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 (2020).
Cancer Cell, 39(12), 1623-1642 https://www.doi.org/10.1016/j.ccell.2021.10.008
Ludwig Center at MIT

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

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

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

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

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

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

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., Lin, J.-R., Sharma-Saha, S., Bynoe, K., Leung, K., Shafran, J., Helmi, H., Maillat, L., Heiss, B., Sorger, P.K., Krishnan, Y., Stadler, W.M., & Patnaik, A.