Article
Author: Mathew, Divij ; Oldridge, Derek ; Ghinnagow, Reem ; Kier, Melanie W ; Han, Nicholas ; Alanio, Cecile ; Xu, Wei ; Giles, Josephine ; Manne, Sasikanth ; Lucas, Minke ; Solis, Sabrina ; Wang, Kevin ; Minn, Andy J ; George, Sangeeth ; Weber, Jeffrey S ; Xu, Xiaowei ; Mitchell, Tara C ; Azar, Tarek ; Wang, Guanning ; Laughlin, Amy I ; Coutifaris, Paulina ; Blank, Christian ; Flowers, Ahron ; Sachar, Chirag ; Kothari, Shawn ; Karakousis, Giorgos C ; Yan, Patrick K ; Amaravadi, Ravi K ; Nandi, Ajeya ; Huang, Alexander C ; Tenney, Daniel J ; Farwell, Michael D ; Schuchter, Lynn M ; Anderson, Shaneaka ; Buggert, Marcus ; Brocks, David ; Herati, Ramin S ; Kiner, Evgeny
Combination checkpoint blockade with anti-PD-1 and anti-CTLA-4 antibodies has shown promising efficacy in melanoma. However, the underlying mechanism in humans remains unclear. Here, we perform paired single-cell RNA and T cell receptor (TCR) sequencing across time in 36 patients with stage IV melanoma treated with anti-PD-1, anti-CTLA-4, or combination therapy. We develop the algorithm Cyclone to track temporal clonal dynamics and underlying cell states. Checkpoint blockade induces waves of clonal T cell responses that peak at distinct time points. Combination therapy results in greater magnitude of clonal responses at 6 and 9 weeks compared to single-agent therapies, including melanoma-specific CD8+ T cells and exhausted CD8+ T cell (TEX) clones. Focused analyses of TEX identify that anti-CTLA-4 induces robust expansion and proliferation of progenitor TEX, which synergizes with anti-PD-1 to reinvigorate TEX during combination therapy. These next generation immune profiling approaches can guide the selection of drugs, schedule, and dosing for novel combination strategies.