Low T-cell Receptor Diversity, High Somatic Mutation Burden, and High Neoantigen Load as Predictors of Clinical Outcome in Muscle-invasive Bladder Cancer

European Urology Focus

Volumn 2, Issue 4, 2016, Pages 445-452

  Choudhury, Noura J ^a   Kiyotani, Kazuma ^a   Yap, Kai Lee ^a   Campanile, Alexa ^a   Antic, Tatjana ^a   Yew, Poh Yin ^a   Steinberg, Gary ^a   Park, Jae Hyun ^a   Nakamura, Yusuke ^a   O'Donnell, Peter H ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Bladder cancer; Immune responses to cancer; Molecular prognosis; Neoantigens; T cell receptor

Indexed keywords

ANTIGEN; NEOANTIGEN; T LYMPHOCYTE RECEPTOR; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CANCER PROGNOSIS; CANCER STAGING; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL EXPANSION; CLINICAL OUTCOME; CONTROLLED STUDY; EXOME; FEMALE; FOLLOW UP; GENE EXPRESSION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; MALE; MIDDLE AGED; MUSCLE INVASIVE BLADDER CANCER; RECURRENCE FREE SURVIVAL; SOMATIC MUTATION; TUMOR ASSOCIATED LEUKOCYTE; VERY ELDERLY;

EID: 84995387448     PISSN: None     EISSN: 24054569     Source Type: Journal    
DOI: 10.1016/j.euf.2015.09.007     Document Type: Article

References (23)

1. [1] Knowles, M.A., Hurst, C.D., Molecular biology of bladder cancer: new insights into pathogenesis and clinical diversity. Nat Rev Cancer 15 (2015), 25–41.
2. [2] Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 504 (2014), 315–322.
3. [3] Gui, Y., Guo, G., Huang, Y., et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet 43 (2011), 875–878.
4. [4] Solomon, D.A., Kim, J.S., Bondaruk, J., et al. Frequent truncating mutations of STAG2 in bladder cancer. Nat Genet 45 (2013), 1428–1430.
5. [5] Iyer, G., Hanrahan, A.J., Milowsky, M.I., et al. Genome sequencing identifies a basis for everolimus sensitivity. Science, 338, 2012, 221.
6. [6] Gubin, M.M., Zhang, X., Schuster, H., et al. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature 515 (2014), 577–581.
7. [7] Carreno, B.M., Magrini, V., Becker-Hapak, M., et al. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 348 (2015), 803–808.
8. [8] Schumacher, T.N., Schreiber, R.D., Neoantigens in cancer immunotherapy. Science 348 (2015), 69–74.
9. [9] Sharma, P., Shen, Y., Wen, S., et al. CD8 tumor-infiltrating lymphocytes are predictive of survival in muscle-invasive urothelial carcinoma. Proc Natl Acad Sci U S A 114 (2007), 3967–3972.
10. [10] van Heijst, J.W., Ceberio, I., Lipuma, L.B., et al. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med 19 (2013), 372–377.
11. [11] Fang, H., Yamaguchi, R., Liu, X., et al. Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor alpha and beta chains using next-generation sequencing (NGS). Oncoimmunology, 3, 2014, e968467.
12. [12] Venturi, V., Kedzierska, K., Turner, S.J., Doherty, P.C., Davenport, M.P., Methods for comparing the diversity of samples of the T cell receptor repertoire. J Immunol Methods 321 (2007), 182–195.
13. [13] Yap, K.L., Kiyotani, K., Tamura, K., et al. Whole-exome sequencing of muscle-invasive bladder cancer identifies recurrent mutations of UNC5C and prognostic importance of DNA repair gene mutations on survival. Clin Cancer Res 20 (2014), 6605–6617.
14. [14] Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G., Hacohen, N., Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160 (2015), 48–61.
15. [15] Robbins, P.F., Lu, Y.C., El-Gamil, M., et al. Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med 19 (2013), 747–752.
16. [16] Hoof, I., Peters, B., Sidney, J., et al. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61 (2009), 1–13.
17. [17] Nielsen, M., Lundegaard, C., Blicher, T., et al. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One, 2, 2007, e796.
18. [18] Snyder, A., Makarov, V., Merghoub, T., et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 371 (2014), 2189–2199.
19. [19] Rizvi, N.A., Hellmann, M.D., Snyder, A., et al. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348 (2015), 124–128.
20. [20] Hamid, O., Schmidt, H., Nissan, A., et al. A prospective phase II trial exploring the association between tumor microenvironment biomarkers and clinical activity of ipilimumab in advanced melanoma. J Transl Med, 9, 2011, 204.
21. [21] Muller, A.J., Sharma, M.D., Chandler, P.R., et al. Chronic inflammation that facilitates tumor progression creates local immune suppression by inducing indoleamine 2,3 dioxygenase. Proc Natl Acad Sci U S A. 105 (2008), 17073–17078.
22. [22] Powles, T., Eder, J.P., Fine, G.D., et al. MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer. Nature 515 (2014), 558–562.
23. [23] Calis, J.J., Maybeno, M., Greenbaum, J.A., et al. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol, 9, 2013, e1003266.