Publications
Ludwig Branch at Lausanne
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.
Duraiswamy, J., Turrini, R., Minasyan, A., Barras, D., Casado, J., Crespo, I., Grimm, A.J., Genolet, R., Benedetti, F., Ioannidou, K., Castro, W., Neal, C., Moriot, A., Tissot, S., Anstett, V., Fahr, N., Tanyi, J. L., Eiva, M., Montone, K. T., Jacobson, C. A., Wulff Westergaard, M. C., Svane, I. M., Kandalaft, L. E., Delorenzi, M., Sorger, P. K., Farkkila, A., Carmona, S., Foukas, P. G., Powell Jr, D. J., Rusakiewicz, S., Dangaj, D., Doucey, M-A., Coukos G (2021).
Cancer Cell, 39(12), 1623-1642 https://www.doi.org/10.1016/j.ccell.2021.10.008
Ludwig Center at MIT
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
Antigen dominance hierarchies shape TCF1+ progenitor CD8 t cell phenotypes in tumors.
Burger, M., Cruz, A.M. Crossland, G.E., Gaglia, G., Ritch, C.C., Blatt, S.E., Bhutkar, A., Canner, D., Kienka, T., Tavana, S., Garmilla, A., Schenkel, J., Hillman, M., de los Rios Kobara, I., Li, A., Hwang, W., Westcott, P. Regev, A., Santagata, S., & Jacks, T.E. (2021).
Cell, 184(19), 4996-5014 http://dx.doi.org/10.2139/ssrn.3770111
Ludwig Center at Harvard
Systematic characterization of antibody-drug conjugate targets in central nervous system tumors.
Coy S, Lee JS, Chan SJ, Woo T, Jones J, Alexandrescu S, Wen PY, Sorger PK, Ligon KL, Santagata S (2024).
Neuro Oncol, 26(3), 458-472. https://doi.org/10.1093/neuonc/noad205
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).
J Invest Dermatol. S0022-202X(24):00107-6. https://doi.org/10.1016/j.jid.2024.01.024
Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity.
Zhang X, Pant SM, Ritch CC, Tang H-Y, Shao H, Dweep H, Gong Y-Y, Brooks R, Brafford P, Wolpaw AJ, Lee Y, Weeraratna A, Sehgal A, Herlyn M, Kossenkov A, Speicher D, Sorger PK, Santagata S, Dang CV. (2024).
Nature Communications, 15(1), 633. https://doi.org/10.1038/s41467-024-44778-2
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).
Clin Cancer Res. https://doi.org/10.1158/1078-0432.CCR-23-2250
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, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK (2023).
Nature Cancer https://doi.org/10.1038/s43018-023-00576-1
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, C.N., Lau, K.S., Santagata, S., Sorger, P.K. (2023).
Cell, 186(19), 363-381.e19. https://doi.org/10.1016/j.cell.2022.12.028
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, P.K. (2022).
Bioinformatics, btac544 https://doi.org/10.1093/bioinformatics/btac544
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution.
Nirmal, A.J., Maliga, Z., Vallius, T., Quattrochi, B., Chen, A.C., Jacobson, C.A., Pelletier, R.J., ... Lian, C.G., Murphy, G.F., Santagata, S., Sorger, P.K. (2022)
Cancer Discovery, 12(6), 1518–1541. https://doi.org/10.1158/2159-8290.CD-21-1357
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, J.L., Lin, J.-R., Krueger, R., Pfister, H., Mitchell, R., Santagata, S., & Sorger, P. K. (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, J.L., Ritch, C.C., Gaglia, G., Coy, S., Chen Y.-A., Lin J-.R., Santagata, S., Sorger, P.K., & 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, G.K., Li, C.M.-C., Rosenbluth, J.M., Selfors, L.M., Girnius, N., Lin, J.-R., Schackmann, R.C.J., Goh, W.L., Moore, K., Shapiro, H.K., Mei, S., D’Andrea, K., Nathanson, K.L., Sorger, P.K., Santagata, S., Regev, A., Garber, J.E., Dillon, D.A., Brugge, J.S. (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
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S.M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J., ... Sorger, P.K. (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, E.J., Kasumova, G.G., Heyde, A., Shi, A., Kraya, A., ... Boland, G.M. (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, A. J., Ericson, N. G., Boswell, S. A., U’Ren, L., Podyminogin, R., Chow, J., Chen, Y.-A., … Sorger, P. K. (2021).
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro, D., Sokolov, A., Yapp, C., Muhlich, J.L., Hess, J., Lin, J-R., Chen, Y-A., Nariya, M.K., Baker, G.J., Ruokonen, J., Maliga, Z., Jacobson, C.A., Farhi, S.L., Abbondanza, D., McKinley, E.T., Betts, C., Regev, A., Coffey, R.J., Coussens, L.M., Santagata, S., & Sorger, P.K. (2022)
Nature Methods 19, 311–315 https://doi.org/10.1038/s41592-021-01308-y
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.
Jerby-Arnon, L., Neftel, C., Shore, M. E., Weisman, H. R., Mathewson, N. D., McBride, M. J., Haas, B., Izar, B., … Regev, A. (2021).
Nature Medicine, 27(2), 289–300. https://doi.org/10.1038/s41591-020-01212-6
HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor.
Hemming, M.L., Coy, S., Lin, J.-R., Andersen, J.L., Przybyl, J., Mazzola, E., Abdelhamid Ahmed, A.H., ... Santagata, S. (2021).
Clinical Cancer Research, 27(6), 1706-19. https://doi.org/10.1158/1078-0432.CCR-20-3538
Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.
Mehta, A.K., Cheney, E.M., Hartl, C.A., Pantelidou, C., Oliwa, M., Castrillon, J.A., Lin, Lin, J.-R., ... Guerriero, J. (2021).
Nature Cancer, 2(1), 66–82. https://doi.org/10.1038/s43018-020-00148-7
Concurrent dexamethasone limits the clinical benefit of immune checkpoint blockade in glioblastoma.
Iorgulescu, J.B., Gokhale, P.C., Speranza, M.C., Eschle, B.K., Poitras, M.J., Wilkens, M.K., Soroko, K.M., ... Reardon, D.A. (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, A.E., Drijvers, J.M., Baker, G.J., Catozzi, A., García-Cañaveras, J.C., Gassaway, B.M., Miller, B.C., ... Haigis, M.C. (2020).
Cell, 183(7), 1848-1866.e26. https://doi.org/10.1016/j.cell.2020.11.009
Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.
Mehta, A.K., Cheney, E.M., Hartl, C.A., Pantelidou,C., Oliwa, M., Castrillon, J.A., Lin, J.-R., Hurst, K.E., de Oliveira Taveira, M., Johnson, N.T., Oldham, W.M., Kalocsay, M., Berberich, M.J., Boswell, S.A., Kothari, A., Johnson, S., Dillon, D.A., Lipschitz, M., Rodig, S., Santagata, S., Garber, J.E., Tung, N., Yélamos, J., Thaxton, J.E., Mittendorf, E.A., Sorger, P.K., Shapiro, G.I., & Guerriero, J.L. (2021).
Nature Cancer, 2(1), 66-82. https://doi.org/10.1038/s43018-020-00148-7
Channel embedding for informative protein identification from highly multiplexed images.
Magid, S.M., Jang, W.-D., Schapiro, D., Wei, D., Tompkin, J., Sorger, P.K., & 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, A.J., Eisert, R.J., Bradshaw, G.A., Solomon, I. H., Chen, Y-A., Pelletier, R.J., ... Sorger, P.K. (2020).
Minerva: A light-weight, narrative image browser for multiplexed tissue images.
Hoffer, J., Rashid, R., Muhlich, J.L., Chen, Y.-A., Russell, D.P.W., Ruokonen, J., Krueger, R., Pfister, H., Santagata, S., & Sorger, P.K. (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, A.J., McMahan, K., Mercado, N.B., Peter, L., Tostanoski, L.H., ... Barach, D.H. (2020).
Science 369(6505): 812–17. https://doi.org/10.1126/science.abc4776
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
Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1.
Hemming, M. L., Nathenson, M. J., Lin, J.-R., Mei, S., Du, Z., Malik, K., Marino-Enriquez, A., Jagannathan, J. P., Sorger, P. K., Bertagnolli, M., Sicinska, E., Demetri, G. D., & 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, D. C., Casado, J., Jacobson, C. A., Nguyen, H., Kochupurakkal, B., Maliga, Z., Yapp, C., Chen, Y.-A., Schapiro, D., Zhou, Y., Graham, J. R., Dezube, B. J., Munster, P., Santagata, S., Garcia, E., Rodig, S., Lako, A., Chowdhury, D., … Konstantinopoulos, P. A. (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, G. N., Li, C. G., Lindquist, S. L., Sarosiek, K. A., Whitesell, L., Sorger, P. K., & Santagata, S. (2020).
Nature Cell Biology, 22(2), 151–158. https://doi.org/10.1038/s41556-019-0458-3
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, Tahara, RK, Anderson, L, Conway, J, He, MX, Shannon, E, Godin, RE, Sorger, PK, D'Andrea, A, Overmoyer, B, Winer, EP, Mittendorf, EA, Van Allen, EM, Shapiro, GI, & Tolaney, SM. (2021).
Clinical Cancer Research, 2(1), 66-82. https://doi.org/10.1158/1078-0432.CCR-20-3089
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.
Krueger, R., Beyer, J., Jang, W.-D., Kim, N. W., Sokolov, A., Sorger, P. K., & 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, J. C., Izar, B., Sorger, P. K., & Santagata, S. (2019).
Nature Protocols, 14(10), 2900–2930. https://doi.org/10.1038/s41596-019-0206-y
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
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, I. F., Du, Z., Touat, M., Sisti, M. B., Wen, P. Y., Umeton, R., Dubuc, A. M., Ducar, M., Canoll, P. D., Severson, E., Elvin, J. A., Ramkissoon, S. H., Lin, J.-R., Cabrera, L., Acevedo, B., Sorger, P. K., Ligon, K. L., Santagata, S., & Reardon, D.A. (2018).
JCO Precision Oncology, 2018(2), 1-12. https://doi.org/10.1200/PO.18.00190
Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity.
Melms, J. C., Vallabhaneni, S., Mills, C. E., Yapp, C., Chen, J.-Y., Morelli, E., Waszyk, P., Kumar, S., Deming, D., Moret, N., Rodriguez, S., Subramanian, K., Rogava, M., Cartwright, A. N. R., Luoma, A., Mei, S., Brinker, T. J., Miller, D. M., Spektor, A., … Izar, B. (2019).
Cancer Research, 2020(80), 798–810. https://doi.org/10.1158/0008-5472.CAN-19-2330
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, P.M., Santagata, S., & Sorger, P.K. (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, J.R., Du, Z., Donson, A.M., Hankinson, T.C., Foreman, N.K., ... 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., Mei, S., Lin, J.-R., Wang, S., Rabasha, B., Liu, D., Zhang, G., Margolais, C., Ashenberg, O., Ott, P.A., Buchbinder, E. I., Haq, R., … 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, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., Fallahi-Sichani, M., Dutton-Regester, K., Lin, J.-R., Cohen, O., Shah, P., Lu, D., Genshaft, A. S., Hughes, T. K., Ziegler, C. G. K., … Garraway, L. A. (2016).
Science (New York, N.Y.), 352(6282), 189–196. https://doi.org/10.1126/science.aad0501
Atlas Technologies
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
Rashid, R., Chen, Y.-A., Hoffer, J., Muhlich, J. L., Lin, J.-R., Krueger, R., Pfister, H., Mitchell, R., Santagata, S., & Sorger, P. K. (2022)
Nature Biomedical Engineering doi.org/10.1038/s41551-021-00789-8
Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.
Krueger, R., Beyer, J., Jang, W.-D., Kim, N. W., Sokolov, A., Sorger, P. K., & 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, J. C., Izar, B., Sorger, P. K., & Santagata, S. (2019).
Nature Protocols, 14(10), 2900–2930. https://doi.org/10.1038/s41596-019-0206-y
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
Ludwig Center at the University of Chicago
PARP and PI3K inhibitor combination therapy eradicates c-MYC-driven murine prostate cancers via cGAS/STING pathway activation within tumor-associated macrophages.
Dutta Gupta, P, Chaudagar, K, Sharma-Saha, S, Bynoe, K, Maillat, L, Heiss, B, Leung KH, Krishnan, Y, Stadler, WM, & Patnaik, A
Cancer Research 81(13_supplement): 1685 https://doi.org/10.1158/1538-7445.AM2021-1685