Our laboratory was the first to describe the immune effects of BRAF-targeted therapy in melanoma. In our initial studies, we first assayed BRAF-mutant and BRAF-with cell lines before and after treatment with targeted therapy, and made the novel observation that treatment with targeted therapy was associated with a significant increase in melanoma antigen expression which was associated with enhanced reactivity to antigen-specific T cells. Next, we characterized the response to BRAF inhibition in patients enrolled in clinical trials of BRAF inhibitors. BRAF inhibition was associated with a dense CD8 T cell infiltrate and increased melanoma antigen expression, which were abrogated on the emergence of resistance to therapy. Interestingly, we also saw high levels of PD-L1 and lower levels of immunosuppressive cytokines (IL-6, IL-8) in patients shortly after initiation of BRAF inhibition. We also studied specificity of the immune response to BRAF-targeted therapy via T cell receptor sequencing. Simultaneously, we characterized the response to BRAF inhibition in an immunocompetent model of BRAF-mutant melanoma, demonstrating a critical contribution of CD8 T cells to the treatment response. We observed an increase on CD4 and CD8 T cell infiltration on treatment of mice with BRAF inhibitor, which was associated with increased interferon gamma and tumor necrosis factor alpha.
- Frederick DT, Piris A, Cogdill AP, Cooper ZA, Lezcano C, Ferrone CR, Mitra D, Boni A, Newton LP, Liu C, Peng W, Sullivan RJ, Lawrence DP, Hodi FS, Overwijk WW, Lizée G, Murphy GF, Hwu P, Flaherty KT, Fisher DE, Wargo JA. BRAF inhibition is associated with enhanced melanoma antigen expression and a more favorable tumor microenvironment in patients with metastatic melanoma. Clin Cancer Res. 2013 Mar 1;19(5):1225-31. PubMed PMID: 23307859; PubMed Central PMCID: PMC3752683.
- Liu C, Peng W, Xu C, Lou Y, Zhang M, Wargo JA, Chen JQ, Li HS, Watowich SS, Yang Y, Tompers Frederick D, Cooper ZA, Mbofung RM, Whittington M, Flaherty KT, Woodman SE, Davies MA, Radvanyi LG, Overwijk WW, Lizée G, Hwu P. BRAF inhibition increases tumor infiltration by T cells and enhances the antitumor activity of adoptive immunotherapy in mice. Clin Cancer Res. 2013 Jan 15;19(2):393-403. PubMed PMID: 23204132; PubMed Central PMCID: PMC4120472.
- Khalili JS, Liu S, Rodríguez-Cruz TG, Whittington M, Wardell S, Liu C, Zhang M, Cooper ZA, Frederick DT, Li Y, Zhang M, Joseph RW, Bernatchez C, Ekmekcioglu S, Grimm E, Radvanyi LG, Davis RE, Davies MA, Wargo JA, Hwu P, Lizée G. Oncogenic BRAF(V600E) promotes stromal cell-mediated immunosuppression via induction of interleukin-1 in melanoma. Clin Cancer Res. 2012 Oct 1;18(19):5329-40. PubMed MID: 22850568; PubMed Central PMCID: PMC3463754.
- Boni A, Cogdill AP, Dang P, Udayakumar D, Njauw CN, Sloss CM, Ferrone CR, Flaherty KT, Lawrence DP, Fisher DE, Tsao H, Wargo JA. Selective BRAFV600E inhibition enhances T-cell recognition of melanoma without affecting lymphocyte function. Cancer Res. 2010 Jul 1;70(13):5213-9. PubMed PMID: 20551059.
We have contributed significantly to the understanding of resistance mechanisms to this form of therapy. This is critical, as resistance to therapy develops in nearly all patients with melanoma who are treated with these agents. To facilitate such studies, we collected longitudinal tumor biopsies and blood samples on patients with metastatic melanoma receiving this treatment, and performed a deep molecular analysis of resistance mechanisms in pre-treatment versus progression samples. We gained a great deal of insight through these analyses, with findings published in high impact journals such as Nature, Cancer Cell, Cancer Discovery, Cancer Research, Nature Medicine, PNAS, and Clinical Cancer Research. We have continued this translational research in other forms of targeted therapy in melanoma as well as in other cancers, with promising findings.
- Chen PL, Roh W, Reuben A, Cooper ZA, Spencer CN, Prieto PA, Miller JP, Bassett RL, Gopalakrishnan V, Wani K, De Macedo MP, Austin-Breneman JL, Jiang H, Chang Q, Reddy SM, Chen WS, Tetzlaff MT, Broaddus RJ, Davies MA, Gershenwald JE, Haydu L, Lazar AJ, Patel SP, Hwu P, Hwu WJ, Diab A, Glitza IC, Woodman SE, Vence LM, Wistuba II, Amaria RN, Kwong LN, Prieto V, Davis RE, Ma W, Overwijk WW, Sharpe AH, Hu J, Futreal PA, Blando J, Sharma P, Allison JP, Chin L, Wargo JA. Analysis of immune signatures in longitudinal tumor samples yields insight into biomarkers of response and mechanisms of resistance to immune checkpoint blockade. Cancer Discov 6(8):827-37, 8/2016. e-Pub 6/2016. PMID: 27301722.
- Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, Rosenberg M, Goetz EM, Sullivan RJ, Farlow DN, Friedrich DC, Anderka K, Perrin D, Johannessen CM, McKenna A, Cibulskis K, Kryukov G, Hodis E, Lawrence DP, Fisher S, Getz G, Gabriel SB, Carter SL, Flaherty KT, Wargo JA, Garraway LA. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 2014 Jan;4(1):61-8. PubMed PMID: 24265154; PubMed Central PMCID: PMC3947296.
Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander ES, Gabriel SB, Getz G, Garraway LA, Chin L. A landscape of driver mutations in melanoma. Cell. 2012 Jul 20;150(2):251-63. PubMed PMID: 22817889; PubMed Central PMCID: PMC3600117.
- Johannessen CM, Boehm JS, Kim SY, Thomas SR, Wardwell L, Johnson LA, Emery CM, Stransky N, Cogdill P, Barretina J, Caponigro G, Hieronymus H, Murray RR, Salehi-Ashtiani K, Hill DE, Vidal M, Zhao JJ, Yang X, Alkan O, Kim S, Harris JL, Wilson CJ, Myer VE, Finan PM, Root DE, Roberts TM, Golub T, Flaherty KT, Dummer R, Weber BL, Sellers WR, Schlegel R, Wargo JA, Hahn WC, Garraway LA. COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature. 2010 Dec 16;468(7326):968-72. PubMed PMID: 21107320; PubMed Central PMCID: PMC3058384.
- Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature. 2012 May 9;485(7399):502-6. PubMed PMID: 22622578;
Our studies of the immune effects of targeted therapy, as well as mechanisms of resistance, led us to generate the hypothesis that combining targeted therapy and immunotherapy would be synergistic in the treatment of melanoma as well as other cancers. We were the first to propose such combinations based on our data, and this has become a productive field of research across cancer types, with combination strategies now being tested in the context of clinical trials in patients with cancer. In our laboratory, we studied potential synergy of BRAF-targeted therapy and immunotherapy through two manners: 1) Longitudinal tumor and blood samples in patients undergoing combined treatment with these modalities and 2) A murine model of BRAF-mutant melanoma. We found evidence of synergy in patients and in our mouse model, and also gained critical insight into optimal timing of therapy.
- V. Gopalakrishnan, C. N. Spencer, L. Nezi, A. Reuben, M. C. Andrews, T. V. Karpinets, P. A. Prieto, D. Vicente, K. Hoffman, S. C. Wei, A. P. Cogdill, L. Zhao, C. W. Hudgens, D. S. Hutchinson, T. Manzo, M. Petaccia de Macedo, T. Cotechini, T. Kumar, W. S. Chen, S. M. Reddy, R. Szczepaniak Sloane, J. Galloway-Pena, H. Jiang, P. L. Chen, E. J. Shpall, K. Rezvani, A. M. Alousi, R. F. Chemaly, S. Shelburne, L. M. Vence, P. C. Okhuysen, V. B. Jensen, A. G. Swennes, F. McAllister, E. Marcelo Riquelme Sanchez, Y. Zhang, E. Le Chatelier, L. Zitvogel, N. Pons, J. L. Austin-Breneman, L. E. Haydu, E. M. Burton, J. M. Gardner, E. Sirmans, J. Hu, A. J. Lazar, T. Tsujikawa, A. Diab, H. Tawbi, I. C. Glitza, W. J. Hwu, S. P. Patel, S. E. Woodman, R. N. Amaria, M. A. Davies, J. E. Gershenwald, P. Hwu, J. E. Lee, J. Zhang, L. M. Coussens, Z. A. Cooper, P. A. Futreal, C. R. Daniel, N. J. Ajami, J. F. Petrosino, M. T. Tetzlaff, P. Sharma, J. P. Allison, R. R. Jenq, J. A. Wargo. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science. 2017 Nov 2. pii: eaan4236. doi: 10.1126/science.aan4236. [Epub ahead of print]PMID29097493
- Wargo JA, Cooper ZA, Flaherty KT. Universes collide: combining immunotherapy with targeted therapy for cancer. Cancer Discov. 2014 Dec;4(12):1377-86. PubMed PMID: 25395294; PubMed Central PMCID: PMC4258160.
- Cooper ZA, Juneja VR, Sage PT, Frederick DT, Piris A, Mitra D, Lo JA, Hodi FS, Freeman GJ, Bosenberg W, McMahon M, Flaherty KT, Fisher DE, Sharpe AH, Wargo JA. Response to BRAF inhibition in melanoma is enhanced when combined with immune checkpoint blockade. Cancer Immunol Res. 2014 Jul;2(7):643-54. PubMed PMID: 24903021; PubMed Central PMCID: PMC4097121.