Atlas Datasets
HTA data is currently organized by the original publication. Our goal is to incorporate these data into multi-functional Atlases. Over time search and other means of accessing data will be added.
Featured Publications
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, 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
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
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
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
Methods and software
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 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
Profiling and Atlasing
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
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
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
Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer.
Keenan, T.E., Li, T., Vallius, T., Guerriero, J.L., Tayob, N., Kochupurakkal, B., Davis, J., Pastorello, R., ... Tolaney, S.M. (2021).
Clinical Cancer Research, 2(1), 66-82. https://doi.org/10.1158/1078-0432.CCR-20-3089