CRATER tumor niches facilitate CD8⁺ T cell engagement and correspond with immunotherapy success

Aya Ludin¹, Georgia L Stirtz², Asaf Tal², Ajit J Nirmal³, Kathleen L Pfaff⁴, Michael Manos⁴, Naomi Besson⁴, Nebiyat Eskndir⁴, Billie Porter⁴, Stephanie M Jones⁴, Hannah M Faulkner⁴, Qiyu Gong⁵, Sophia Liu⁶, Irving Barrera⁵, Lijian Wu⁷, Cecilia Pessoa Rodrigues¹, Aditi Sahu⁸, Elizabeth Jerison⁹, Joao V Alessi¹⁰, Biagio Ricciuti¹⁰, Douglas S Richardson¹¹, Jodi D Weiss², Hadley M Moreau², Meredith E Stanhope², Alexander B Afeyan², James Sefton², Wyatt D McCall², Emily Formato¹, Song Yang¹², Yi Zhou¹², David P Hoytema van Konijnenburg¹³, Hannah L Cole², Miguel Cordova⁸, Liang Deng⁸, Milind Rajadhyaksha⁸, Stephen R Quake¹⁴, Mark M Awad¹⁰, Fei Chen¹⁵, Kai W Wucherpfennig⁷, Peter K Sorger¹⁶, F Stephen Hodi¹⁷, Scott J Rodig¹⁸, George F Murphy¹⁹, Leonard I Zon²⁰

Affiliations

¹ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.
² Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA.
³ Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁴ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
⁷ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
⁸ Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.
⁹ Department of Physics, University of Chicago, Chicago, IL 60637, USA.
¹⁰ Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
¹¹ Harvard Center for Biological Imaging, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
¹² Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.
¹³ Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
¹⁴ Department of Bioengineering and Applied Sciences, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
¹⁵ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
¹⁶ Ludwig Center at Harvard, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
¹⁷ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy, Boston, MA, USA.
¹⁸ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁹ Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
²⁰ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: leonard.zon@enders.tch.harvard.edu.

PMID: 41109214
DOI: 10.1016/j.cell.2025.09.021

Free article

CRATER tumor niches facilitate CD8⁺ T cell engagement and correspond with immunotherapy success

Aya Ludin et al. Cell. 2025.

Free article

. 2025 Oct 17:S0092-8674(25)01089-X.

doi: 10.1016/j.cell.2025.09.021. Online ahead of print.

Authors

Affiliations

¹ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.
² Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA.
³ Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁴ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
⁷ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
⁸ Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.
⁹ Department of Physics, University of Chicago, Chicago, IL 60637, USA.
¹⁰ Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
¹¹ Harvard Center for Biological Imaging, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
¹² Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.
¹³ Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
¹⁴ Department of Bioengineering and Applied Sciences, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
¹⁵ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
¹⁶ Ludwig Center at Harvard, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
¹⁷ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy, Boston, MA, USA.
¹⁸ Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁹ Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
²⁰ Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: leonard.zon@enders.tch.harvard.edu.

PMID: 41109214
DOI: 10.1016/j.cell.2025.09.021

Abstract

T cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identify domains facilitating the immune response during immunotherapy. We identified cancer regions of antigen presentation and T cell engagement and retention (CRATERs) as pockets at the stroma-melanocyte boundaries of zebrafish and human melanoma. CRATERs are rich in antigen-recognition molecules, harboring the highest density of CD8⁺ T cells in tumors. In zebrafish, CD8⁺ T cells formed prolonged interactions with melanoma cells within CRATERs, characteristic of antigen recognition. Following immunostimulatory treatment, CRATERs expanded, becoming the major sites of activated CD8⁺ T cell accumulation and tumor killing. In humans, elevation in CRATER density in biopsies following immune checkpoint blockade (ICB) therapy correlated with a clinical response to therapy. CRATERs are structures that show active tumor killing and may be useful as a diagnostic indicator for immunotherapy success.

Keywords: CD8+ T cells; cancer; immune response; immunotherapy; melanoma; zebrafish.

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Conflict of interest statement

Declaration of interests L.I.Z. is a founder and stockholder of Fate Therapeutics, CAMP4 Therapeutics, Amagma Therapeutics, Scholar Rock, and Branch Biosciences and a consultant for Celularity and Cellarity. F.S.H. reports grants and personal fees related to the submitted work from Bristol-Myers Squibb and Novartis and personal fees from Merck, Surface, Compass Therapeutics, Apricity, 7 Hills Pharma, Bicara, Checkpoint Therapeutics, Bioentre, Gossamer, Iovance, Catalym, Immunocore, Kairos, Rheos, Zumutor, Corner Therapeuitcs, Puretech, Curis, Astra Zeneca, and Solu Therapeutics. Outside the submitted work, F.S.H. has the following patents: Methods for Treating MICA-Related Disorders (#20100111973) with royalties paid; Tumor antigens and uses thereof (#7250291) (issued); Angiopoiten-2 Biomarkers Predictive of Anti-immune checkpoint response (#20170248603) (pending); Compositions and Methods for Identification, Assessment, Prevention, and Treatment of Melanoma using PD-L1 Isoforms (#20160340407) (pending); Therapeutic peptides (#20160046716) (pending); Therapeutic Peptides (#20140004112) (pending); Therapeutic Peptides (#20170022275) (pending); Therapeutic Peptides (#20170008962) (pending); THERAPEUTIC PEPTIDES (#9402905) (issued); METHODS OF USING PEMBROLIZUMAB AND TREBANANIB (pending); Vaccine compositions and methods for restoring NKG2D pathway function against cancers (#10279021) (issued); Antibodies that bind to MHC class I polypeptide-related Sequence A (#10106611) (issued); ANTI-GALECTIN ANTIBODY BIOMARKERS PREDICTIVE OF ANTI-IMMUNE CHECKPOINT AND ANTI-ANGIOGENESIS RESPONSES (#20170343552) (pending); and Antibodies against EDIL3 and methods of use thereof (pending). J.V.A. is on the advisory board of BMS and AstraZeneca and consultant for MSD, Janssen. K.W.W. serves on the scientific advisory boards of DEM BioPharma, Solu Therapeutics, D2M Biotherapeutics, DoriNano, Inc., and Nextechinvest. He is a co-founder of Immunitas Therapeutics and receives sponsored research funding from Fate Therapeutics. He holds equity in TScan Therapeutics. These activities are not related to the research reported in this publication.

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CRATER tumor niches facilitate CD8⁺ T cell engagement and correspond with immunotherapy success

Affiliations

CRATER tumor niches facilitate CD8⁺ T cell engagement and correspond with immunotherapy success

Authors

Affiliations

Abstract

Conflict of interest statement

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Full Text Sources

Research Materials