014067.54","unstructured":"Lee MY , Sherman AR , Martinez Ramirez L , et al . Data from: Single-cell spatial transcriptomics uncovers niches that govern response to PD-1\/PD-L1 blockade in cutaneous squamous cell carcinoma. Dryad Digital Repository 2025. Available: https:\/\/doi.org\/10.5061\/dryad.s4mw6m9jh"},{"key":"2026013003350726000_14.1.e014067.55","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol"},{"key":"2026013003350726000_14.1.e014067.56","doi-asserted-by":"crossref","unstructured":"Danaher P , Zhao E , Yang Z , et al . Insitutype: likelihood-based cell typing for single cell spatial transcriptomics. Bioinformatics 2022. doi:10.1101\/2022.10.19.512902","DOI":"10.1101\/2022.10.19.512902"},{"key":"2026013003350726000_14.1.e014067.57","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-024-03435-z","article-title":"Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment","volume":"25","author":"Soupir","year":"2024","journal-title":"Genome Biol"}],"container-title":["Journal for ImmunoTherapy of Cancer"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1136\/jitc-2025-014067","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T11:35:17Z","timestamp":1769772917000},"score":1,"resource":{"primary":{"URL":"https:\/\/jitc.bmj.com\/lookup\/doi\/10.1136\/jitc-2025-014067"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":57,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,30]]},"published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1136\/jitc-2025-014067"],"URL":"https:\/\/doi.org\/10.1136\/jitc-2025-014067","relation":{},"ISSN":["2051-1426"],"issn-type":[{"value":"2051-1426","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]}}}