Radiation and dual checkpoint blockade activate non-redundant immune mechanisms in cancer

Pardoll, D. M. The blockade of immune checkpoints in cancer immunotherapy. Nature Rev. Cancer 12, 252–264 (2012)

Hodi, F. S. et al. Improved survival with ipilimumab in patients with metastatic melanoma. N. Engl. J. Med. 363, 711–723 (2010)

Hamid, O. et al. Safety and tumor responses with lambrolizumab (anti-PD-1) in melanoma. N. Engl. J. Med. 369, 134–144 (2013)

Topalian, S. L. et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N. Engl. J. Med. 366, 2443–2454 (2012)

Brahmer, J. R. et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N. Engl. J. Med. 366, 2455–2465 (2012)

Wolchok, J. D. et al. Nivolumab plus ipilimumab in advanced melanoma. N. Engl. J. Med. 369, 122–133 (2013)

Postow, M. A. et al. Immunologic correlates of the abscopal effect in a patient with melanoma. N. Engl. J. Med. 366, 925–931 (2012)

Ishwaran, H., Kogalur, U. B., Gorodeski, E. Z., Minn, A. J. & Lauer, M. S. High-dimensional variable selection for survival data. J. Am. Stat. Assoc. 105, 205–217 (2010)

Ishwaran, H., Kogalur, U. B., Chen, X. & Minn, A. J. Random survival forests for high-dimensional data. Statistical Analy Data Mining 4, 115–132 (2011)

Wilson, E. B. et al. Blockade of chronic type I interferon signaling to control persistent LCMV infection. Science 340, 202–207 (2013)

Teijaro, J. R. et al. Persistent LCMV infection is controlled by blockade of type I interferon signaling. Science 340, 207–211 (2013)

Jönsson, G. et al. Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome. Clin. Cancer Res. 16, 3356–3367 (2010)

Wherry, E. J. T cell exhaustion. Nature Immunol. 12, 492–499 (2011)

Paley, M. A. et al. Progenitor and terminal subsets of CD8+ T cells cooperate to contain chronic viral infection. Science 338, 1220–1225 (2012)

Thomas, N. et al. Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. Bioinformatics 30, 3181–3188 (2014)

Atchley, W. R., Zhao, J., Fernandes, A. D. & Druke, T. Solving the protein sequence metric problem. Proc. Natl Acad. Sci. USA 102, 6395–6400 (2005)

Curran, M. A., Montalvo, W., Yagita, H. & Allison, J. P. PD-1 and CTLA-4 combination blockade expands infiltrating T cells and reduces regulatory T and myeloid cells within B16 melanoma tumors. Proc. Natl Acad. Sci. USA 107, 4275–4280 (2010)

Cha, E. et al. Improved survival with T cell clonotype stability after anti-CTLA-4 treatment in cancer patients. Sci. Transl. Med. 6, 238ra70–238ra70 (2014)

Robert, L. et al. CTLA4 blockade broadens the peripheral T-cell receptor repertoire. Clin. Cancer Res. 20, 2424–2432 (2014)

Reits, E. A. Radiation modulates the peptide repertoire, enhances MHC class I expression, and induces successful antitumor immunotherapy. J. Exp. Med. 203, 1259–1271 (2006)

Eisenhauer, E. A. et al. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur. J. Cancer 45, 228–247 (2009)

Bayne, L. J. et al. Tumor-derived granulocyte-macrophage colony-stimulating factor regulates myeloid inflammation and T cell immunity in pancreatic cancer. Cancer Cell 21, 822–835 (2012)

Lee, Y. et al. Therapeutic effects of ablative radiation on local tumor require CD8+ T cells: changing strategies for cancer treatment. Blood 114, 589–595 (2009)

Dewan, M. Z. et al. Fractionated but not single-dose radiotherapy induces an immune-mediated abscopal effect when combined with anti-CTLA-4 antibody. Clin. Cancer Res. 15, 5379–5388 (2009)

Green, M. R. et al. Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma. Blood 116, 3268–3277 (2010)

Holets, L. M. Trophoblast CD274 (B7-H1) is differentially expressed across gestation: influence of oxygen concentration. Biol. Reprod. 74, 352–358 (2006)

Cheadle, C., Vawter, M. P., Freed, W. J. & Becker, K. G. Analysis of microarray data using Z score transformation. J. Mol. Diagn. 5, 73–81 (2003)

Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)

Efron, B. & Tibshirani, R. On testing the significance of sets of genes. Ann. Appl. Stat. 1, 107–129 (2007)

Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001)

Chen, X. & Ishwaran, H. Random forests for genomic data analysis. Genomics 99, 323–329 (2012)

Ishwaran, H. & Kogalur, U. B. Random forests for survival, regression and classification (RF-SRC) (2013)

Rempala, G. A. & Seweryn, M. Methods for diversity and overlap analysis in T-cell receptor populations. J. Math. Biol. 67, 1339–1368 (2013)