{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T04:05:47Z","timestamp":1789617947633,"version":"build-2803163510"},"reference-count":141,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T00:00:00Z","timestamp":1774569600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010449","name":"National Center for Tumor Diseases Heidelberg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010449","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["342751"],"award-info":[{"award-number":["342751"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Forschung, Technologie und Raumfahrt","doi-asserted-by":"publisher","award":["01KT2313"],"award-info":[{"award-number":["01KT2313"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Forschung, Technologie und Raumfahrt","doi-asserted-by":"publisher","award":["TRANSCAN-2021-228-ImmuMet"],"award-info":[{"award-number":["TRANSCAN-2021-228-ImmuMet"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001661","name":"Heidelberg University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005677","name":"German Jos\u00e9 Carreras Foundation for Leucemia","doi-asserted-by":"publisher","award":["03R\/2021"],"award-info":[{"award-number":["03R\/2021"]}],"id":[{"id":"10.13039\/501100005677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005941","name":"Dietmar Hopp Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005941","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010441","name":"Heidelberg University Medical Faculty Heidelberg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010441","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005972","name":"Deutsche Krebshilfe","doi-asserted-by":"publisher","award":["70116064"],"award-info":[{"award-number":["70116064"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005972","name":"Deutsche Krebshilfe","doi-asserted-by":"publisher","award":["70116282"],"award-info":[{"award-number":["70116282"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["NFDI46\/1"],"award-info":[{"award-number":["NFDI46\/1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["501864659"],"award-info":[{"award-number":["501864659"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["404521405"],"award-info":[{"award-number":["404521405"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cancer Cell"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.ccell.2026.03.016","type":"journal-article","created":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T19:22:03Z","timestamp":1777317723000},"page":"1290-1311.e16","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"title":["Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes"],"prefix":"10.1016","volume":"44","author":[{"given":"Lena","family":"Jassowicz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangyoumin","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolf","family":"Warta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatima","family":"Heinicke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Am\u00e9lie","family":"W\u00f6llner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Briesch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furkan","family":"Sor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Soller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catharina","family":"Lotsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John K.L.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang-Gyun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Aubert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Scheer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoqing","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Knoll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Schlegel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas","family":"Frank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Dao Trong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerhard","family":"Jungwirth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amin I.","family":"Nohman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kendra","family":"Maa\u00df","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niels","family":"Grabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mandy","family":"Barthel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Butz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Lulay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Zucknick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Bortolomeazzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pooja","family":"Sant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Thewes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Michel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo","family":"Fremd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Schneeweiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chong","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karsten","family":"Rippe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Abdollahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"von Deimling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Unterberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandro M.","family":"Krieg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan-Philipp","family":"Mallm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Lichter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Zapatka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Seiffert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christel","family":"Herold-Mende","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ccell.2026.03.016_bib1","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":"10.1016\/j.ccell.2026.03.016_bib2","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/s41572-019-0111-2","article-title":"Breast cancer","volume":"5","author":"Harbeck","year":"2019","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.ccell.2026.03.016_bib3","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1200\/PO.20.00248","article-title":"CATCH: A Prospective Precision Oncology Trial in Metastatic Breast Cancer","volume":"5","author":"Hlevnjak","year":"2021","journal-title":"JCO Precis. Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib4","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1056\/NEJMoa1813904","article-title":"Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer","volume":"380","author":"Andr\u00e9","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib5","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1002\/ijc.70208","article-title":"Delivering precision oncology in metastatic breast cancer: Clinical impact of comprehensive genomic profiling-The CATCH experience","volume":"158","author":"Hlevnjak","year":"2026","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib6","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1093\/neuonc\/noaa285","article-title":"The Incidence of Brain Metastases Among Patients with Metastatic Breast Cancer: A Systematic Review and Meta-Analysis","volume":"23","author":"Kuksis","year":"2021","journal-title":"Neuro Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib7","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1016\/j.annonc.2021.07.016","article-title":"EANO-ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up of patients with brain metastasis from solid tumours","volume":"32","author":"Le Rhun","year":"2021","journal-title":"Ann. Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib8","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.1200\/JCO.20.01255","article-title":"Survival in Patients With Brain Metastases: Summary Report on the Updated Diagnosis-Specific Graded Prognostic Assessment and Definition of the Eligibility Quotient","volume":"38","author":"Sperduto","year":"2020","journal-title":"J. Clin. Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib9","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1007\/s10549-011-1372-y","article-title":"Unfavourable pattern of metastases in M0 breast cancer patients during 1978-2008: a population-based analysis of the Munich Cancer Registry","volume":"128","author":"van den Hurk","year":"2011","journal-title":"Breast Cancer Res. Treat."},{"key":"10.1016\/j.ccell.2026.03.016_bib10","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/nrclinonc.2015.215","article-title":"Clinical relevance of host immunity in breast cancer: from TILs to the clinic","volume":"13","author":"Savas","year":"2016","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib11","doi-asserted-by":"crossref","first-page":"6175","DOI":"10.1038\/s41467-020-19933-0","article-title":"Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome","volume":"11","author":"Park","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib12","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1056\/NEJMoa2202809","article-title":"Pembrolizumab plus Chemotherapy in Advanced Triple-Negative Breast Cancer","volume":"387","author":"Cortes","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib13","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1056\/NEJMoa2112651","article-title":"Event-free Survival with Pembrolizumab in Early Triple-Negative Breast Cancer","volume":"386","author":"Schmid","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib14","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1016\/j.cell.2020.05.007","article-title":"Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells","volume":"181","author":"Klemm","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib15","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1016\/j.cell.2020.04.055","article-title":"Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes","volume":"181","author":"Friebel","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib16","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41586-022-05680-3","article-title":"Single-cell spatial immune landscapes of primary and metastatic brain tumours","volume":"614","author":"Karimi","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib17","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.cell.2021.12.043","article-title":"Cellular architecture of human brain metastases","volume":"185","author":"Gonzalez","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib18","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2021-002684","article-title":"Spatially resolved analysis of the T cell immune contexture in lung cancer-associated brain metastases","volume":"9","author":"Lu","year":"2021","journal-title":"J. Immunother. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib19","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s00401-020-02256-1","article-title":"Multi-omic molecular profiling reveals potentially targetable abnormalities shared across multiple histologies of brain metastasis","volume":"141","author":"Fukumura","year":"2021","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.ccell.2026.03.016_bib20","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1056\/NEJMoa1805453","article-title":"Combined Nivolumab and Ipilimumab in Melanoma Metastatic to the Brain","volume":"379","author":"Tawbi","year":"2018","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib21","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/S1470-2045(18)30139-6","article-title":"Combination nivolumab and ipilimumab or nivolumab alone in melanoma brain metastases: a multicentre randomised phase 2 study","volume":"19","author":"Long","year":"2018","journal-title":"Lancet Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib22","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/S1470-2045(20)30111-X","article-title":"Pembrolizumab for management of patients with NSCLC and brain metastases: long-term results and biomarker analysis from a non-randomised, open-label, phase 2 trial","volume":"21","author":"Goldberg","year":"2020","journal-title":"Lancet Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib23","doi-asserted-by":"crossref","DOI":"10.15252\/emmm.202013412","article-title":"The immune suppressive microenvironment affects efficacy of radio-immunotherapy in brain metastasis","volume":"13","author":"Niesel","year":"2021","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib24","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1158\/1078-0432.CCR-23-0433","article-title":"CDK4\/6 inhibition sensitizes intracranial tumors to PD-1 blockade in preclinical models of brain metastasis","volume":"30","author":"Nayyar","year":"2024","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib25","doi-asserted-by":"crossref","DOI":"10.1172\/JCI169314","article-title":"Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors","volume":"133","author":"Sun","year":"2023","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.ccell.2026.03.016_bib26","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1038\/s41591-023-02392-7","article-title":"Pembrolizumab in brain metastases of diverse histologies: phase 2 trial results","volume":"29","author":"Brastianos","year":"2023","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib27","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1158\/2159-8290.CD-21-0976","article-title":"Tumor Immune Microenvironment of Brain Metastases: Toward Unlocking Antitumor Immunity","volume":"12","author":"Strickland","year":"2022","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.03.016_bib28","doi-asserted-by":"crossref","DOI":"10.1080\/2162402X.2015.1057388","article-title":"Density of tumor-infiltrating lymphocytes correlates with extent of brain edema and overall survival time in patients with brain metastases","volume":"5","author":"Berghoff","year":"2016","journal-title":"OncoImmunology"},{"key":"10.1016\/j.ccell.2026.03.016_bib29","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13058-016-0702-8","article-title":"Immune response in breast cancer brain metastases and their microenvironment: the role of the PD-1\/PD-L axis","volume":"18","author":"Duchnowska","year":"2016","journal-title":"Breast Cancer Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib30","doi-asserted-by":"crossref","first-page":"2146","DOI":"10.1093\/neuonc\/noac136","article-title":"A comprehensive profiling of the immune microenvironment of breast cancer brain metastases","volume":"24","author":"Griguolo","year":"2022","journal-title":"Neuro Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib31","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/j.ijrobp.2009.08.025","article-title":"Diagnosis-specific prognostic factors, indexes, and treatment outcomes for patients with newly diagnosed brain metastases: a multi-institutional analysis of 4,259 patients","volume":"77","author":"Sperduto","year":"2010","journal-title":"Int. J. Radiat. Oncol. Biol. Phys."},{"key":"10.1016\/j.ccell.2026.03.016_bib32","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1073\/pnas.1322098111","article-title":"Human breast cancer metastases to the brain display GABAergic properties in the neural niche","volume":"111","author":"Neman","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.03.016_bib33","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1038\/346648a0","article-title":"Cerebellar GABAA receptor selective for a behavioural alcohol antagonist","volume":"346","author":"L\u00fcddens","year":"1990","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib34","doi-asserted-by":"crossref","first-page":"2014","DOI":"10.1158\/2159-8290.CD-20-0841","article-title":"Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome","volume":"11","author":"Liudahl","year":"2021","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.03.016_bib35","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1172\/JCI96313","article-title":"Spatially distinct tumor immune microenvironments stratify triple-negative breast cancers","volume":"129","author":"Gruosso","year":"2019","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.ccell.2026.03.016_bib36","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/s41577-019-0127-6","article-title":"Macrophages as regulators of tumour immunity and immunotherapy","volume":"19","author":"DeNardo","year":"2019","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.ccell.2026.03.016_bib37","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1016\/j.celrep.2017.08.078","article-title":"Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites","volume":"20","author":"Kumar","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.ccell.2026.03.016_bib38","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1126\/science.abl5447","article-title":"Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers","volume":"375","author":"Lowery","year":"2022","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib39","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.adh9562","article-title":"Transcriptome-based identification of tumor-reactive and bystander CD8(+) T cell receptor clonotypes in human pancreatic cancer","volume":"15","author":"Meng","year":"2023","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib40","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1186\/s12859-023-05440-8","article-title":"scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis","volume":"24","author":"Wong","year":"2023","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ccell.2026.03.016_bib41","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1038\/s41588-021-00911-1","article-title":"A single-cell and spatially resolved atlas of human breast cancers","volume":"53","author":"Wu","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ccell.2026.03.016_bib42","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41593-020-00789-y","article-title":"Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization","volume":"24","author":"Pombo Antunes","year":"2021","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.ccell.2026.03.016_bib43","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/s41586-019-0903-2","article-title":"Altered human oligodendrocyte heterogeneity in multiple sclerosis","volume":"566","author":"J\u00e4kel","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib44","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41586-021-03465-8","article-title":"Comparative cellular analysis of motor cortex in human, marmoset and mouse","volume":"598","author":"Bakken","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib45","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1038\/s41467-023-36790-9","article-title":"A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data","volume":"14","author":"De Falco","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib46","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1126\/science.1254257","article-title":"Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma","volume":"344","author":"Patel","year":"2014","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib47","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib48","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature20123","article-title":"Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma","volume":"539","author":"Tirosh","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib49","doi-asserted-by":"crossref","DOI":"10.1126\/science.aai8478","article-title":"Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq","volume":"355","author":"Venteicher","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.ccell.2026.03.016_bib50","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1016\/j.cell.2017.10.044","article-title":"Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer","volume":"171","author":"Puram","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib52","doi-asserted-by":"crossref","first-page":"2098","DOI":"10.1038\/s41593-019-0532-y","article-title":"Mapping microglia states in the human brain through the integration of high-dimensional techniques","volume":"22","author":"Sankowski","year":"2019","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.ccell.2026.03.016_bib53","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","article-title":"A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease","volume":"169","author":"Keren-Shaul","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib54","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1016\/j.cell.2022.02.021","article-title":"Tissue-resident FOLR2(+) macrophages associate with CD8(+) T cell infiltration in human breast cancer","volume":"185","author":"Nalio Ramos","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib55","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1038\/s41591-018-0078-7","article-title":"Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis","volume":"24","author":"Savas","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib56","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.immuni.2020.06.010","article-title":"Sensing of ATP via the Purinergic Receptor P2RX7 Promotes CD8(+) Trm Cell Generation by Enhancing Their Sensitivity to the Cytokine TGF-\u03b2","volume":"53","author":"Borges da Silva","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.03.016_bib57","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abe6968","article-title":"Human cytomegalovirus expands a CD8(+) T cell population with loss of BCL11B expression and gain of NK cell identity","volume":"6","author":"Sottile","year":"2021","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.ccell.2026.03.016_bib58","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1016\/j.cell.2023.03.006","article-title":"Immune checkpoint therapy-current perspectives and future directions","volume":"186","author":"Sharma","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib59","doi-asserted-by":"crossref","first-page":"6439","DOI":"10.4049\/jimmunol.179.10.6439","article-title":"Preferential migration of T regulatory cells induced by IL-16","volume":"179","author":"McFadden","year":"2007","journal-title":"J. Immunol."},{"key":"10.1016\/j.ccell.2026.03.016_bib60","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/s41568-019-0144-6","article-title":"Tertiary lymphoid structures in the era of cancer immunotherapy","volume":"19","author":"Saut\u00e8s-Fridman","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib61","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1158\/0008-5472.CAN-13-1342","article-title":"Dendritic cells in tumor-associated tertiary lymphoid structures signal a Th1 cytotoxic immune contexture and license the positive prognostic value of infiltrating CD8+ T cells","volume":"74","author":"Goc","year":"2014","journal-title":"Cancer Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib62","first-page":"1015","article-title":"MSIsensor: microsatellite instability detection using paired tumor-normal sequence data","volume":"30","author":"Niu","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"key":"10.1016\/j.ccell.2026.03.016_bib63","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/s41523-022-00465-3","article-title":"RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer","volume":"8","author":"Staaf","year":"2022","journal-title":"npj Breast Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib64","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.ccell.2019.01.003","article-title":"Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1\/Anti-CTLA-4 Combined Therapy","volume":"35","author":"Gide","year":"2019","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib65","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1038\/s41591-018-0101-z","article-title":"Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer","volume":"24","author":"Kim","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib66","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.1038\/s12276-020-00493-8","article-title":"Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer","volume":"52","author":"Cho","year":"2020","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib67","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.ccell.2021.05.009","article-title":"Durvalumab with olaparib and paclitaxel for high-risk HER2-negative stage II\/III breast cancer: Results from the adaptively randomized I-SPY2 trial","volume":"39","author":"Pusztai","year":"2021","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib68","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.ccell.2022.05.005","article-title":"Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies","volume":"40","author":"Wolf","year":"2022","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib69","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1016\/S1470-2045(20)30445-9","article-title":"Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study","volume":"21","author":"Marabelle","year":"2020","journal-title":"Lancet Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib70","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.aan6733","article-title":"Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade","volume":"357","author":"Le","year":"2017","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib71","doi-asserted-by":"crossref","DOI":"10.1155\/2014\/651751","article-title":"Microarray-based RNA profiling of breast cancer: batch effect removal improves cross-platform consistency","volume":"2014","author":"Larsen","year":"2014","journal-title":"BioMed Res. Int."},{"key":"10.1016\/j.ccell.2026.03.016_bib72","doi-asserted-by":"crossref","first-page":"2024","DOI":"10.1158\/1078-0432.CCR-10-2567","article-title":"A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance","volume":"17","author":"Miller","year":"2011","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib73","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0028403","article-title":"Homogeneous datasets of triple negative breast cancers enable the identification of novel prognostic and predictive signatures","volume":"6","author":"Karn","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.ccell.2026.03.016_bib74","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"Koboldt","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib75","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/s41467-022-27987-5","article-title":"Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities","volume":"13","author":"Cosgrove","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib76","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abo5871","article-title":"The evolving role of tissue-resident memory T cells in infections and cancer","volume":"8","author":"Yenyuwadee","year":"2022","journal-title":"Sci. Adv."},{"key":"10.1016\/j.ccell.2026.03.016_bib77","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.jhep.2022.02.032","article-title":"T cell exhaustion and residency dynamics inform clinical outcomes in hepatocellular carcinoma","volume":"77","author":"Barsch","year":"2022","journal-title":"J. Hepatol."},{"key":"10.1016\/j.ccell.2026.03.016_bib78","doi-asserted-by":"crossref","DOI":"10.3390\/biomedicines10102454","article-title":"The Abundance of Tumor-Infiltrating CD8(+) Tissue Resident Memory T Lymphocytes Correlates with Patient Survival in Glioblastoma","volume":"10","author":"La Manna","year":"2022","journal-title":"Biomedicines"},{"key":"10.1016\/j.ccell.2026.03.016_bib79","doi-asserted-by":"crossref","first-page":"1828","DOI":"10.1038\/s41416-023-02202-4","article-title":"Cancer-specific tissue-resident memory T-cells express ZNF683 in colorectal cancer","volume":"128","author":"Kitakaze","year":"2023","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib80","doi-asserted-by":"crossref","first-page":"e20201605","DOI":"10.1084\/jem.20201605","article-title":"Tissue-resident memory T cells in tumor immunity and immunotherapy","volume":"218","author":"Ok\u0142a","year":"2021","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib81","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/s41467-023-36430-2","article-title":"FGL2-targeting T cells exhibit antitumor effects on glioblastoma and recruit tumor-specific brain-resident memory T cells","volume":"14","author":"Zhao","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib82","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1038\/s41591-021-01323-8","article-title":"A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer","volume":"27","author":"Bassez","year":"2021","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib83","doi-asserted-by":"crossref","first-page":"3615","DOI":"10.21873\/anticanres.17184","article-title":"Tertiary Lymphoid Structures in Brain Metastases of Lung Cancer: Prognostic Significance and Correlation With Clinical Outcomes","volume":"44","author":"Nohira","year":"2024","journal-title":"Anticancer Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib84","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2024-009232","article-title":"Density of tertiary lymphoid structures predicts clinical outcome in breast cancer brain metastasis","volume":"12","author":"Zhao","year":"2024","journal-title":"J. Immunother. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib85","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/s40478-025-02007-x","article-title":"Identification and characterization of tertiary lymphoid structures in brain metastases","volume":"13","author":"Mughal","year":"2025","journal-title":"Acta Neuropathol. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib86","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/s41586-019-1906-8","article-title":"B cells are associated with survival and immunotherapy response in sarcoma","volume":"577","author":"Petitprez","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib87","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/s41586-019-1922-8","article-title":"B cells and tertiary lymphoid structures promote immunotherapy response","volume":"577","author":"Helmink","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib88","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/s41586-019-1914-8","article-title":"Tertiary lymphoid structures improve immunotherapy and survival in melanoma","volume":"577","author":"Cabrita","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.03.016_bib89","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1016\/S0140-6736(20)32531-9","article-title":"Pembrolizumab plus chemotherapy versus placebo plus chemotherapy for previously untreated locally recurrent inoperable or metastatic triple-negative breast cancer (KEYNOTE-355): a randomised, placebo-controlled, double-blind, phase 3 clinical trial","volume":"396","author":"Cortes","year":"2020","journal-title":"Lancet (London, England)"},{"key":"10.1016\/j.ccell.2026.03.016_bib90","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1056\/NEJMoa1500596","article-title":"PD-1 Blockade in Tumors with Mismatch-Repair Deficiency","volume":"372","author":"Le","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib91","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1038\/s41467-020-17414-y","article-title":"Exhausted T cell signature predicts immunotherapy response in ER-positive breast cancer","volume":"11","author":"Terranova-Barberio","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib92","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1016\/S1470-2045(20)30465-4","article-title":"Trastuzumab emtansine plus atezolizumab versus trastuzumab emtansine plus placebo in previously treated, HER2-positive advanced breast cancer (KATE2): a phase 2, multicentre, randomised, double-blind trial","volume":"21","author":"Emens","year":"2020","journal-title":"Lancet Oncol."},{"key":"10.1016\/j.ccell.2026.03.016_bib93","doi-asserted-by":"crossref","first-page":"4546","DOI":"10.1016\/j.cell.2023.08.043","article-title":"The local microenvironment drives activation of neutrophils in human brain tumors","volume":"186","author":"Maas","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib94","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/s43018-023-00519-w","article-title":"Reciprocal interactions between innate immune cells and astrocytes facilitate neuroinflammation and brain metastasis via lipocalin-2","volume":"4","author":"Adler","year":"2023","journal-title":"Nat. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib95","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1016\/j.ccell.2024.08.012","article-title":"Fibrotic response to anti-CSF-1R therapy potentiates glioblastoma recurrence","volume":"42","author":"Watson","year":"2024","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib96","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.ccell.2023.12.018","article-title":"Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms","volume":"42","author":"Bejarano","year":"2024","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.03.016_bib97","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1038\/s43018-021-00254-0","article-title":"Compensatory CSF2-driven macrophage activation promotes adaptive resistance to CSF1R inhibition in breast-to-brain metastasis","volume":"2","author":"Klemm","year":"2021","journal-title":"Nat. Cancer"},{"key":"10.1016\/j.ccell.2026.03.016_bib98","doi-asserted-by":"crossref","first-page":"1627","DOI":"10.1016\/j.celrep.2019.01.041","article-title":"RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types","volume":"26","author":"Monaco","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.ccell.2026.03.016_bib99","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1038\/s41467-021-22973-9","article-title":"The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments","volume":"12","author":"Grieshaber-Bouyer","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib100","article-title":"Computational framework for prioritizing candidate compounds overcoming the resistance of pancancer immunotherapy","volume":"6","author":"Feng","year":"2025","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib101","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.03.016_bib102","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.ccell.2026.03.016_bib103","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"GigaScience"},{"key":"10.1016\/j.ccell.2026.03.016_bib104","first-page":"882","article-title":"STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data","volume":"37","author":"Andreatta","year":"2021","journal-title":"Bioinformatics (Oxford, England)"},{"key":"10.1016\/j.ccell.2026.03.016_bib105","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1038\/s41467-024-45240-z","article-title":"Semi-supervised integration of single-cell transcriptomics data","volume":"15","author":"Andreatta","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib106","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.03.016_bib107","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","article-title":"Cellpose: a generalist algorithm for cellular segmentation","volume":"18","author":"Stringer","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.03.016_bib108","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/s41592-025-02595-5","article-title":"Cellpose3: one-click image restoration for improved cellular segmentation","volume":"22","author":"Stringer","year":"2025","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.03.016_bib109","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/s41587-021-01044-w","article-title":"Cell segmentation in imaging-based spatial transcriptomics","volume":"40","author":"Petukhov","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.03.016_bib110","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.453","article-title":"scikit-image: image processing in Python","volume":"2","author":"van der Walt","year":"2014","journal-title":"PeerJ"},{"key":"10.1016\/j.ccell.2026.03.016_bib111","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.03.016_bib112","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/s41587-021-00830-w","article-title":"Robust decomposition of cell type mixtures in spatial transcriptomics","volume":"40","author":"Cable","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.03.016_bib113","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1038\/s41592-025-02817-w","article-title":"Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem","volume":"22","author":"Chen","year":"2025","journal-title":"Nat Methods"},{"key":"10.1016\/j.ccell.2026.03.016_bib114","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s13059-021-02286-2","article-title":"Giotto: a toolbox for integrative analysis and visualization of spatial expression data","volume":"22","author":"Dries","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib115","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/s13059-022-02734-7","article-title":"BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies","volume":"23","author":"Li","year":"2022","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib116","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","author":"Gu","year":"2022","journal-title":"iMeta"},{"key":"10.1016\/j.ccell.2026.03.016_bib117","first-page":"2847","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics (Oxford, England)"},{"key":"10.1016\/j.ccell.2026.03.016_bib118","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1038\/s41591-020-0844-1","article-title":"A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors","volume":"26","author":"Slyper","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib119","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-025-97053-9","article-title":"A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues","volume":"15","author":"Ernst","year":"2025","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ccell.2026.03.016_bib121","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1093\/bioinformatics\/btab358","article-title":"Cellsnp-lite: an efficient tool for genotyping single cells","volume":"37","author":"Huang","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.03.016_bib122","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/s13059-019-1865-2","article-title":"Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference","volume":"20","author":"Huang","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib123","doi-asserted-by":"crossref","first-page":"e20","DOI":"10.1182\/blood-2016-05-716480","article-title":"A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation","volume":"128","author":"Nestorowa","year":"2016","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.03.016_bib124","doi-asserted-by":"crossref","DOI":"10.1126\/science.abe6474","article-title":"Pan-cancer single-cell landscape of tumor-infiltrating T cells","volume":"374","author":"Zheng","year":"2021","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib125","doi-asserted-by":"crossref","DOI":"10.1126\/science.abl5197","article-title":"Cross-tissue immune cell analysis reveals tissue-specific features in humans","volume":"376","author":"Dom\u00ednguez Conde","year":"2022","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ccell.2026.03.016_bib126","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.immuni.2024.01.006","article-title":"An atlas of cells in the human tonsil","volume":"57","author":"Massoni-Badosa","year":"2024","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.03.016_bib127","doi-asserted-by":"crossref","first-page":"7303","DOI":"10.4049\/jimmunol.177.10.7303","article-title":"Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression","volume":"177","author":"Martinez","year":"2006","journal-title":"J. Immunol."},{"key":"10.1016\/j.ccell.2026.03.016_bib128","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1038\/nn.4597","article-title":"Transcriptomic analysis of purified human cortical microglia reveals age-associated changes","volume":"20","author":"Galatro","year":"2017","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.ccell.2026.03.016_bib129","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/s41591-023-02673-1","article-title":"Multiomic spatial landscape of innate immune cells at human central nervous system borders","volume":"30","author":"Sankowski","year":"2024","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.03.016_bib131","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib132","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41596-024-01045-4","article-title":"CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics","volume":"20","author":"Jin","year":"2025","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ccell.2026.03.016_bib133","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1186\/s13059-021-02548-z","article-title":"geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq","volume":"22","author":"Missarova","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib134","first-page":"979","article-title":"EBImage--an R package for image processing with applications to cellular phenotypes","volume":"26","author":"Pau","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"10.1016\/j.ccell.2026.03.016_bib135","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0165530","article-title":"DRAQ5 and Eosin ('D&E') as an Analog to Hematoxylin and Eosin for Rapid Fluorescence Histology of Fresh Tissues","volume":"11","author":"Elfer","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.ccell.2026.03.016_bib136","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/B978-0-12-336156-1.50061-6","article-title":"Contrast Limited Adaptive Histogram Equalization","volume":"4","author":"Zuiderveld","year":"1994","journal-title":"Graphics gems"},{"key":"10.1016\/j.ccell.2026.03.016_bib139","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btac805","article-title":"Benchmarking and integration of methods for deconvoluting spatial transcriptomic data","volume":"39","author":"Yan","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.03.016_bib140","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1038\/s41467-023-37168-7","article-title":"A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics","volume":"14","author":"Li","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.03.016_bib142","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/s13059-021-02404-0","article-title":"SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies","volume":"22","author":"Zhu","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib143","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1158\/2159-8290.CD-21-0126","article-title":"Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers","volume":"11","author":"Horak","year":"2021","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.03.016_bib146","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-Seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ccell.2026.03.016_bib147","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1093\/nar\/gkv1507","article-title":"TCGAbiolinks: an R\/Bioconductor package for integrative analysis of TCGA data","volume":"44","author":"Colaprico","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.03.016_bib148","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.03.016_bib149","first-page":"1097","article-title":"Genefu: an R\/Bioconductor package for computation of gene expression-based signatures in breast cancer","volume":"32","author":"Gendoo","year":"2015","journal-title":"Bioinformatics (Oxford, England)"}],"container-title":["Cancer Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535610826001704?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535610826001704?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T12:21:11Z","timestamp":1783081271000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535610826001704"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":141,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S1535610826001704"],"URL":"https:\/\/doi.org\/10.1016\/j.ccell.2026.03.016","relation":{},"ISSN":["1535-6108"],"issn-type":[{"value":"1535-6108","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes","name":"articletitle","label":"Article Title"},{"value":"Cancer Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ccell.2026.03.016","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}