Publications
Featured Publications
Multimodal spatial profiling reveals immune suppression and microenvironment remodeling in fallopian tube precursors to high-grade serous ovarian carcinoma
Kader T, Lin J-R, Hug C, Coy S, Chen Y-A, de Bruijn I, Shih N, Jung, E, ... Santagata S
Cancer Discovery. 2024 Dec 20. https://doi.org/10.1158/2159-8290.CD-24-1366
Ovarian cancer-derived IL-4 promotes immunotherapy resistance
Mollaoglu G, Tepper A, Falcomatà C, Potak HT, Pia L, Amabile A, Mateus-Tique J, Rabinovich N,... Baccarini A, Brown BD. (2024).
AKT and EZH2 inhibitors kill TNBCs by hijacking mechanisms of involution
Schade A, Perurena N, Yang Y, Rodriguez CL, Krishnan A, Loi P, Mastellone GM, Pilla NF,... Cichowski K. (2024).
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution.
Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AC, Jacobson CA, Pelletier RJ,... Lian CG, Murphy GF, Santagata S, Sorger, PK. (2022)
Cancer Discovery, 12(6), 1518–1541. https://doi.org/10.1158/2159-8290.CD-21-1357
Development and validation of time-to-event models to predict metastatic recurrence of localized cutaneous melanoma.
Wan G, Leung BW, DeSimone MS, Nguyen N, Rajeh A, Collier MR, Rashdan H, Roster K,...Semenov YR. (2024).
Journal of the American Academy of Dermatology, 90(2):288-298. https://doi.org/10.1016/j.jaad.2023.08.105
Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer
Guerriero JL, Lin JR, Pastorello RG, Du Z, Chen YA, Townsend M, Shimada K, Hughes ME ... Santagata S (2024).
npj Breast Cancer, 10(2). https://doi.org/10.1038/s41523-023-00605-3
High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers.
Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E,...Sorger PK (2023).
Nature Cancer https://doi.org/10.1038/s43018-023-00576-1
Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma.
Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S.(2023).
Cancer Cell, 41(5):871-886.e10. https://doi.org/10.1016/j.ccell.2023.03.015
Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer.
Lin J-R, Wang S, Coy S, Tyler M, Yapp C, Chen Y-A, Heiser CN, Lau KS, Santagata S, Sorger PK. (2023).
Cell, 186(19), 363-381.e19. https://doi.org/10.1016/j.cell.2022.12.028
Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.
Mehta AK, Cheney EM, Hartl CA, Pantelidou C, Oliwa M, Castrillon JA, Lin, J-R,... Guerriero, J. (2021).
Nature Cancer, 2(1), 66–82. https://doi.org/10.1038/s43018-020-00148-7
Temporal and spatial topography of cell proliferation in cancer.
Gaglia G, Kabraji S, Angyropoulu D, Dai Y, Wang S, Bergholz J, Coy S, Lin J-R, ... Santagata, P. (2022).
Nature Cell Biology, 24(3), 316-326 https://doi.org/10.1038/s41556-022-00860-9
Other Publications
Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.
Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin J-R, Muhlich JL, Mittendorf EA., Santagata S, Guerriero JL, Sorger PK. (2024).
Nature Methods https://doi.org/10.1038/s41592-024-02328-0
Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers
Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M,... Cichowski K. (2024).
Cancer Discovery https://doi.org/10.1158/2159-8290.CD-23-0866
Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence: A Pilot Study.
Maliga Z, Kim DY, Bui AN, Lin JR, Dewan AK, Jadeja S, Murphy GF, Nirmal AJ, Lian CG, Sorger PK, LeBoeuf NR. (2024).
Journal of the American Academy of Dermatology, 90(2):288-298. https://doi.org/10.1016/j.jid.2024.01.024
Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft Tissue Sarcomas: Clinical Outcomes and Biological Correlates
Haddox CL, Nathenson MJ, Mazzola E, Lin JR, Baginska J, Nau A, Weirather JL, Choy E, Marino-Enriquez A, Morgan JA, Cote GM, Merriam P, Wagner AJ, Sorger PK, Santagata S, George S. (2024).
Clinical Cancer Research https://doi.org/10.1158/1078-0432.CCR-23-2250
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data.
Wan G, Maliga Z, Yan B, Vallius T, Shi Y, Khattab S, Chang C, Nirmal AJ, Yu K-H, Liu D, Lian CG, DeSimone MS, Sorger PK, Semenov YR.(2024).
Briefings in Bioinformatics https://doi.org/10.1093/bib/bbae189
Influence of melanoma type on incidence and downstream implications of cutaneous immune-related adverse events in the setting of immune checkpoint inhibitor therapy.
Nguyen N, Wan G, Ugwu-Dike P, Alexander NA, Raval N, Zhang S, Jairath R, Phillipps J,... Semenov YR. (2023).
Journal of the American Academy of Dermatology. 88(6):1308-1316 https://doi.org/10.1016/j.jaad.2023.02.014
Increased risk of cutaneous immune-related adverse events in patients treated with talimogene laherparepvec and immune checkpoint inhibitors: A multi-hospital cohort study
Leung BW, Wan G, Nguyen N, Rashdan H, Zhang S, Chen W, Cohen S, Boland GM, Sullivan RJ, Fadden RM, Kaufman HL, Kwatra SG, LeBoeuf NR, Semenov YR.(2023).
Journal of the American Academy of Dermatology, 88(6):1265-1270 https://doi.org/10.1016/j.jaad.2023.02.017
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues.
Yapp C, Novikov E, Jang W-D, Chen Y-A, Cicconet M, Maliga Z, Jacobson CA, Wei D, Santagata S, Pfister H, Sorger PK. (2022).
Nature Communications Biology https://doi.org/10.1038/s42003-022-04076-3
Prediction of early-stage melanoma recurrence using clinical and histopathologic features.
Wan G, Nguyen N, Liu F, DeSimone MS, Leung BW, Rajeh A, Collier MR, Choi MS,... Semenov YR. (2022).
NPJ Precision Oncology. 6(1):79 https://doi.org/10.1038/s41698-022-00321-4
The impact of stage-related features in melanoma recurrence prediction: A machine learning approach.
Wan G, Leung B, Nguyen N, DeSimone MS, Liu F, Choi MS, Ho D, Laucks V, Semenov YR (2022).
JAAD International, 10: P28-30 https://doi.org/10.1016/j.jdin.2022.08.014
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.
Muhlich J, Chen Y-A, Yapp C, Russell R, Santagata S, Sorger PK. (2022).
Bioinformatics, btac544 https://doi.org/10.1093/bioinformatics/btac544
Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients.
Wu H-J, Temko D, Maliga M, Moreira A, Sei E, Conterno Minussi D, Dean J, Lee C, Xu Q,... Michor F. (2022).
Cell Genomics, 2(8), 100165. https://doi.org/10.1016/j.xgen.2022.100165
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
Rumana R, Chen Y-A, Hoffer J, Muhlich JL, Lin J-R, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. (2022).
Nature Biomedical Engineering, 6(5):515-526. https://pubmed.ncbi.nlm.nih.gov/34750536/
Scope2Screen: Focus+context techniques for pathology tumor assessment in multivariate image data.
Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich JL, Ritch CC, Gaglia G, Coy S, Chen Y-A, Lin J-R, Santagata S, Sorger PK, Pfister H. (2022).
IEEE Transactions on Visualization and Computer Graphics, 28(1), 259-269. https://pubmed.ncbi.nlm.nih.gov/34606456/
A human breast atlas integrating single-cell proteomics and transcriptomics.
Gray GK, Li CM-C, Rosenbluth JM, Selfors LM, Girnius N, Lin J-R, Schackmann RCJ, Goh WL, Moore K,...Brugge JS. (2022).
Developmental Cell, 57(22), 1400-1420. https://doi.org/10.1016/j.devcel.2022.05.003
The immunoregulatory landscape of human tuberculosis granulomas.
McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF,... Angelo M. (2022).
Nature Immunology, 23(2):318–329. https://doi.org/10.1038/s41590-021-01121-x
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro D, Sokolov A, Yapp C, Muhlich JL, Hess J, Lin J-R, Chen Y-A, Nariya MK,... Sorger PK. (2021)
Nature Methods, 19, 311–315 https://doi.org/10.1038/s41592-021-01308-y
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen Y-A, Sudar D, Xie Y, Muhlich J, ... Sorger PK. (2022).
Nature Methods, 19, 262–267 https://doi.org/10.1038/s41592-022-01415-4
Evolution of delayed resistance to immunotherapy in a melanoma responder.
Liu D, Lin J-R, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A,... Boland, GM. (2021).
Nature Medicine, 27, 985–992. https://doi.org/10.1038/s41591-021-01331-8
Micro-region transcriptomics of fixed human tissue using pick-seq.
Maliga Z, Nirmal AJ, Ericson NG, Boswell SA, U’Ren L, Podyminogin R, Chow J, Chen Y-A,… Sorger PK. (2021).
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.
Jerby-Arnon L, Neftel C, Shore ME, Weisman HR, Mathewson ND, McBride MJ, Haas B, Izar B, … Regev A. (2021).
Nature Medicine, 27(2), 289–300. https://doi.org/10.1038/s41591-020-01212-6
Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer.
Keenan TE, Li T, Vallius T, Guerriero JL, Tayob N, Kochupurakkal B, Davis J, Pastorello R,... Tolaney SM. (2021).
Clinical Cancer Research, 2(1), 66-82. https://doi.org/10.1158/1078-0432.CCR-20-3089
HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor.
Hemming ML, Coy S, Lin J-R, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH,... Santagata S. (2021).
Clinical Cancer Research, 27(6), 1706-19. https://doi.org/10.1158/1078-0432.CCR-20-3538
Concurrent dexamethasone limits the clinical benefit of immune checkpoint blockade in glioblastoma.
Iorgulescu JB, Gokhale PC, Speranza MC, Eschle BK, Poitras MJ, Wilkens MK, Soroko KM,... Reardon DA. (2021).
Clinical Cancer Research, 27(1), 276–87. https://doi.org/10.1158/1078-0432.CCR-20-2291
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity.
Ringel AE, Drijvers JM, Baker GJ, Catozzi A, García-Cañaveras JC, Gassaway BM, Miller BC, ... Haigis MC. (2020).
Cell, 183(7), 1848-1866.e26. https://doi.org/10.1016/j.cell.2020.11.009
Channel embedding for informative protein identification from highly multiplexed images.
Magid SM, Jang W-D, Schapiro D, Wei D, Tompkin J, Sorger PK, Pfister, H. (2020).
Medical Image Computing and Computer-Assisted Intervention (MICCAI), 12265, 3–13. https://doi.org/10.1007/978-3-030-59722-1_1
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung.
Kalocsay M, Maliga Z, Nirmal AJ, Eisert RJ, Bradshaw GA, Solomon IH, Chen Y-A, Pelletier RJ, ... Sorger PK. (2020).
Minerva: A light-weight, narrative image browser for multiplexed tissue images.
Hoffer J, Rashid R, Muhlich JL, Chen Y-A, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. (2020).
Journal of Open Source Software, 5(54), 2579 https://doi.org/10.21105/joss.02579
SARS-CoV-2 infection protects against rechallenge in rhesus macaques.
Chandrashekar A, Liu J, Martinot AJ, McMahan K, Mercado NB, Peter L, Tostanoski LH,... Barach DH. (2020).
Science 369(6505): 812–17. https://doi.org/10.1126/science.abc4776
Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1.
Hemming ML, Nathenson MJ, Lin J-R, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M, Sicinska E, Demetri GD, Santagata S. (2020).
JCO Precision Oncology, 4, 79–90. https://doi.org/10.1200/po.19.00287
Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.
Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C,… Konstantinopoulos PA. (2020).
Nature Communications, 11(1), 1459. https://doi.org/10.1038/s41467-020-15315-8
HSF1 phase transition mediates stress adaptation and cell fate decisions.
Gaglia G, Rashid R, Yapp C, Joshi GN, Li CG, Lindquist SL, Sarosiek KA, Whitesell L, Sorger PK, Santagata S. (2020).
Nature Cell Biology, 22(2), 151–158. https://doi.org/10.1038/s41556-019-0458-3
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.
Krueger R, Beyer J, Jang W-D, Kim NW, Sokolov A, Sorger PK, Pfister H. (2020).
IEEE Transactions on Visualization and Computer Graphics, 26(1), 227–237. https://doi.org/10.1109/TVCG.2019.2934547
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.
Du Z, Lin J-R, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. (2019).
Nature Protocols, 14(10), 2900–2930. https://doi.org/10.1038/s41596-019-0206-y
Mismatch repair deficiency in high-grade meningioma: A rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade.
Dunn IF, Du Z, Touat M, Sisti MB, Wen PY, Umeton R, Dubuc AM, Ducar M,... Reardon DA. (2018).
JCO Precision Oncology, 2018. https://doi.org/10.1200/PO.18.00190
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.
Rashid R, Gaglia G, Chen Y-A, Lin J-R, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. (2019).
Scientific Data, 6(1), 323. https://doi.org/10.1038/s41597-019-0332-y
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-cycif and conventional optical microscopes.
Lin J-R, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger, PK. (2018).
ELife, 7. https://doi.org/10.7554/eLife.31657
Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma.
Coy S, Rashid R, Lin JR, Du Z, Donson AM, Hankinson TC, Foreman NK, ... Santagata S. (2018).
Neuro-Oncology, 20(8), 1101-12. https://doi.org/10.1093/neuonc/noy035
A cancer cell program promotes t cell exclusion and resistance to checkpoint blockade.
Jerby-Arnon, L., Shah, P., Cuoco, M. S., Rodman, C., Su, M.-J., Melms, J. C., Leeson, R., Kanodia, A., … Regev, A. (2018).
Cell, 175(4), 984-997.e24. https://doi.org/10.1016/j.cell.2018.09.006
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C,… Garraway LA. (2016).
Science, 352(6282), 189–196. https://doi.org/10.1126/science.aad0501