A Novel Natural Killer Cell-related Gene Signature for Improving the Prediction of Prognosis and Immunotherapy Response in Bladder Cancer

Lenis, A.T.; Lec, P.M.; Chamie, K.; Mshs, M. Bladder Cancer. JAMA, 2020, 324(19), 1980-1991.
[http://dx.doi.org/10.1001/jama.2020.17598] [PMID: 33201207]

Rosenberg, J.E.; Hoffman-Censits, J.; Powles, T.; van der Heijden, M.S.; Balar, A.V.; Necchi, A.; Dawson, N.; O’Donnell, P.H.; Balmanoukian, A.; Loriot, Y.; Srinivas, S.; Retz, M.M.; Grivas, P.; Joseph, R.W.; Galsky, M.D.; Fleming, M.T.; Petrylak, D.P.; Perez-Gracia, J.L.; Burris, H.A.; Castellano, D.; Canil, C.; Bellmunt, J.; Bajorin, D.; Nickles, D.; Bourgon, R.; Frampton, G.M.; Cui, N.; Mariathasan, S.; Abidoye, O.; Fine, G.D.; Dreicer, R. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: A single-arm, multicentre, phase 2 trial. Lancet, 2016, 387(10031), 1909-1920.
[http://dx.doi.org/10.1016/S0140-6736(16)00561-4] [PMID: 26952546]

Witjes, J.A.; Bruins, H.M.; Cathomas, R.; Compérat, E.M.; Cowan, N.C.; Gakis, G.; Hernández, V.; Linares Espinós, E.; Lorch, A.; Neuzillet, Y.; Rouanne, M.; Thalmann, G.N.; Veskimäe, E.; Ribal, M.J.; van der Heijden, A.G. European association of urology guidelines on muscle-invasive and metastatic bladder cancer: Summary of the 2020 guidelines. Eur. Urol., 2021, 79(1), 82-104.
[http://dx.doi.org/10.1016/j.eururo.2020.03.055] [PMID: 32360052]

Wu, S.Y.; Fu, T.; Jiang, Y.Z.; Shao, Z.M. Natural killer cells in cancer biology and therapy. Mol. Cancer, 2020, 19(1), 120.
[http://dx.doi.org/10.1186/s12943-020-01238-x] [PMID: 32762681]

Bald, T.; Krummel, M.F.; Smyth, M.J.; Barry, K.C. The NK cell–cancer cycle: Advances and new challenges in NK cell–based immunotherapies. Nat. Immunol., 2020, 21(8), 835-847.
[http://dx.doi.org/10.1038/s41590-020-0728-z] [PMID: 32690952]

Guillerey, C.; Huntington, N.D.; Smyth, M.J. Targeting natural killer cells in cancer immunotherapy. Nat. Immunol., 2016, 17(9), 1025-1036.
[http://dx.doi.org/10.1038/ni.3518] [PMID: 27540992]

Hodgins, J.J.; Khan, S.T.; Park, M.M.; Auer, R.C.; Ardolino, M. Killers 2.0: NK cell therapies at the forefront of cancer control. J. Clin. Invest., 2019, 129(9), 3499-3510.
[http://dx.doi.org/10.1172/JCI129338] [PMID: 31478911]

Ferreira-Teixeira, M.; Paiva-Oliveira, D.; Parada, B.; Alves, V.; Sousa, V.; Chijioke, O.; Münz, C.; Reis, F.; Rodrigues-Santos, P.; Gomes, C. Natural killer cell-based adoptive immunotherapy eradicates and drives differentiation of chemo resistant bladder cancer stem-like cells. BMC Med., 2016, 14(1), 163.
[http://dx.doi.org/10.1186/s12916-016-0715-2] [PMID: 27769244]

Sun, H.; Huang, Q.; Huang, M.; Wen, H.; Lin, R.; Zheng, M.; Qu, K.; Li, K.; Wei, H.; Xiao, W.; Sun, R.; Tian, Z.; Sun, C. Human CD96 correlates to natural killer cell exhaustion and predicts the prognosis of human hepatocellular carcinoma. Hepatology, 2019, 70(1), 168-183.
[http://dx.doi.org/10.1002/hep.30347] [PMID: 30411378]

Chauvin, J.M.; Ka, M.; Pagliano, O.; Menna, C.; Ding, Q.; DeBlasio, R.; Sanders, C.; Hou, J.; Li, X.Y.; Ferrone, S.; Davar, D.; Kirkwood, J.M.; Johnston, R.J.; Korman, A.J.; Smyth, M.J.; Zarour, H.M. IL15 stimulation with TIGIT blockade reverses CD155-mediated NK-cell dysfunction in melanoma. Clin. Cancer Res., 2020, 26(20), 5520-5533.
[http://dx.doi.org/10.1158/1078-0432.CCR-20-0575] [PMID: 32591463]

Khatua, S.; Cooper, L.J.N.; Sandberg, D.I.; Ketonen, L.; John son, J.M.; Rytting, M.E.; Liu, D.D.; Meador, H.; Trikha, P.; Nakkula, R.J.; Behbehani, G.K.; Ragoonanan, D.; Gupta, S.; Kotrotsou, A.; Idris, T.; Shpall, E.J.; Rezvani, K.; Colen, R.; Zaky, W.; Lee, D.A.; Gopalakrishnan, V. Phase I study of intraventricular infusions of autologous ex vivo expanded NK cells in children with recurrent medulloblastoma and ependymoma. Neuro-oncol., 2020, 22(8), 1214-1225.
[http://dx.doi.org/10.1093/neuonc/noaa047] [PMID: 32152626]

McWilliams, E.M.; Mele, J.M.; Cheney, C.; Timmerman, E.A.; Fiazuddin, F.; Strattan, E.J.; Mo, X.; Byrd, J.C.; Muthusamy, N.; Awan, F.T. Therapeutic CD94/NKG2A blockade improves natural killer cell dysfunction in chronic lymphocytic leukemia. OncoImmunology, 2016, 5(10), e1226720.
[http://dx.doi.org/10.1080/2162402X.2016.1226720] [PMID: 27853650]

Zhang, S.; Liu, W.; Hu, B.; Wang, P.; Lv, X.; Chen, S.; Shao, Z. Prognostic significance of tumor-infiltrating natural killer cells in solid tumors: A systematic review and meta-analysis. Front. Immunol., 2020, 11, 1242.
[http://dx.doi.org/10.3389/fimmu.2020.01242] [PMID: 32714321]

Alderdice, M.; Dunne, P.D.; Cole, A.J.; O’Reilly, P.G.; McArt, D.G.; Bingham, V.; Fuchs, M.A.; McQuaid, S.; Loughrey, M.B.; Murray, G.I.; Samuel, L.M.; Lawler, M.; Wilson, R.H.; Salto-Tellez, M.; Coyle, V.M. Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival. Mod. Pathol., 2017, 30(9), 1287-1298.
[http://dx.doi.org/10.1038/modpathol.2017.47] [PMID: 28621318]

Li, C.; Liu, F.; Sun, L.; Liu, Z.; Zeng, Y. Natural killer cell-related gene signature predicts malignancy of glioma and the survival of patients. BMC Cancer, 2022, 22(1), 230.
[http://dx.doi.org/10.1186/s12885-022-09230-y] [PMID: 35236310]

Thorsson, V.; Gibbs, D.L.; Brown, S.D.; Wolf, D.; Bortone, D.S.; Ou Yang, T.H.; Porta-Pardo, E.; Gao, G.F.; Plaisier, C.L.; Eddy, J.A.; Ziv, E.; Culhane, A.C.; Paull, E.O.; Sivakumar, I.K.A.; Gentles, A.J.; Malhotra, R.; Farshidfar, F.; Colaprico, A.; Parker, J.S.; Mose, L.E.; Vo, N.S.; Liu, J.; Liu, Y.; Rader, J.; Dhankani, V.; Reynolds, S.M.; Bowlby, R.; Califano, A.; Cherniack, A.D.; Anastassiou, D.; Bedognetti, D.; Mokrab, Y.; Newman, A.M.; Rao, A.; Chen, K.; Krasnitz, A.; Hu, H.; Malta, T.M.; Noushmehr, H.; Pedamallu, C.S.; Bullman, S.; Ojesina, A.I.; Lamb, A.; Zhou, W.; Shen, H.; Choueiri, T.K.; Weinstein, J.N.; Guinney, J.; Saltz, J.; Holt, R.A.; Rabkin, C.S.; Lazar, A.J.; Serody, J.S.; Demicco, E.G.; Disis, M.L.; Vincent, B.G.; Shmulevich, I.; Caesar-Johnson, S.J.; Demchok, J.A.; Felau, I.; Kasapi, M.; Ferguson, M.L.; Hutter, C.M.; Sofia, H.J.; Tarnuzzer, R.; Wang, Z.; Yang, L.; Zenklusen, J.C.; Zhang, J.J.; Chudamani, S.; Liu, J.; Lolla, L.; Naresh, R.; Pihl, T.; Sun, Q.; Wan, Y.; Wu, Y.; Cho, J.; DeFreitas, T.; Frazer, S.; Gehlenborg, N.; Getz, G.; Heiman, D.I.; Kim, J.; Lawrence, M.S.; Lin, P.; Meier, S.; Noble, M.S.; Saksena, G.; Voet, D.; Zhang, H.; Bernard, B.; Chambwe, N.; Dhankani, V.; Knijnenburg, T.; Kramer, R.; Leinonen, K.; Liu, Y.; Miller, M.; Reynolds, S.; Shmulevich, I.; Thorsson, V.; Zhang, W.; Akbani, R.; Broom, B.M.; Hegde, A.M.; Ju, Z.; Kanchi, R.S.; Korkut, A.; Li, J.; Liang, H.; Ling, S.; Liu, W.; Lu, Y.; Mills, G.B.; Ng, K-S.; Rao, A.; Ryan, M.; Wang, J.; Weinstein, J.N.; Zhang, J.; Abeshouse, A.; Armenia, J.; Chakravarty, D.; Chatila, W.K.; de Bruijn, I.; Gao, J.; Gross, B.E.; Heins, Z.J.; Kundra, R.; La, K.; Ladanyi, M.; Luna, A.; Nissan, M.G.; Ochoa, A.; Phillips, S.M.; Reznik, E.; Sanchez-Vega, F.; Sander, C.; Schultz, N.; Sheridan, R.; Sumer, S.O.; Sun, Y.; Taylor, B.S.; Wang, J.; Zhang, H.; Anur, P.; Peto, M.; Spellman, P.; Benz, C.; Stuart, J.M.; Wong, C.K.; Yau, C.; Hayes, D.N.; Parker, J.S.; Wilkerson, M.D.; Ally, A.; Balasundaram, M.; Bowlby, R.; Brooks, D.; Carlsen, R.; Chuah, E.; Dhalla, N.; Holt, R.; Jones, S.J.M.; Kasaian, K.; Lee, D.; Ma, Y.; Marra, M.A.; Mayo, M.; Moore, R.A.; Mungall, A.J.; Mungall, K.; Robertson, A.G.; Sadeghi, S.; Schein, J.E.; Sipahimalani, P.; Tam, A.; Thiessen, N.; Tse, K.; Wong, T.; Berger, A.C.; Beroukhim, R.; Cherniack, A.D.; Cibulskis, C.; Gabriel, S.B.; Gao, G.F.; Ha, G.; Meyerson, M.; Schumacher, S.E.; Shih, J.; Kucherlapati, M.H.; Kucherlapati, R.S.; Baylin, S.; Cope, L.; Danilova, L.; Bootwalla, M.S.; Lai, P.H.; Maglinte, D.T.; Van Den Berg, D.J.; Weisenberger, D.J.; Auman, J.T.; Balu, S.; Bodenheimer, T.; Fan, C.; Hoadley, K.A.; Hoyle, A.P.; Jefferys, S.R.; Jones, C.D.; Meng, S.; Mieczkowski, P.A.; Mose, L.E.; Perou, A.H.; Perou, C.M.; Roach, J.; Shi, Y.; Simons, J.V.; Skelly, T.; Soloway, M.G.; Tan, D.; Veluvolu, U.; Fan, H.; Hinoue, T.; Laird, P.W.; Shen, H.; Zhou, W.; Bellair, M.; Chang, K.; Covington, K.; Creighton, C.J.; Dinh, H.; Doddapaneni, H.V.; Donehower, L.A.; Drummond, J.; Gibbs, R.A.; Glenn, R.; Hale, W.; Han, Y.; Hu, J.; Korchina, V.; Lee, S.; Lewis, L.; Li, W.; Liu, X.; Morgan, M.; Morton, D.; Muzny, D.; Santibanez, J.; Sheth, M.; Shinbrot, E.; Wang, L.; Wang, M.; Wheeler, D.A.; Xi, L.; Zhao, F.; Hess, J.; Appelbaum, E.L.; Bailey, M.; Cordes, M.G.; Ding, L.; Fronick, C.C.; Fulton, L.A.; Fulton, R.S.; Kandoth, C.; Mardis, E.R.; McLellan, M.D.; Miller, C.A.; Schmidt, H.K.; Wilson, R.K.; Crain, D.; Curley, E.; Gardner, J.; Lau, K.; Mallery, D.; Morris, S.; Paulauskis, J.; Penny, R.; Shelton, C.; Shelton, T.; Sherman, M.; Thompson, E.; Yena, P.; Bowen, J.; Gastier-Foster, J.M.; Gerken, M.; Leraas, K.M.; Lichtenberg, T.M.; Ramirez, N.C.; Wise, L.; Zmuda, E.; Corcoran, N.; Costello, T.; Hovens, C.; Carvalho, A.L.; de Carvalho, A.C.; Fregnani, J.H.; Longatto-Filho, A.; Reis, R.M.; Scapulatempo-Neto, C.; Silveira, H.C.S.; Vidal, D.O.; Burnette, A.; Eschbacher, J.; Hermes, B.; Noss, A.; Singh, R.; Anderson, M.L.; Castro, P.D.; Ittmann, M.; Huntsman, D.; Kohl, B.; Le, X.; Thorp, R.; Andry, C.; Duffy, E.R.; Lyadov, V.; Paklina, O.; Setdikova, G.; Shabunin, A.; Tavobilov, M.; McPherson, C.; Warnick, R.; Berkowitz, R.; Cramer, D.; Feltmate, C.; Horowitz, N.; Kibel, A.; Muto, M.; Raut, C.P.; Malykh, A.; Barnholtz-Sloan, J.S.; Barrett, W.; Devine, K.; Fulop, J.; Ostrom, Q.T.; Shimmel, K.; Wolinsky, Y.; Sloan, A.E.; De Rose, A.; Giuliante, F.; Goodman, M.; Karlan, B.Y.; Hagedorn, C.H.; Eckman, J.; Harr, J.; Myers, J.; Tucker, K.; Zach, L.A.; Deyarmin, B.; Hu, H.; Kvecher, L.; Larson, C.; Mural, R.J.; Somiari, S.; Vicha, A.; Zelinka, T.; Bennett, J.; Iacocca, M.; Rabeno, B.; Swanson, P.; Latour, M.; Lacombe, L.; Têtu, B.; Bergeron, A.; McGraw, M.; Staugaitis, S.M.; Chabot, J.; Hibshoosh, H.; Sepulveda, A.; Su, T.; Wang, T.; Potapova, O.; Voronina, O.; Desjardins, L.; Mariani, O.; Roman-Roman, S.; Sastre, X.; Stern, M-H.; Cheng, F.; Signoretti, S.; Berchuck, A.; Bigner, D.; Lipp, E.; Marks, J.; McCall, S.; McLendon, R.; Secord, A.; Sharp, A.; Behera, M.; Brat, D.J.; Chen, A.; Delman, K.; Force, S.; Khuri, F.; Magliocca, K.; Maithel, S.; Olson, J.J.; Owonikoko, T.; Pickens, A.; Ramalingam, S.; Shin, D.M.; Sica, G.; Van Meir, E.G.; Zhang, H.; Eijckenboom, W.; Gillis, A.; Korpershoek, E.; Looijenga, L.; Oosterhuis, W.; Stoop, H.; van Kessel, K.E.; Zwarthoff, E.C.; Calatozzolo, C.; Cuppini, L.; Cuzzubbo, S.; DiMeco, F.; Finocchiaro, G.; Mattei, L.; Perin, A.; Pollo, B.; Chen, C.; Houck, J.; Lohavanichbutr, P.; Hartmann, A.; Stoehr, C.; Stoehr, R.; Taubert, H.; Wach, S.; Wullich, B.; Kycler, W.; Murawa, D.; Wiznerowicz, M.; Chung, K.; Edenfield, W.J.; Martin, J.; Baudin, E.; Bubley, G.; Bueno, R.; De Rienzo, A.; Richards, W.G.; Kalkanis, S.; Mikkelsen, T.; Noushmehr, H.; Scarpace, L.; Girard, N.; Aymerich, M.; Campo, E.; Giné, E.; Guillermo, A.L.; Van Bang, N.; Hanh, P.T.; Phu, B.D.; Tang, Y.; Colman, H.; Evason, K.; Dottino, P.R.; Martignetti, J.A.; Gabra, H.; Juhl, H.; Akeredolu, T.; Stepa, S.; Hoon, D.; Ahn, K.; Kang, K.J.; Beuschlein, F.; Breggia, A.; Birrer, M.; Bell, D.; Borad, M.; Bryce, A.H.; Castle, E.; Chandan, V.; Cheville, J.; Copland, J.A.; Farnell, M.; Flotte, T.; Giama, N.; Ho, T.; Kendrick, M.; Kocher, J-P.; Kopp, K.; Moser, C.; Nagorney, D.; O’Brien, D.; O’Neill, B.P.; Patel, T.; Petersen, G.; Que, F.; Rivera, M.; Roberts, L.; Smallridge, R.; Smyrk, T.; Stanton, M.; Thompson, R.H.; Torbenson, M.; Yang, J.D.; Zhang, L.; Brimo, F.; Ajani, J.A.; Gonzalez, A.M.A.; Behrens, C.; Bondaruk, J.; Broaddus, R.; Czerniak, B.; Esmaeli, B.; Fujimoto, J.; Gershenwald, J.; Guo, C.; Lazar, A.J.; Logothetis, C.; Meric-Bernstam, F.; Moran, C.; Ramondetta, L.; Rice, D.; Sood, A.; Tamboli, P.; Thompson, T.; Troncoso, P.; Tsao, A.; Wistuba, I.; Carter, C.; Haydu, L.; Hersey, P.; Jakrot, V.; Kakavand, H.; Kefford, R.; Lee, K.; Long, G.; Mann, G.; Quinn, M.; Saw, R.; Scolyer, R.; Shannon, K.; Spillane, A.; Stretch,; Synott, M.; Thompson, J.; Wilmott, J.; Al-Ahmadie, H.; Chan, T.A.; Ghossein, R.; Gopalan, A.; Levine, D.A.; Reuter, V.; Singer, S.; Singh, B.; Tien, N.V.; Broudy, T.; Mirsaidi, C.; Nair, P.; Drwiega, P.; Miller, J.; Smith, J.; Zaren, H.; Park, J-W.; Hung, N.P.; Kebebew, E.; Linehan, W.M.; Metwalli, A.R.; Pacak, K.; Pinto, P.A.; Schiffman, M.; Schmidt, L.S.; Vocke, C.D.; Wentzensen, N.; Worrell, R.; Yang, H.; Moncrieff, M.; Goparaju, C.; Melamed, J.; Pass, H.; Botnariuc, N.; Caraman, I.; Cernat, M.; Chemencedji, I.; Clipca, A.; Doruc, S.; Gorincioi, G.; Mura, S.; Pirtac, M.; Stancul, I.; Tcaciuc, D.; Albert, M.; Alexopoulou, I.; Arnaout, A.; Bartlett, J.; Engel, J.; Gilbert, S.; Parfitt, J.; Sekhon, H.; Thomas, G.; Rassl, D.M.; Rintoul, R.C.; Bifulco, C.; Tamakawa, R.; Urba, W.; Hayward, N.; Timmers, H.; Antenucci, A.; Facciolo, F.; Grazi, G.; Marino, M.; Merola, R.; de Krijger, R.; Gimenez-Roqueplo, A-P.; Piché, A.; Chevalier, S.; McKercher, G.; Birsoy, K.; Barnett, G.; Brewer, C.; Farver, C.; Naska, T.; Pennell, N.A.; Raymond, D.; Schilero, C.; Smolenski, K.; Williams, F.; Morrison, C.; Borgia, J.A.; Liptay, M.J.; Pool, M.; Seder, C.W.; Junker, K.; Omberg, L.; Dinkin, M.; Manikhas, G.; Alvaro, D.; Bragazzi, M.C.; Cardinale, V.; Carpino, G.; Gaudio, E.; Chesla, D.; Cottingham, S.; Dubina, M.; Moiseenko, F.; Dhanasekaran, R.; Becker, K-F.; Janssen, K-P.; Slotta-Huspenina, J.; Abdel-Rahman, M.H.; Aziz, D.; Bell, S.; Cebulla, C.M.; Davis, A.; Duell, R.; Elder, J.B.; Hilty, J.; Kumar, B.; Lang, J.; Lehman, N.L.; Mandt, R.; Nguyen, P.; Pilarski, R.; Rai, K.; Schoenfield, L.; Senecal, K.; Wakely, P.; Hansen, P.; Lechan, R.; Powers, J.; Tischler, A.; Grizzle, W.E.; Sexton, K.C.; Kastl, A.; Henderson, J.; Porten, S.; Waldmann, J.; Fassnacht, M.; Asa, S.L.; Schadendorf, D.; Couce, M.; Graefen, M.; Huland, H.; Sauter, G.; Schlomm, T.; Simon, R.; Tennstedt, P.; Olabode, O.; Nelson, M.; Bathe, O.; Carroll, P.R.; Chan, J.M.; Disaia, P.; Glenn, P.; Kelley, R.K.; Landen, C.N.; Phillips, J.; Prados, M.; Simko, J.; Smith-McCune, K.; VandenBerg, S.; Roggin, K.; Fehrenbach, A.; Kendler, A.; Sifri, S.; Steele, R.; Jimeno, A.; Carey, F.; Forgie, I.; Mannelli, M.; Carney, M.; Hernandez, B.; Campos, B.; Herold-Mende, C.; Jungk, C.; Unterberg, A.; von Deimling, A.; Bossler, A.; Galbraith, J.; Jacobus, L.; Knudson, M.; Knutson, T.; Ma, D.; Milhem, M.; Sigmund, R.; Godwin, A.K.; Madan, R.; Rosenthal, H.G.; Adebamowo, C.; Adebamowo, S.N.; Boussioutas, A.; Beer, D.; Giordano, T.; Mes-Masson, A-M.; Saad, F.; Bocklage, T.; Landrum, L.; Mannel, R.; Moore, K.; Moxley, K.; Postier, R.; Walker, J.; Zuna, R.; Feldman, M.; Valdivieso, F.; Dhir, R.; Luketich, J.; Pinero, E.M.M.; Quintero-Aguilo, M.; Carlotti, C.G., Jr; Dos Santos, J.S.; Kemp, R.; Sankarankuty, A.; Tirapelli, D.; Catto, J.; Agnew, K.; Swisher, E.; Creaney, J.; Robinson, B.; Shelley, C.S.; Godwin, E.M.; Kendall, S.; Shipman, C.; Bradford, C.; Carey, T.; Haddad, A.; Moyer, J.; Peterson, L.; Prince, M.; Rozek, L.; Wolf, G.; Bowman, R.; Fong, K.M.; Yang, I.; Korst, R.; Rathmell, W.K.; Fantacone-Campbell, J.L.; Hooke, J.A.; Kovatich, A.J.; Shriver, C.D.; DiPersio, J.; Drake, B.; Govindan, R.; Heath, S.; Ley, T.; Van Tine, B.; Westervelt, P.; Rubin, M.A.; Lee, J.I.; Aredes, N.D.; Mariamidze, A. The immune landscape of cancer. Immunity, 2018, 48(4), 812-830.e14.
[http://dx.doi.org/10.1016/j.immuni.2018.03.023] [PMID: 29628290]

Gaudet, P.; Škunca, N.; Hu, J.C.; Dessimoz, C. Primer on the gene ontology. Methods Mol. Biol., 2017, 1446, 25-37.
[http://dx.doi.org/10.1007/978-1-4939-3743-1_3] [PMID: 27812933]

Kanehisa, M.; Furumichi, M.; Tanabe, M.; Sato, Y.; Morishima, K. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 2017, 45(D1), D353-D361.
[http://dx.doi.org/10.1093/nar/gkw1092] [PMID: 27899662]

Yu, G.; Wang, L.G.; Han, Y.; He, Q.Y. clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS, 2012, 16(5), 284-287.
[http://dx.doi.org/10.1089/omi.2011.0118] [PMID: 22455463]

Choi, W.; Porten, S.; Kim, S.; Willis, D.; Plimack, E.R.; Hoffman-Censits, J.; Roth, B.; Cheng, T.; Tran, M.; Lee, I.L.; Melquist, J.; Bondaruk, J.; Majewski, T.; Zhang, S.; Pretzsch, S.; Baggerly, K.; Siefker-Radtke, A.; Czerniak, B.; Dinney, C.P.N.; McConkey, D.J. Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell, 2014, 25(2), 152-165.
[http://dx.doi.org/10.1016/j.ccr.2014.01.009] [PMID: 24525232]

Damrauer, J.S.; Hoadley, K.A.; Chism, D.D.; Fan, C.; Tiganelli, C.J.; Wobker, S.E.; Yeh, J.J.; Milowsky, M.I.; Iyer, G.; Parker, J.S.; Kim, W.Y. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc. Natl. Acad. Sci., 2014, 111(8), 3110-3115.
[http://dx.doi.org/10.1073/pnas.1318376111] [PMID: 24520177]

Mo, Q.; Nikolos, F.; Chen, F.; Tramel, Z.; Lee, Y.C.; Hayashi, K.; Xiao, J.; Shen, J.; Chan, K.S. Prognostic power of a tumor differentiation gene signature for bladder urothelial carcinomas. J. Natl. Cancer Inst., 2018, 110(5), 448-459.
[http://dx.doi.org/10.1093/jnci/djx243] [PMID: 29342309]

Kamoun, A.; de Reyniès, A.; Allory, Y.; Sjödahl, G.; Robertson, A.G.; Seiler, R.; Hoadley, K.A.; Groeneveld, C.S.; Al-Ahmadie, H.; Choi, W.; Castro, M.A.A.; Fontugne, J.; Eriksson, P.; Mo, Q.; Kardos, J.; Zlotta, A.; Hartmann, A.; Dinney, C.P.; Bellmunt, J.; Powles, T.; Malats, N.; Chan, K.S.; Kim, W.Y.; McConkey, D.J.; Black, P.C.; Dyrskjøt, L.; Höglund, M.; Lerner, S.P.; Real, F.X.; Radvanyi, F.; Aine, M.; Al-Ahmadie, H.; Allory, Y.; Bellmunt, J.; Bernard-Pierrot, I.; Black, P.C.; Castro, M.A.A.; Chan, K.S.; Choi, W.; Czerniak, B.; Dinney, C.P.; Dyrskjøt, L.; Eriksson, P.; Fontugne, J.; Gibb, E.A.; Groeneveld, C.S.; Hartmann, A.; Hoadley, K.A.; Höglund, M.; Kamoun, A.; Kardos, J.; Kim, J.; Kim, W.Y.; Kwiatkowski, D.J.; Lebret, T.; Lerner, S.P.; Liedberg, F.; Malats, N.; McConkey, D.J.; Mo, Q.; Powles, T.; Radvanyi, F.; Real, F.X.; de Reyniès, A.; Robertson, A.G.; Siefker-Radtke, A.; Sirab, N.; Seiler, R.; Sjödahl, G.; Taber, A.; Weinstein, J.; Zlotta, A. A consensus molecular classification of muscle-invasive bladder cancer. Eur. Urol., 2020, 77(4), 420-433.
[http://dx.doi.org/10.1016/j.eururo.2019.09.006] [PMID: 31563503]

Robertson, A.G.; Kim, J.; Al-Ahmadie, H.; Bellmunt, J.; Guo, G.; Cherniack, A.D.; Hinoue, T.; Laird, P.W.; Hoadley, K.A.; Akbani, R.; Castro, M.A.A.; Gibb, E.A.; Kanchi, R.S.; Gordenin, D.A.; Shukla, S.A.; Sanchez-Vega, F.; Hansel, D.E.; Czerniak, B.A.; Reuter, V.E.; Su, X.; de Sa Carvalho, B.; Chagas, V.S.; Mungall, K.L.; Sadeghi, S.; Pedamallu, C.S.; Lu, Y.; Klimczak, L.J.; Zhang, J.; Choo, C.; Ojesina, A.I.; Bullman, S.; Leraas, K.M.; Lichtenberg, T.M.; Wu, C.J.; Schultz, N.; Getz, G.; Meyerson, M.; Mills, G.B.; McConkey, D.J.; Weinstein, J.N.; Kwiatkowski, D.J.; Lerner, S.P. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cancer Cell, 2018, 174(4), 1033.
[PMID: 30096301]

Rebouissou, S.; Bernard-Pierrot, I.; de Reyniès, A.; Lepage, M.L.; Krucker, C.; Chapeaublanc, E.; Hérault, A.; Kamoun, A.; Caillault, A.; Letouzé, E.; Elarouci, N.; Neuzillet, Y.; Denoux, Y.; Molinié, V.; Vordos, D.; Laplanche, A.; Maillé, P.; Soyeux, P.; Ofualuka, K.; Reyal, F.; Biton, A.; Sibony, M.; Paoletti, X.; Southgate, J.; Benhamou, S.; Lebret, T.; Allory, Y.; Radvanyi, F. EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype. Sci. Transl. Med., 2014, 6(244), 244ra91.
[http://dx.doi.org/10.1126/scitranslmed.3008970] [PMID: 25009231]

Sjödahl, G.; Lauss, M.; Lövgren, K.; Chebil, G.; Gudjonsson, S.; Veerla, S.; Patschan, O.; Aine, M.; Fernö, M.; Ringnér, M.; Månsson, W.; Liedberg, F.; Lindgren, D.; Höglund, M. A molecular taxonomy for urothelial carcinoma. Clin. Cancer Res., 2012, 18(12), 3377-3386.
[http://dx.doi.org/10.1158/1078-0432.CCR-12-0077-T] [PMID: 22553347]

Hänzelmann, S.; Castelo, R.; Guinney, J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 2013, 14(1), 7.
[http://dx.doi.org/10.1186/1471-2105-14-7] [PMID: 23323831]

Mayakonda, A.; Lin, D.C.; Assenov, Y.; Plass, C.; Koeffler, H.P. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res., 2018, 28(11), 1747-1756.
[http://dx.doi.org/10.1101/gr.239244.118] [PMID: 30341162]

Bindea, G.; Mlecnik, B.; Tosolini, M.; Kirilovsky, A.; Waldner, M.; Obenauf, A.C.; Angell, H.; Fredriksen, T.; Lafontaine, L.; Berger, A.; Bruneval, P.; Fridman, W.H.; Becker, C.; Pagès, F.; Speicher, M.R.; Trajanoski, Z.; Galon, J. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity, 2013, 39(4), 782-795.
[http://dx.doi.org/10.1016/j.immuni.2013.10.003] [PMID: 24138885]

Newman, A.M.; Liu, C.L.; Green, M.R.; Gentles, A.J.; Feng, W.; Xu, Y.; Hoang, C.D.; Diehn, M.; Alizadeh, A.A. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods, 2015, 12(5), 453-457.
[http://dx.doi.org/10.1038/nmeth.3337] [PMID: 25822800]

Yoshihara, K.; Shahmoradgoli, M.; Martínez, E.; Vegesna, R.; Kim, H.; Torres-Garcia, W.; Treviño, V.; Shen, H.; Laird, P.W.; Levine, D.A.; Carter, S.L.; Getz, G.; Stemke-Hale, K.; Mills, G.B.; Verhaak, R.G.W. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun., 2013, 4(1), 2612.
[http://dx.doi.org/10.1038/ncomms3612] [PMID: 24113773]

Mariathasan, S.; Turley, S.J.; Nickles, D.; Castiglioni, A.; Yuen, K.; Wang, Y.; Kadel, E.E., III; Koeppen, H.; Astarita, J.L.; Cubas, R.; Jhunjhunwala, S.; Banchereau, R.; Yang, Y.; Guan, Y.; Chalouni, C.; Ziai, J.; Şenbabaoğlu, Y.; Santoro, S.; Sheinson, D.; Hung, J.; Giltnane, J.M.; Pierce, A.A.; Mesh, K.; Lianoglou, S.; Riegler, J.; Carano, R.A.D.; Eriksson, P.; Höglund, M.; Somarriba, L.; Halligan, D.L.; van der Heijden, M.S.; Loriot, Y.; Rosenberg, J.E.; Fong, L.; Mellman, I.; Chen, D.S.; Green, M.; Derleth, C.; Fine, G.D.; Hegde, P.S.; Bourgon, R.; Powles, T. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature, 2018, 554(7693), 544-548.
[http://dx.doi.org/10.1038/nature25501] [PMID: 29443960]

Ayers, M.; Lunceford, J.; Nebozhyn, M.; Murphy, E.; Loboda, A.; Kaufman, D.R.; Albright, A.; Cheng, J.D.; Kang, S.P.; Shankaran, V.; Piha-Paul, S.A.; Yearley, J.; Seiwert, T.Y.; Ribas, A.; McClanahan, T.K. IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade. J. Clin. Invest., 2017, 127(8), 2930-2940.
[http://dx.doi.org/10.1172/JCI91190] [PMID: 28650338]

Fu, J.; Li, K.; Zhang, W.; Wan, C.; Zhang, J.; Jiang, P.; Liu, X.S. Large-scale public data reuse to model immunotherapy response and resistance. Genome Med., 2020, 12(1), 21.
[http://dx.doi.org/10.1186/s13073-020-0721-z] [PMID: 32102694]

Geeleher, P.; Cox, N.; Huang, R.S. pRRophetic: An R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One, 2014, 9(9), e107468.
[http://dx.doi.org/10.1371/journal.pone.0107468] [PMID: 25229481]

Gao, J.; Zheng, Q.; Xin, N.; Wang, W.; Zhao, C. CD 155, an onco‐immunologic molecule in human tumors. Cancer Sci., 2017, 108(10), 1934-1938.
[http://dx.doi.org/10.1111/cas.13324] [PMID: 28730595]

Lupo, K.B.; Matosevic, S. CD155 immunoregulation as a target for natural killer cell immunotherapy in glioblastoma. J. Hematol. Oncol., 2020, 13(1), 76.
[http://dx.doi.org/10.1186/s13045-020-00913-2] [PMID: 32532329]

Kearney, C.J.; Ramsbottom, K.M.; Voskoboinik, I.; Darcy, P.K.; Oliaro, J. Loss of DNAM-1 ligand expression by acute myeloid leukemia cells renders them resistant to NK cell killing. Onco Immunology, 2016, 5(8), e1196308.
[http://dx.doi.org/10.1080/2162402X.2016.1196308] [PMID: 27622064]

Zhang, J.; Zhu, Y.; Wang, Q.; Kong, Y.; Sheng, H.; Guo, J.; Xu, J.; Dai, B. Poliovirus receptor CD155 is up-regulated in muscle-invasive bladder cancer and predicts poor prognosis. Urol. Oncol., 2020, 38(2), 41.e11-41.e18.
[http://dx.doi.org/10.1016/j.urolonc.2019.07.006] [PMID: 31383549]

Luo, C.; Ye, W.; Hu, J.; Othmane, B.; Li, H.; Chen, J.; Zu, X. A poliovirus receptor (CD155)-related risk signature predicts the prognosis of bladder cancer. Front. Oncol., 2021, 11, 660273.
[http://dx.doi.org/10.3389/fonc.2021.660273] [PMID: 34150627]

Li, X.; Zhou, Q.; Sunkara, M.; Kutys, M.L.; Wu, Z.; Rychahou, P.; Morris, A.J.; Zhu, H.; Evers, B.M.; Huang, C. Ubiquitylation of phosphatidylinositol 4-phosphate 5-kinase type I γ by HECTD1 regulates focal adhesion dynamics and cell migration. J. Cell Sci., 2013, 126(Pt 12), 2617-2628.
[PMID: 23572508]

Bennett, L.; Madders, E.C.E.T.; Parsons, J.L. HECTD1 promotes base excision repair in nucleosomes through chromatin remodelling. Nucleic Acids Res., 2020, 48(3), 1301-1313.
[http://dx.doi.org/10.1093/nar/gkz1129] [PMID: 31799632]

de Curtis, I. The Rac3 GTPase in neuronal development, neurodevelopmental disorders, and cancer. Cells, 2019, 8(9), 1063.
[http://dx.doi.org/10.3390/cells8091063] [PMID: 31514269]

Sun, S.; Wang, Y.; Wang, J.; Bi, J. Wnt pathway-related three mRNA clinical outcome signature in bladder urothelial carcinoma: computational biology and experimental analyses. J. Transl. Med., 2021, 19(1), 409.
[http://dx.doi.org/10.1186/s12967-021-03061-4] [PMID: 34579753]

Zhu, W.L.; Hossain, M.S.; Guo, D.Y.; Liu, S.; Tong, H.; Khakpoor, A.; Casey, P.J.; Wang, M. A role for Rac3 GTPase in the regulation of autophagy. J. Biol. Chem., 2011, 286(40), 35291-35298.
[http://dx.doi.org/10.1074/jbc.M111.280990] [PMID: 21852230]

Rao, A.; Luo, C.; Hogan, P.G. Transcription factors of the nfat family:Regulation and function. Annu. Rev. Immunol., 1997, 15(1), 707-747.
[http://dx.doi.org/10.1146/annurev.immunol.15.1.707] [PMID: 9143705]

Peng, S.L.; Gerth, A.J.; Ranger, A.M.; Glimcher, L.H. NFATc1 and NFATc2 together control both T and B cell acti-vation and differentiation. Immunity, 2001, 14(1), 13-20.
[http://dx.doi.org/10.1016/S1074-7613(01)00085-1] [PMID: 11163226]

Heim, L.; Friedrich, J.; Engelhardt, M.; Trufa, D.I.; Geppert, C.I.; Rieker, R.J.; Sirbu, H.; Finotto, S. NFATc1 promotes antitumoral effector functions and memory CD8+ T-cell differentiation during non–small cell lung cancer development. Cancer Res., 2018, 78(13), 3619-3633.
[http://dx.doi.org/10.1158/0008-5472.CAN-17-3297] [PMID: 29691251]

Tsai, F.Y.; Keller, G.; Kuo, F.C.; Weiss, M.; Chen, J.; Rosenblatt, M.; Alt, F.W.; Orkin, S.H. An early haematopoietic defect in micelacking the transcription factor GATA-2. Nature, 1994, 371(6494), 221-226.
[http://dx.doi.org/10.1038/371221a0] [PMID: 8078582]

Katerndahl, C.D.S.; Rogers, O.R.S.; Day, R.B.; Cai, M.A.; Rooney, T.P.; Helton, N.M.; Hoock, M.; Ramakrishnan, S.M.; Nonavinkere Srivatsan, S.; Wartman, L.D.; Miller, C.A.; Ley, T.J. Tumor suppressor function of Gata2 in acute promyelocytic leukemia. Blood, 2021, 138(13), 1148-1161.
[http://dx.doi.org/10.1182/blood.2021011758] [PMID: 34125173]

Mace, E.M.; Hsu, A.P.; Monaco-Shawver, L.; Makedonas, G.; Rosen, J.B.; Dropulic, L.; Cohen, J.I.; Frenkel, E.P.; Bagwell, J.C.; Sullivan, J.L.; Biron, C.A.; Spalding, C.; Zerbe, C.S.; Uzel, G.; Holland, S.M.; Orange, J.S. Mutations in GATA2 cause human NK cell deficiency with specific loss of the CD56bright subset. Blood, 2013, 121(14), 2669-2677.
[http://dx.doi.org/10.1182/blood-2012-09-453969] [PMID: 23365458]

Dell’Angelica, E.C. The building BLOC(k)s of lysosomes and related organelles. Curr. Opin. Cell Biol., 2004, 16(4), 458-464.
[http://dx.doi.org/10.1016/j.ceb.2004.05.001] [PMID: 15261680]

Morgan, N.V.; Pasha, S.; Johnson, C.A.; Ainsworth, J.R.; Eady, R.A.J.; Dawood, B.; McKeown, C.; Trembath, R.C.; Wilde, J.; Watson, S.P.; Maher, E.R. A germline mutation in BLOC1S3/reduced pigmentation causes a novel variant of Hermansky-Pudlak syndrome (HPS8). Am. J. Hum. Genet., 2006, 78(1), 160-166.
[http://dx.doi.org/10.1086/499338] [PMID: 16385460]

Balar, A.V.; Kamat, A.M.; Kulkarni, G.S.; Uchio, E.M.; Boormans, J.L.; Roumiguié, M.; Krieger, L.E.M.; Singer, E.A.; Bajorin, D.F.; Grivas, P.; Seo, H.K.; Nishiyama, H.; Konety, B.R.; Li, H.; Nam, K.; Kapadia, E.; Frenkl, T.; de Wit, R. Pembrolizumab monotherapy for the treatment of high-risk non-muscle-invasive bladder cancer unresponsive to BCG (KEYNOTE-057): An open-label, single-arm, multicentre, phase 2 study. Lancet Oncol., 2021, 22(7), 919-930.
[http://dx.doi.org/10.1016/S1470-2045(21)00147-9] [PMID: 34051177]

Li, M.O.; Wolf, N.; Raulet, D.H.; Akkari, L.; Pittet, M.J.; Ro-driguez, P.C.; Kaplan, R.N.; Munitz, A.; Zhang, Z.; Cheng, S.; Bhardwaj, N. Innate immune cells in the tumor microenvironment. Cancer Cell, 2021, 39(6), 725-729.
[http://dx.doi.org/10.1016/j.ccell.2021.05.016] [PMID: 34129817]

Ranti, D.; Bieber, C.; Wang, Y.S.; Sfakianos, J.P.; Horowitz, A. Natural killer cells: Unlocking new treatments for bladder cancer. Trends Cancer, 2022, 8(8), 698-710.
[http://dx.doi.org/10.1016/j.trecan.2022.03.007] [PMID: 35581130]

Rosenberg, J.; Huang, J. CD8+ T cells and NK cells: Parallel and complementary soldiers of immunotherapy. Curr. Opin. Chem. Eng., 2018, 19, 9-20.
[http://dx.doi.org/10.1016/j.coche.2017.11.006] [PMID: 29623254]

Tsujihashi, H.; Matsuda, H.; Uejima, S.; Akiyama, T.; Kurita, T. Role of natural killer cells in bladder tumor. Eur. Urol., 1989, 16(6), 444-449.
[http://dx.doi.org/10.1159/000471637] [PMID: 2591428]

Moretta, A.; Biassoni, R.; Bottino, C.; Pende, D.; Vitale, M.; Poggi, A.; Mingari, M.C.; Moretta, L. Major histocompatibility complex class I-specific receptors on human natural killer and T lymphocytes. Immunol. Rev., 1997, 155(1), 105-117.
[http://dx.doi.org/10.1111/j.1600-065X.1997.tb00943.x] [PMID: 9059886]

Buckle, I.; Guillerey, C. Inhibitory receptors and immune checkpoints regulating natural killer cell responses to cancer. Cancers., 2021, 13(17), 4263.
[http://dx.doi.org/10.3390/cancers13174263] [PMID: 34503073]

Khan, M.; Arooj, S.; Wang, H. NK cell-based immune check point inhibition. Front. Immunol., 2020, 11, 167.
[http://dx.doi.org/10.3389/fimmu.2020.00167] [PMID: 32117298]

Galot, R.; Le Tourneau, C.; Saada-Bouzid, E.; Daste, A.; Even, C.; Debruyne, P.; Henry, S.; Zanetta, S.; Rutten, A.; Licitra, L.; Canon, J.L.; Kaminsky, M.C.; Specenier, P.; Rottey, S.; Guigay, J.; Kong, A.; Tinhofer, I.; Borcoman, E.; Dirix, L.; Raveloarivahy, T.; Fortpied, C.; Vanlancker, M.; Morfouace, M.; Govaerts, A.S.; Machiels, J.P. A phase II study of monalizumab in patients with recurrent/metastatic squamous cell carcinoma of the head and neck: The I1 cohort of the EORTC-HNCG-1559 UPSTREAM trial. Eur. J. Cancer, 2021, 158, 17-26.
[http://dx.doi.org/10.1016/j.ejca.2021.09.003] [PMID: 34638090]

Ruggeri, L.; Urbani, E.; André, P.; Mancusi, A.; Tosti, A.; Topini, F.; Bléry, M.; Animobono, L.; Romagné, F.; Wagtmann, N.; Velardi, A. Effects of anti-NKG2A antibody administration on leukemia and normal hematopoietic cells. Haematologica, 2016, 101(5), 626-633.
[http://dx.doi.org/10.3324/haematol.2015.135301] [PMID: 26721894]

Jandus, C.; Boligan, K.F.; Chijioke, O.; Liu, H.; Dahlhaus, M.; Démoulins, T.; Schneider, C.; Wehrli, M.; Hunger, R.E.; Baerlocher, G.M.; Simon, H.U.; Romero, P.; Münz, C.; von Gunten, S. Interactions between Siglec-7/9 receptors and ligands influence NK cell–dependent tumor immunosurveillance. J. Clin. Invest., 2014, 124(4), 1810-1820.
[http://dx.doi.org/10.1172/JCI65899] [PMID: 24569453]

Matlung, H.L.; Szilagyi, K.; Barclay, N.A.; van den Berg, T.K. The CD47-SIRPα signaling axis as an innate immune check point in cancer. Immunol. Rev., 2017, 276(1), 145-164.
[http://dx.doi.org/10.1111/imr.12527] [PMID: 28258703]