The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging
Open accessAbstract
The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of tumor-immune populations across individuals, reconciled by overall immune infiltration and enriched co-occurrence of immune subpopulations and checkpoint expression. Spatial enrichment analysis showed immune mixed and compartmentalized tumors, coinciding with expression of PD1, PD-L1, and IDO in a cell-type- and location-specific manner. Ordered immune structures along the tumor-immune border were associated with compartmentalization and linked to survival. These data demonstrate organization in the tumor-immune microenvironment that is structured in cellular composition, spatial arrangement, and regulatory-protein expression and provide a framework to apply multiplexed imaging to immune oncology.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Nuclear segmentation was performed with DeepCell (Van Valen et al., 2016) (https://github.com/vanvalenlab/deepcell-tf) as previously described (Keren et al., 2018), using in-house training and validation MIBI imaging datasets from a variety of human clinical tissue types to ensure reproducibility.”
From Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma (2020) · cites this paper as Keren et al., 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
NIH Image to ImageJ: 25 years of image analysis
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012) · Nature Methods · doi:10.1038/nmeth.2089 · Cited by 64,638
PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989
Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review
Wanchoo, R., Karam, S., Uppal, N. N., Barta, V. S., Deray, G., Devoe, C., Launay‐Vacher, V., Jhaveri, K. D., & on behalf of Cancer and Kidney International Network Workgroup on Immune Checkpoint Inhibitors (2017) · American Journal of Nephrology · doi:10.1159/000455014 · Cited by 15,320
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883 · cited 1×
“Since H3K9ac was shown to be correlated with open chromatin and H3K27me3 with closed chromatin (Kouzarides, 2007), these global changes in their ratios may indicate that cells on the tumor border are more transcriptionally active than those in the tumor center.”
Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma
Larkin, J., Chiarion-Sileni, V., Gonzalez, R., Grob, J. J., Cowey, C. L., Lao, C. D., Schadendorf, D., Dummer, R., Smylie, M., Rutkowski, P., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1504030 · Cited by 8,157
Cancer immunotherapy using checkpoint blockade
Ribas, A., & Wolchok, J. D. (2018) · Science · doi:10.1126/science.aar4060 · Cited by 6,791
Myeloid-derived-suppressor cells as regulators of the immune system
Gabrilovich, D. I., & Nagaraj, S. (2009) · Nature Reviews Immunology · doi:10.1038/nri2506 · Cited by 6,753
PD-1 blockade induces responses by inhibiting adaptive immune resistance
Tumeh, P. C., Harview, C. L., Yearley, J. H., Shintaku, I. P., Taylor, E. J. M., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014) · Nature · doi:10.1038/nature13954 · Cited by 6,609
Elements of cancer immunity and the cancer–immune set point
Chen, D. S., & Mellman, I. (2017) · Nature · doi:10.1038/nature21349 · Cited by 5,352
Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients
Herbst, R. S., Soria, J.-C., Kowanetz, M., Fine, G. D., Hamid, O., Gordon, M. S., Sosman, J. A., McDermott, D. F., Powderly, J. D., Gettinger, S. N., et al. (2014) · Nature · doi:10.1038/nature14011 · Cited by 5,231
Flagged first, then by citations
Research works printed but not linked: 1
- Haralick, 1973, Textural Features for Image Classification. IEEE Trans. Syst. Man. Cybern, SMC, 3, 610
Cited by
Sorted by citations
Items 601–700 of 1,000
Spatial proteomics of tumor microenvironments reveal why location matters
Piyadasa, H., Angelo, M., & Bendall, S. C. (2023) · Nature Immunology · doi:10.1038/s41590-023-01471-8 · Cited by 9
Immune mechanisms shape the clonal landscape during early progression of prostate cancer
Tshering, L. F., Luo, F., Russ, S., Szenk, M., Rubel, D., Tutuska, K., Rail, J. G., Balázsi, G., Shen, M. M., & Talos, F. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.04.010 · Cited by 9
Komforti, M. K., Badve, S., Harmon, B. E., Lo, Y., & Fineberg, S. (2020) · Histopathology · doi:10.1111/his.14181 · Cited by 9
Fang, T., Wang, Z., Yin, X., Wang, H., Zhang, L., Lin, X., Zhang, X., Wang, Y., & Xue, Y. (2022) · Disease Markers · doi:10.1155/2022/2893336 · Cited by 9
Mass Spectrometry and Mass Spectrometry Imaging-based Thyroid Cancer Analysis
Wang, H.-J., Li, B., Zhang, M., Chai, C., Li, X., Li, N., Xiao, H., & Bian, W. (2022) · Journal of Analysis and Testing · doi:10.1007/s41664-022-00218-y · Cited by 9
Protein Profiling of Breast Cancer for Treatment Decision-Making
Badve, S., & Gökmen‐Polar, Y. (2022) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk_351207 · Cited by 9
Baharlou, H., Canete, N. P., Vine, E. E., Hu, K., Yuan, D., Sandgren, K. J., Bertram, K. M., Nasr, N., Rhodes, J. W., Gosselink, M. P., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111385 · Cited by 9
Recent advancement in the spatial immuno-oncology
To, A., Zou, Y., & Sugimura, R. (2024) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2024.12.003 · Cited by 8
IL-32–producing CD8+ memory T cells define immunoregulatory niches in human cutaneous leishmaniasis
Dey, N. S., Dey, S., Brown, N., Senarathne, S., Reis, L. C., Sengupta, R., Lindoso, J. Â. L., James, S. R., Gilbert, L., Boucher, D., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci182040 · Cited by 11
Engineering tumor spatial heterogeneity in vitro
Chen, C., Zhao, Z., Seah, D. H., Wu, K. Z., Mohanaselvi, S., & Fong, E. L. S. (2025) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2025.115757 · Cited by 9
Yang, F., Li, Z., Lei, L., Zhou, Y., Zhang, X., & Song, G. (2026) · Chemical Society Reviews · doi:10.1039/d4cs00445k · Cited by 8
Robust High-Throughput Phenotyping with Deep Segmentation Enabled by a Web-Based Annotator
Yuan, J., Kaur, D., Zhou, Z., Nagle, M. F., Kiddle, N. G., Doshi, N. A., Behnoudfar, A., Peremyslova, E., Ma, C., Strauss, S. H., et al. (2022) · Plant Phenomics · doi:10.34133/2022/9893639 · Cited by 8
Insights into highly multiplexed tissue images: A primer for Mass Cytometry Imaging data analysis
Zhao, J., Liu, Y., Wang, M., Ma, J., Yang, P., Wang, S., Wu, Q., Gao, J., Chen, M., Qu, G., et al. (2022) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2022.116794 · Cited by 8
PD-L1 protein expression in breast cancer
Saastad, S. A., Skjervold, A. H., Ytterhus, B., Engstrøm, M. J., & Bofin, A. M. (2023) · Journal of Clinical Pathology · doi:10.1136/jcp-2023-208942 · Cited by 8
Self-supervised deep learning for highly efficient spatial immunophenotyping
Zhang, H., AbdulJabbar, K., Grunewald, T., Akarca, A. U., Hagos, Y. B., Sobhani, F., Lecat, C. S. Y., Patel, D., Lee, L. S. H., Rodriguez‐Justo, M., et al. (2023) · EBioMedicine · doi:10.1016/j.ebiom.2023.104769 · Cited by 9
Ehsani, R., Jonassen, I., Akslen, L. A., & Kleftogiannis, D. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad146 · Cited by 8
Identification of cells of leukemic stem cell origin with non-canonical regenerative properties
Hollands, C. G., Boyd, A. L., Zhao, X., Reid, J. C., Henly, C., Elrafie, A., Boylan, D., Broder, E., Kalau, O., Johnson, P. M., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101485 · Cited by 8
SPOT: spatial proteomics through on-site tissue-protein-labeling
Xu, Y., Lih, T. M., Marzo, A. M. D., Li, Q. K., & Zhang, H. (2024) · Clinical Proteomics · doi:10.1186/s12014-024-09505-5 · Cited by 8
Proteomics advances for precision therapy in ovarian cancer
Labrie, M., Kendsersky, N. D., Ma, H., Campbell, L. G., Eng, J. R., Chin, K., & Mills, G. B. (2019) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1666004 · Cited by 8
Identification of non-cancer cells from cancer transcriptomic data
Bortolomeazzi, M., Keddar, M. R., Ciccarelli, F. D., & Benedetti, L. G. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.194445 · Cited by 10
McMahon, N. P., Solanki, A., Wang, L. G., Montaño, A. R., Jones, J. A., Samkoe, K. S., Tichauer, K. M., & Gibbs, S. L. (2021) · Molecular Imaging and Biology · doi:10.1007/s11307-021-01589-x · Cited by 8
Apolipoprotein B Is Associated With the Microenvironment of Cholangiocarcinoma
Xu, X., Chen, D., Feng, X., Hu, J., Ge, J., Yan, C., Zhang, D., Ling, Z., Chen, J., & Wu, J. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.654689 · Cited by 8
Seal, S., Wrobel, J., Johnson, A. M., Nemenoff, R. A., Schenk, E. L., Bitler, B. G., Jordan, K. R., & Ghosh, D. (2022) · BMC Research Notes · doi:10.1186/s13104-022-06097-x · Cited by 8
Rangamuwa, K., Aloe, C. A., Christie, M., Asselin-Labat, M.-L., Batey, D., Irving, L., John, T., Bozinovski, S., Leong, T. L., & Steinfort, D. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1129195 · Cited by 9
PET/CT in Patients with Breast Cancer Treated with Immunotherapy
Vaz, S. C., Graff, S. L., Ferreira, A. R., Debiasi, M., & de Geus‐Oei, L. (2023) · Cancers · doi:10.3390/cancers15092620 · Cited by 9
Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Cytotoxic Human T CellsPreprint
Hartmann, F. J., Mrdjen, D., McCaffrey, E., Glass, D. R., Greenwald, N. F., Bharadwaj, A., Khair, Z., Baranski, A., Baskar, R., Angelo, M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.17.909796 · Cited by 8
Spatial Epitope Barcoding Reveals Subclonal Tumor Patch BehaviorsPreprint
Clavé, X. R., Drainas, A. P., Jiang, S., Bai, Y., Baron, M., Zhu, B., Markovic, M., Coles, G. L., Bassik, M. C., Sage, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.29.449991 · Cited by 8
Greenbaum, S., Averbukh, I., Soon, E., Rizzuto, G. A., Baranski, A., Greenwald, N. F., Kagel, A., Bosse, M. M., Greenwood, E. A., Khair, Z., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.08.459490 · Cited by 8
Creason, A., Watson, C., Gu, Q., Persson, D., Sargent, L., Chen, Y., Lin, J., Sivagnanam, S., Wünnemann, F., Nirmal, A. J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.18.504436 · Cited by 9
Multi-modal mass spectrometry imaging reveals single-cell metabolic states in mammalian liverPreprint
Tian, H., Rajbhandari, P., Tarolli, J. G., Decker, A., Neelakantan, T. V., Angerer, T. B., Zandkarimi, F., Daniels, J., Remotti, H. E., Frache, G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.26.508878 · Cited by 9
A Hitchhiker's guide to high-dimensional tissue imaging with multiplexed ion beam imaging
Yeo, Y. Y., Cramer, P., Deisher, A., Bai, Y., Zhu, B., Yeo, W.-J., Shipp, M. A., Rodig, S. J., & Jiang, S. (2024) · Methods in cell biology · doi:10.1016/bs.mcb.2024.02.018 · Cited by 7
ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma
Wang, W., Liu, D., Yao, J., Yuan, Z., Liang, Y., & Cao, B. (2024) · Medical Science Monitor · doi:10.12659/msm.943523 · Cited by 7
Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data
Samorodnitsky, S., & Wu, M. C. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae522 · Cited by 7
Soupir, A. C., Gadiyar, I., Helm, B. R., Harris, C. R., Vandekar, S., Peres, L. C., Coffey, R. J., Wrobel, J., Ma, S., & Fridley, B. L. (2025) · Statistics and data science in imaging. · doi:10.1080/29979676.2024.2437947 · Cited by 7
Natural killer cells occupy unique spatial neighborhoods in HER2- and HER2+ human breast cancers
Ehlers, F. A. I., Blise, K. E., Betts, C. B., Sivagnanam, S., Kooreman, L. F. S., Hwang, E. S., Bos, G. M. J., Wieten, L., & Coussens, L. M. (2025) · Breast Cancer Research · doi:10.1186/s13058-025-01964-4 · Cited by 7
Guo, X., Chang, M., Li, W., Qian, Z., Guo, H., Xie, C., Bi, W. L., Xing, B., Zhang, F., & Huang, Y. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115584 · Cited by 7
Topological classification of tumour-immune interactions and dynamics
Yang, J., Fang, H., Dhesi, J., Yoon, I. H. R., Bull, J. A., Byrne, H. M., Harrington, H. A., & Grindstaff, G. (2025) · Journal of Mathematical Biology · doi:10.1007/s00285-025-02253-6 · Cited by 11
Dong, K., Gao, Y., Zou, Q., Cui, Y., Han, C., Lin, S., Wang, Z., Tang, C., Cheng, X., Meng, F., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03796-z · Cited by 8
Hanson, G. F., Goundry, K. A., Wessel, R. E., Brown, M. G., Bullock, T. N. J., & Dolatshahi, S. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1642527 · Cited by 7
Coullomb, A., Foulon, C., Haastrecht, B. V., Monsarrat, P., & Pancaldi, V. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101536 · Cited by 6
Abikenari, M. A., Nageeb, G., Ha, J. H., Sjöholm, M., Liu, J., Bergsneider, B. H.-L., Valenzuela, J., Poe, J., Cho, K. B., Verma, R., et al. (2026) · Metabolites · doi:10.3390/metabo16030185 · Cited by 9
The immunology of human breast cancer
Torralba, E. G., Loi, S., Salgado, R., Galluzzi, L., & Buqué, A. (2026) · Nature reviews. Immunology · doi:10.1038/s41577-026-01307-0 · Cited by 8
Pejovic, T. B., Abate, P.-V., Ma, H., Thiessen, J., Corless, C. L., Peterson, A., Allard‐Chamard, H., & Labrie, M. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.903806 · Cited by 10
Opportunities and Challenges in Understanding Atherosclerosis by Human Biospecimen Studies
Elishaev, M., Hodonsky, C. J., Ghosh, S., Finn, A. V., von Scheidt, M., & Wang, Y. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.948492 · Cited by 7
Carpino, G., Overi, D., Onori, P., Franchitto, A., Cardinale, V., Alvaro, D., & Gaudio, E. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231710065 · Cited by 7
Vascular phenotyping of the invasive front in breast cancer using a 3D angiogenesis atlas
Bhargava, A., Popel, A. S., & Pathak, A. P. (2023) · Microvascular Research · doi:10.1016/j.mvr.2023.104555 · Cited by 7
Park, M., Casini, A., & Strittmatter, N. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117304 · Cited by 7
Bhattacharyya, S., Ehsan, S., & Karacosta, L. G. (2023) · Frontiers in Network Physiology · doi:10.3389/fnetp.2023.1256104 · Cited by 7
Saiding, A., Maimaitiyiming, D., Chen, M., Yan, F., Chen, D., Hu, X., & Shi, P. (2023) · PeerJ · doi:10.7717/peerj.16006 · Cited by 7
Radio-immunomics in hepatocellular carcinoma: Unraveling the tumor immune microenvironment
Liu, Q., Zhu, W., Song, F., Lou, T., He, L., Zhou, W., & Feng, Z. (2024) · Meta-Radiology · doi:10.1016/j.metrad.2024.100098 · Cited by 7
UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples
Kochetov, B., Bell, P. D., Garcia, P. S., Shalaby, A. S., Raphael, R., Raymond, B., Leibowitz, B. J., Schoedel, K. E., Brand, R. M., Brand, R. E., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06714-4 · Cited by 7
Yee, W.-L. S., & Drum, C. L. (2020) · Advanced Therapeutics · doi:10.1002/adtp.201900163 · Cited by 7
MIAMI: mutual information-based analysis of multiplex imaging data
Seal, S., & Ghosh, D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac414 · Cited by 7
Changes in the immune landscape of TNBC after neoadjuvant chemotherapy: correlation with relapse
Moamin, M. R., Allen, R. J., Woods, S. L., Brown, J. E., Nunns, H., Juncker‐Jensen, A., & Lewis, C. E. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1291643 · Cited by 7
Batra, H. V., Ding, Q., Pandurengan, R. K., Ibarguen, H. P., Rabassedas, N. B., Şahin, A. A., Wistuba, I. I., Parra, E. R., & Raso, M. G. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1281650 · Cited by 7
Computational modelling in single-cell cancer genomics: methods and future directions
Zhang, A. W., & Campbell, K. R. (2020) · Physical Biology · doi:10.1088/1478-3975/abacfe · Cited by 7
Kalra, J., Baker, J. H. E., Song, J., Kyle, A. H., Minchinton, A. I., & Bally, M. B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22126336 · Cited by 7
Qian, H., Li, H., Xie, J., Lu, X., Li, F., Wang, W., Tang, X., Shi, M., Jiang, L., Li, H., et al. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.682261 · Cited by 7
Spatial Biology of Breast CancerPreprint
Ali, H. R., & West, R. B. (2023) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041335 · Cited by 7
QUICHE reveals structural definitions of anti-tumor responses in triple negative breast cancerPreprint
Ranek, J. S., Greenwald, N. F., Goldston, M., Fullaway, C. C., Sowers, C., Kong, A., Mouron, S. A., Quintela-Fandiño, M., West, R. B., & Angelo, M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.06.631548 · Cited by 6
Greenwald, N. F., Nederlof, I., Sowers, C., Ding, D., Park, S., Kong, A., Houlahan, K. E., Varra, S. R., Graaf, M. D., Geurts, V., et al. (2025) · bioRxiv · doi:10.1101/2025.01.26.634557 · Cited by 7
Advances in spatial multi-omics in tumors
Wang, J., Alhaskawi, A., Dong, Y., Tian, T., Abdalbary, S. A., & Lü, H. (2024) · Tumori Journal · doi:10.1177/03008916241271458 · Cited by 6
Li, Q., Meng, F., Yang, L., García, A. M. D., Parkhats, M. V., Lee, J., Kusamori, K., Nishikawa, M., Gu, H., Li, Q., et al. (2025) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.5c00342 · Cited by 7
Yu, Y., Wang, S., Li, J., Yu, M., McCrocklin, K., Kang, J., Ma, A., Ma, Q., Xu, D. H., & Wang, J. (2025) · Nature Communications · doi:10.1038/s41467-025-63141-7 · Cited by 5
Ennis, C. S., Seen, M., Chen, A., Kang, H., Ilinski, A., Mahdaviani, K., Ko, N. Y., Monti, S., & Denis, G. V. (2025) · Communications Biology · doi:10.1038/s42003-025-08663-y · Cited by 7
Traxel, S., Schmidt, F., Beerli, C., Vuong, D.-V., Speck, R. F., & Bredl, S. (2025) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2024-011057 · Cited by 7
Evaluating cell AI foundation models in kidney pathology with human-in-the-loop enrichment
Guo, J., Lu, S., Cui, C., Deng, R., Yao, T., Tao, Z., Lin, Y., Lionts, M., Liu, Q., Xiong, J., et al. (2025) · Communications Medicine · doi:10.1038/s43856-025-01205-x · Cited by 9
Li, Y., Zhang, Y., Zhang, Y., Wang, Q., Ji, B., Yang, H., & Li, X. (2026) · Precision Clinical Medicine · doi:10.1093/pcmedi/pbaf040 · Cited by 7
Decoding myeloid heterogeneity in glioblastoma: spatial insights from transcriptomics
Cheng, Y., Zhao, W., Xie, M., Zheng, X., Ding, F., & Du, J. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-07873-0 · Cited by 6
Desmoplasia and therapeutic resistance in pancreatic ductal adenocarcinoma
Ghanwatkar, Y., Ramanathan, R., & Mahato, R. I. (2026) · Cancer Letters · doi:10.1016/j.canlet.2026.218618 · Cited by 6
Einhaus, J. F., Gaudilliere, D. K., Hedou, J. J., Feyaerts, D., Ozawa, M. G., Masaki, S., Ganio, E. A., Tsai, A. S., Stelzer, I. A., Bruckman, K. C., et al. (2023) · iScience · doi:10.1016/j.isci.2023.108486 · Cited by 6
Complementing Cell Taxonomies with a Multicellular Analysis of Tissues
Flores, R. O. R., Schäfer, P. S. L., Küchenhoff, L., & Sáez-Rodríguez, J. (2024) · Physiology · doi:10.1152/physiol.00001.2024 · Cited by 8
Bartemes, K. R., Moore, R. M., Novotny, B. C., Pavelko, K. D., Sherman, W. A., Rivera, M., García, J. J., Yin, L. X., Ma, D. J., Moore, E. J., et al. (2025) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-24-2425 · Cited by 6
Kumar, R., Hartmann, F. J., Favaro, P. M. B., Ho, D., Bruce, T., Goldston, M., Spence, A., McCaffrey, E., Bendall, S. C., & Angelo, M. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c04300 · Cited by 6
Prioritizing perturbation-responsive gene patterns using interpretable deep learning
Cui, Y., & Yuan, Z. (2025) · Nature Communications · doi:10.1038/s41467-025-61476-9 · Cited by 6
Spider: a flexible and unified framework for simulating spatial transcriptomics data
Yang, J., Wei, N., Qu, Y., Hu, C., Zhang, W., Liu, L., Wu, H., & Zheng, X. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf562 · Cited by 6
Exploiting Molecular Barcodes in High-Throughput Cellular Assays
Binan, L., Drobetsky, E. A., & Costantino, S. (2019) · SLAS TECHNOLOGY · doi:10.1177/2472630318824337 · Cited by 6
Self-Organizing Maps for Cellular In Silico Staining and Cell Substate Classification
Yuan, E. C., Matusiak, M., Sirinukunwattana, K., Varma, S., Kidziński, Ł., & West, R. B. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.765923 · Cited by 6
High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging
Elhanani, O., Keren, L., & Angelo, M. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1771-7_10 · Cited by 6
Marin‐Carbonne, J., Kiss, A., Bouvier, A., Meibom, A., Baumgartner, L. P., Bovay, T., Plane, F., Escrig, S., & Rubatto, D. (2022) · CHIMIA International Journal for Chemistry · doi:10.2533/chimia.2022.26 · Cited by 6
Chen, H. Y., Palendira, U., & Feng, C. G. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.09.005 · Cited by 6
Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers
Lo, Y., Liu, Y., Kammersgaard, M. B., Koladiya, A., Keyes, T., & Davis, K. L. (2023) · Seminars in Immunopathology · doi:10.1007/s00281-022-00981-1 · Cited by 6
The most likely but largely ignored triggering factor for breast (or all) cancer invasion
Man, Y., Mannion, C. M., Stojadinovic, A., Peoples, G. E., Cho, W. C. S., Fu, S. W., Tan, X., Hsiao, Y.-H., Liu, A., Semczuk, A., et al. (2023) · Journal of Cancer · doi:10.7150/jca.82291 · Cited by 6
Lee, E., Chern, K. T., Nissen, M. D., Wang, X., Huang, C. C., Gandhi, A. K., Bouchard‐Côté, A., Weng, A. P., & Roth, A. J. L. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad242 · Cited by 6
Balcioglu, H. E., Wijers, R., Smid, M., Hammerl, D., Trapman-Jansen, A., Oostvogels, A. A. M., Timmermans, M. A. M., Martens, J. W. M., & Debets, R. (2024) · npj Imaging · doi:10.1038/s44303-024-00022-6 · Cited by 5
Sun, D., Liu, H., & Wang, T. (2020) · Cancer Management and Research · doi:10.2147/cmar.s237981 · Cited by 6
New Technologies to Image Tumors
McNamara, G. T., Lucas, J., Beeler, J. F., Basavanhally, A. N., Lee, G., Hedvat, C. V., Baxi, V. A., Locke, D., Borowsky, A. D., & Levenson, R. M. (2020) · Cancer treatment and research · doi:10.1007/978-3-030-38862-1_2 · Cited by 6
Pourmir, I., Gazeau, B., Basile, H. D. S., & Fabre, E. (2020) · Cancer Drug Resistance · doi:10.20517/cdr.2020.14 · Cited by 5
The prospects of single‐cell analysis in autoimmunity
Sulen, A., Islam, S., Wolff, A. S. B., & Oftedal, B. E. (2020) · Scandinavian Journal of Immunology · doi:10.1111/sji.12964 · Cited by 6
A brief glimpse of a tangled web in a small world: Tumor microenvironment
Talaat, I. M., & Kim, B. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.1002715 · Cited by 6
A Graph Based Neural Network Approach to Immune Profiling of Multiplexed Tissue Samples
Garcia-Martin, N., Malacrino, S., Wojciechowska, M., Campo, L., Jones, H. J. S., Wedge, D. C., Holmes, C. C., Sirinukunwattana, K., Sailem, H., Verrill, C. L., et al. (2022) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc48229.2022.9871251 · Cited by 6
The triple negative breast cancer drugs graveyard: a review of failed clinical trials 2017-2022
Salimbeni, B. T., Corvaja, C., Valenza, C., Zagami, P., & Curigliano, G. (2022) · Expert Opinion on Investigational Drugs · doi:10.1080/13543784.2022.2151433 · Cited by 6
Wang, B. G., Yao, Y., Huang, H., Zhou, J., & Ni, C. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1131259 · Cited by 6
Unraveling the cartography of the cancer ecosystem
Rabbie, R., Lau, D., White, R. M., & Adams, D. J. (2021) · Genome biology · doi:10.1186/s13059-021-02310-5 · Cited by 6
Subcellular localization of drug distribution by super-resolution ion beam imagingPreprint
Rovira‐Clavé, X., Jiang, S., Bai, Y., Barlow, G. L., Bhate, S. S., Coskun, A. F., Han, G., Zhu, B., Ho, C. K., Hitzman, C., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/557603 · Cited by 6
ImPartial: Partial Annotations for Cell Instance SegmentationPreprint
Martinez, N., Sapiro, G., Tannenbaum, A., Hollmann, T. J., & Nadeem, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.20.427458 · Cited by 6
emObject: domain specific data abstraction for spatial omicsPreprint
Baker, E. A. G., Huang, M., Lam, A., Rahim, M. K., Bieniosek, M. F., Wang, B., Zhang, N. R., Mayer, A. T., & Trevino, A. E. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.07.543950 · Cited by 5
High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironmentPreprint
Du, W., Zhou, B., Forjaz, A., Shin, S. M., Wu, F., Crawford, A. J., Nair, P. R., Johnston, A. C., West‐Foyle, H., Tang, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.16.603739 · Cited by 6
Tajima, T., Zhang, W., Han, S., Reitsma, A. J., Harden, J. T., Fuentes, S., Sonehara, A., Esquivel, C. O., Martinez, O. M., & Krams, S. M. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1584916 · Cited by 6
Peng, X., Smithy, J. W., Yosofvand, M., Kostrzewa, C. E., Bleile, M., Ehrich, F. D., Lee, J., Postow, M. A., Callahan, M. K., Panageas, K. S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61821-y · Cited by 5
Metadata
- Authors
- Keren, L., Bosse, M., Marquez, D., Angoshtari, R., Jain, S., Varma, S., Yang, S.-R., Kurian, A., Van Valen, D., West, R., Bendall, S. C., & Angelo, M.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- Corresponding author
- Bendall, Sean C.
- Angelo, Michael
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-09
- Volume
- 174
- Issue
- 6
- Pages
- 1373-1387.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6132072
- OpenAlex
- W2890156321
- Cited by
- 1,183
- References
- 54
- Citations by year
- 2026: 222 · 2025: 147 · 2024: 141 · 2023: 164 · 2022: 153 · 2021: 167 · 2020: 105 · 2019: 74 · 2018: 9
- FWCI
- 33.83
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- Damon Runyon Cancer Research Foundation (DRG-2292-17, DRG-2017-09)
- EMBO Long-Term fellowship (ALTF 1128-2016)
- NIH F32 Postdoctoral Fellowship
- Burroughs Wellcome PDEP award
- The Allen Discovery Center at Stanford University
- Crowdflower A.I.
- NIH (5R01CA18390402, 1DP2OD022550-01, 1-R00-GM104148-01, 5U19AI116484-02, U19 AI104209, 1-DP5-OD019822, 1R01AG056287-01, 1R01AG057915-01, 1U24CA224309-01)
- Bill and Melinda Gates Foundation
- Stanford Cancer Institute (NSF ECCS-1542152)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
- Keywords
- triple-negative breast cancer, tumor immune microenvironment, MIBI, immune checkpoint molecules, PD-1, PD-L1, IDO, immune cell infiltration, patient survival
- MeSH terms
- Machine Learning, Lymphocyte Activation Gene 3 Protein, Female, Humans, Lymphocytes, Mass Spectrometry, Antigens, CD, Cluster Analysis, Principal Component Analysis, Indoleamine-Pyrrole 2,3,-Dioxygenase, Kaplan-Meier Estimate, Tumor Microenvironment, B7-H1 Antigen, Programmed Cell Death 1 Receptor, Spatial Analysis, Triple Negative Breast Neoplasms
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
