Publications

Ludwig Branch at Lausanne

Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.

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.

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

Spatio-temporal effects of genetic and therapeutic perturbation on the immune microenvironment in murine models of lung and pancreatic adenocarcinomas.

Manuscript in preparation

Ludwig Center at Harvard

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.
Manuscript submitted