Genomics-and transcriptomics-based patient selection for cancer treatmentwith immune checkpoint inhibitors a review

JAMA Oncology

Volumn 2, Issue 11, 2016, Pages 1490-1495

  Dijkstra, Krijn K ^a   Voabil, Paula ^a   Schumacher, Ton N ^a   Voest, Emile E ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; IMMUNOLOGIC FACTOR; TRANSCRIPTOME; TUMOR MARKER;

GENETICS; GENOMICS; HUMAN; IMMUNOLOGY; METABOLISM; NEOPLASMS; PATIENT SELECTION; TREATMENT OUTCOME;

ANTINEOPLASTIC AGENTS; BIOMARKERS, TUMOR; GENOMICS; HUMANS; IMMUNOLOGIC FACTORS; NEOPLASMS; PATIENT SELECTION; TRANSCRIPTOME; TREATMENT OUTCOME;

EID: 85013040069     PISSN: 23742437     EISSN: 23742445     Source Type: Journal    
DOI: 10.1001/jamaoncol.2016.2214     Document Type: Review

References (53)

1. Sharma P, Allison JP. Immune checkpoint targeting in cancer therapy. Cell. 2015;161(2):205-214.
2. Hodi FS, O'Day SJ, McDermott DF, et al. Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med. 2010;363(8): 711-723.
3. Larkin J, Chiarion-Sileni V, Gonzalez R, et al. Combined nivolumab and ipilimumab or monotherapy in untreated melanoma. N Engl J Med. 2015;373(1):23-34.
4. Schadendorf D, Hodi FS, Robert C, et al. Pooled analysis of long-Term survival data from phase II and phase III clinical trials of ipilimumab in unresectable or metastatic melanoma. J Clin Oncol. 2015;33(17): 1889-1894.
5. Garon EB, Rizvi NA, Hui R, et al; KEYNOTE-001 Investigators. Pembrolizumab for the treatment of non-small-cell lung cancer. N Engl J Med. 2015;372 (21):2018-2028.
6. Robert C, Schachter J, Long GV, et al; KEYNOTE-006 investigators. Pembrolizumab vs ipilimumab in advanced melanoma. N Engl J Med. 2015;372(26):2521-2532.
7. Borghaei H, Paz-Ares L, Horn L, et al. Nivolumab vs docetaxel in advanced nonsquamous non-small-cell lung cancer. N Engl J Med. 2015;373 (17):1627-1639.
8. Voest EE, Bernards R. DNA-guided precision medicine Cancer Discov. 2016;6(2):130-132.
9. Tumeh PC, Harview CL, Yearley JH, et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014;515(7528):568-571.
10. Heemskerk B, Kvistborg P, Schumacher TN. The cancer antigenome. EMBO J. 2013;32(2):194-203.
11. Kvistborg P, van Buuren MM, Schumacher TN. Human cancer regression antigens. Curr Opin Immunol. 2013;25(2):284-290.
12. Robbins PF, Lu YC, El-Gamil M, et al. Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med. 2013;19(6):747-752.
13. Gubin MM, Zhang X, Schuster H, et al. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature. 2014;515(7528):577-581.
14. Linnemann C, van Buuren MM, Bies L, et al. High-Throughput epitope discovery reveals frequent recognition of neo-Antigens by CD4+ T cells in human melanoma. Nat Med. 2015;21(1):81-85.
15. Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348 (6230):69-74.
16. van Rooij N, van Buuren MM, Philips D, et al. Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol. 2013;31(32):e439-e442.
17. Rizvi NA, Hellmann MD, Snyder A, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348(6230):124-128.
18. Alexandrov LB, Nik-Zainal S, Wedge DC, et al; Australian Pancreatic Cancer Genome Initiative; ICGC Breast Cancer Consortium; ICGC MMML-Seq Consortium; ICGC PedBrain. Signatures of mutational processes in human cancer. Nature. 2013;500(7463):415-421.
19. RooneyMS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160(1-2):48-61.
20. Snyder A, Makarov V, Merghoub T, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med. 2014;371(23): 2189-2199.
21. Van Allen EM, Miao D, Schilling B, et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015;350(6257): 207-211.
22. Le DT, Uram JN, Wang H, et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372(26):2509-2520.
23. Kelderman S, Schumacher TN, Kvistborg P. Mismatch repair-deficient cancers are targets for anti-PD1 therapy. Cancer Cell. 2015;28(1):11-13.
24. Howitt BE, Shukla SA, Sholl LM, et al. Association of polymerase e-mutated and microsatellite-instable endometrial cancers with neoantigen load, number of tumor-infiltrating lympocytes, and expression of PD-1 and PD-L1. JAMA Oncol. 2015;1(9):1319-1323.
25. Tian S, Roepman P, Popovici V, et al. A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency. J Pathol. 2012;228(4):586-595.
26. Angelova M, Charoentong P, Hackl H, et al. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 2015;16(64):64-80.
27. Schumacher TN, Kesmir C, van Buuren MM. Biomarkers in cancer immunotherapy. Cancer Cell. 2015;27(1):12-14.
28. Gubin MM, Schreiber RD. CANCER. The odds of immunotherapy success. Science. 2015;350(6257): 158-159.
29. Kvistborg P, Philips D, Kelderman S, et al. Anti-CTLA-4 therapy broadens the melanoma-reactive CD8+ T cell response. Sci Transl Med. 2014;6(254):254ra128.
30. Tran E, Ahmadzadeh M, Lu YC, et al. Immunogenicity of somatic mutations in human gastrointestinal cancers. Science. 2015;350(6266): 1387-1390.
31. Green MR, Rodig S, Juszczynski P, et al. Constitutive AP-1 activity and EBV infection induce PD-L1 in Hodgkin lymphomas and posttransplant lymphoproliferative disorders: implications for targeted therapy. Clin Cancer Res. 2012;18(6): 1611-1618.
32. Chen BJ, Chapuy B, Ouyang J, et al. PD-L1 expression is characteristic of a subset of aggressive B-cell lymphomas and virus-Associated malignancies. Clin Cancer Res. 2013;19(13):3462-3473.
33. FangW, Zhang J, Hong S, et al. EBV-driven LMP1 and IFN-γ up-regulate PD-L1 in nasopharyngeal carcinoma. Oncotarget. 2014;5 (23):12189-12202.
34. Ji RR, Chasalow SD, Wang L, et al. An immune-Active tumor microenvironment favors clinical response to ipilimumab. Cancer Immunol Immunother. 2012;61(7):1019-1031.
35. Herbst RS, Soria JC, Kowanetz M, et al. Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature. 2014;515(7528):563-567.
36. Spranger S, Bao R, Gajewski TF. Melanoma-intrinsic β-catenin signalling prevents anti-Tumour immunity. Nature. 2015;523(7559): 231-235.
37. Panarelli NC, Vaughn CP, SamowitzWS, Yantiss RK. Sporadic microsatellite instability-high colon cancers rarely display immunohistochemical evidence ofWnt signaling activation. Am J Surg Pathol. 2015;39(3):313-317.
38. PengW, Chen JQ, Liu C, et al. Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov. 2016;6(2):202-216.
39. Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453-457.
40. Gentles AJ, Newman AM, Liu CL, et al. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med. 2015; 21(8):938-945.
41. Galon J, Mlecnik B, Bindea G, et al. Towards the introduction of the 'Immunoscore' in the classification of malignant tumours. J Pathol. 2014; 232(2):199-209.
42. Leone P, Shin EC, Perosa F, Vacca A, Dammacco F, Racanelli V. MHC class I antigen processing and presenting machinery. J Natl Cancer Inst. 2013;105 (16):1172-1187.
43. Shukla SA, RooneyMS, Rajasagi M, et al. Comprehensive analysis of cancer-Associated somatic mutations in class I HLA genes. Nat Biotechnol. 2015;33(11):1152-1158.
44. Dierssen JW, de Miranda NF, Ferrone S, et al. HNPCC versus sporadic microsatellite-unstable colon cancers follow different routes toward loss of HLA class I expression. BMC Cancer. 2007;7:33-43.
45. Johnson DB, Estrada MV, Salgado R, et al. Melanoma-specific MHC-II expression represents a tumour-Autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy. Nat Commun. 2016;7:10582-10591.
46. Tran E, Turcotte S, Gros A, et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science. 2014;344(6184):641-645.
47. Ansell SM, Lesokhin AM, Borrello I, et al. PD-1 blockade with nivolumab in relapsed or refractory Hodgkin's lymphoma. N Engl J Med. 2015;372(4): 311-319.
48. Topalian SL, Hodi FS, Brahmer JR, et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med. 2012;366(26): 2443-2454.
49. Powles T, Eder JP, Fine GD, et al. MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer. Nature. 2014;515(7528): 558-562.
50. Sun T, Zhou Y, Yang M, et al. Functional genetic variations in cytotoxic T-lymphocyte antigen 4 and susceptibility to multiple types of cancer. Cancer Res. 2008;68(17):7025-7034.
51. Breunis WB, Tarazona-Santos E, Chen R, Kiley M, Rosenberg SA, Chanock SJ. Influence of cytotoxic T lymphocyte-Associated antigen 4 (CTLA4) common polymorphisms on outcome in treatment of melanoma patients with CTLA-4 blockade. J Immunother. 2008;31(6):586-590.
52. Sivan A, Corrales L, Hubert N, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015;350 (6264):1084-1089.
53. Vizou M, Pitt JM, Daille R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079-1084.