Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma

Sung, H.; Ferlay, J.; Siegel, R.L.; Laversanne, M.; Soerjomataram, I.; Jemal, A.; Bray, F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin., 2021, 71(3), 209-249.
[http://dx.doi.org/10.3322/caac.21660] [PMID: 33538338]

Wu, F.; Wang, L.; Zhou, C. Lung cancer in China: Current and prospect. Curr. Opin. Oncol., 2021, 33(1), 40-46.
[http://dx.doi.org/10.1097/CCO.0000000000000703] [PMID: 33165004]

Dan, AK; Manna, A; Ghosh, S; Sikdar, S; Sahu, R; Parhi, PK Molecular mechanisms of the lipopeptides from Bacillus subtilis in the apoptosis of cancer cells - A review on its current status in different cancer cell lines. Advances in Cancer Biology - Metastasis, 2021, 3, 100019.

Wang, M.; Herbst, R.S.; Boshoff, C. Toward personalized treatment approaches for non-small-cell lung cancer. Nat. Med., 2021, 27(8), 1345-1356.
[http://dx.doi.org/10.1038/s41591-021-01450-2] [PMID: 34385702]

Jones, P.A.; Baylin, S.B. The epigenomics of cancer. Cell, 2007, 128(4), 683-692.
[http://dx.doi.org/10.1016/j.cell.2007.01.029] [PMID: 17320506]

Flavahan, W.A.; Gaskell, E.; Bernstein, B.E. Epigenetic plasticity and the hallmarks of cancer. Science, 2017, 357(6348), eaal2380.
[http://dx.doi.org/10.1126/science.aal2380] [PMID: 28729483]

Aamna, B.; Kumar Dan, A.; Sahu, R.; Behera, S.K.; Parida, S. Deciphering the signaling mechanisms of β-arrestin1 and β-arrestin2 in regulation of cancer cell cycle and metastasis. J. Cell. Physiol., 2022, 237(10), 3717-3733.
[http://dx.doi.org/10.1002/jcp.30847] [PMID: 35908197]

Gaudet, F.; Hodgson, J.G.; Eden, A.; Jackson-Grusby, L.; Dausman, J.; Gray, J.W.; Leonhardt, H.; Jaenisch, R. Induction of tumors in mice by genomic hypomethylation. Science, 2003, 300(5618), 489-492.
[http://dx.doi.org/10.1126/science.1083558] [PMID: 12702876]

Jun, H.J.; Woolfenden, S.; Coven, S.; Lane, K.; Bronson, R.; Housman, D.; Charest, A. Epigenetic regulation of c-ROS receptor tyrosine kinase expression in malignant gliomas. Cancer Res., 2009, 69(6), 2180-2184.
[http://dx.doi.org/10.1158/0008-5472.CAN-08-3351] [PMID: 19276365]

Kakaradov, B.; Arsenio, J.; Widjaja, C.E.; He, Z.; Aigner, S.; Metz, P.J.; Yu, B.; Wehrens, E.J.; Lopez, J.; Kim, S.H.; Zuniga, E.I.; Goldrath, A.W.; Chang, J.T.; Yeo, G.W. Early transcriptional and epigenetic regulation of CD8⁺ T cell differentiation revealed by single-cell RNA sequencing. Nat. Immunol., 2017, 18(4), 422-432.
[http://dx.doi.org/10.1038/ni.3688] [PMID: 28218746]

Xie, S.; Chen, W.; Chen, K.; Chang, Y.; Yang, F.; Lin, A.; Shu, Q.; Zhou, T.; Yan, X. Emerging roles of RNA methylation in gastrointestinal cancers. Cancer Cell Int., 2020, 20(1), 585.
[http://dx.doi.org/10.1186/s12935-020-01679-w] [PMID: 33372610]

Ma, L.; Xue, X.; Zhang, X.; Yu, K.; Xu, X.; Tian, X.; Miao, Y.; Meng, F.; Liu, X.; Guo, S.; Qiu, S.; Wang, Y.; Cui, J.; Guo, W.; Li, Y.; Xia, J.; Yu, Y.; Wang, J. The essential roles of m⁶A RNA modification to stimulate ENO1-dependent glycolysis and tumorigenesis in lung adenocarcinoma. J. Exp. Clin. Cancer Res., 2022, 41(1), 36.
[http://dx.doi.org/10.1186/s13046-021-02200-5] [PMID: 35078505]

Yu, W.; Zhang, C.; Wang, Y.; Tian, X.; Miao, Y.; Meng, F.; Ma, L.; Zhang, X.; Xia, J. YAP 5-methylcytosine modification increases its mRNA stability and promotes the transcription of exosome secretion-related genes in lung adenocarcinoma. Cancer Gene Ther., 2023, 30(1), 149-162.
[http://dx.doi.org/10.1038/s41417-022-00533-7] [PMID: 36123390]

Ma, S.; Zhu, J.; Wang, M.; Zhu, J.; Wang, W.; Xiong, Y.; Jiang, R.; Liu, L.; Jiang, T. Comprehensive analysis of m⁷G modification patterns based on potential m⁷G regulators and tumor microenvironment infiltration characterization in lung adenocarcinoma. Front. Genet., 2022, 13, 996950.
[http://dx.doi.org/10.3389/fgene.2022.996950] [PMID: 36246663]

Ouyang, W.; Jiang, Y.; Bu, S.; Tang, T.; Huang, L.; Chen, M.; Tan, Y.; Ou, Q.; Mao, L.; Mai, Y.; Yao, H.; Yu, Y.; Lin, X. A prognostic risk score based on hypoxia-, immunity-, and epithelialto-mesenchymal transition-related genes for the prognosis and immunotherapy response of lung adenocarcinoma. Front. Cell Dev. Biol., 2022, 9, 758777.
[http://dx.doi.org/10.3389/fcell.2021.758777] [PMID: 35141229]

Zhang, M.; Song, J.; Yuan, W.; Zhang, W.; Sun, Z. Roles of RNA methylation on tumor immunity and clinical implications. Front. Immunol., 2021, 12, 641507.
[http://dx.doi.org/10.3389/fimmu.2021.641507] [PMID: 33777035]

Okayama, H.; Kohno, T.; Ishii, Y.; Shimada, Y.; Shiraishi, K.; Iwakawa, R.; Furuta, K.; Tsuta, K.; Shibata, T.; Yamamoto, S.; Watanabe, S.; Sakamoto, H.; Kumamoto, K.; Takenoshita, S.; Gotoh, N.; Mizuno, H.; Sarai, A.; Kawano, S.; Yamaguchi, R.; Miyano, S.; Yokota, J. Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res., 2012, 72(1), 100-111.
[http://dx.doi.org/10.1158/0008-5472.CAN-11-1403] [PMID: 22080568]

Schabath, M.B.; Welsh, E.A.; Fulp, W.J.; Chen, L.; Teer, J.K.; Thompson, Z.J.; Engel, B.E.; Xie, M.; Berglund, A.E.; Creelan, B.C.; Antonia, S.J.; Gray, J.E.; Eschrich, S.A.; Chen, D-T.; Cress, W.D.; Haura, E.B.; Beg, A.A. Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma. Oncogene, 2016, 35(24), 3209-3216.
[http://dx.doi.org/10.1038/onc.2015.375] [PMID: 26477306]

Shen, W.; Song, Z.; Zhong, X.; Huang, M.; Shen, D.; Gao, P.; Qian, X.; Wang, M.; He, X.; Wang, T.; Li, S.; Song, X. Sangerbox: A comprehensive, interaction-friendly clinical bioinformatics analysis platform. iMeta, 2022, 1(3), e36.
[http://dx.doi.org/10.1002/imt2.36]

Frankish, A.; Carbonell-Sala, S.; Diekhans, M.; Jungreis, I.; Loveland, J.E.; Mudge, J.M.; Sisu, C.; Wright, J.C.; Arnan, C.; Barnes, I.; Banerjee, A.; Bennett, R.; Berry, A.; Bignell, A.; Boix, C.; Calvet, F.; Cerdán-Vélez, D.; Cunningham, F.; Davidson, C.; Donaldson, S.; Dursun, C.; Fatima, R.; Giorgetti, S.; Giron, C.G.; Gonzalez, J.M.; Hardy, M.; Harrison, P.W.; Hourlier, T.; Hollis, Z.; Hunt, T.; James, B.; Jiang, Y.; Johnson, R.; Kay, M.; Lagarde, J.; Martin, F.J.; Gómez, L.M.; Nair, S.; Ni, P.; Pozo, F.; Ramalingam, V.; Ruffier, M.; Schmitt, B.M.; Schreiber, J.M.; Steed, E.; Suner, M.M.; Sumathipala, D.; Sycheva, I.; Uszczynska-Ratajczak, B.; Wass, E.; Yang, Y.T.; Yates, A.; Zafrulla, Z.; Choudhary, J.S.; Gerstein, M.; Guigo, R.; Hubbard, T.J.P.; Kellis, M.; Kundaje, A.; Paten, B.; Tress, M.L.; Flicek, P. GENCODE: Reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res., 2023, 51(D1), D942-D949.
[http://dx.doi.org/10.1093/nar/gkac1071] [PMID: 36420896]

Zhang, M.; Zhu, K.; Pu, H.; Wang, Z.; Zhao, H.; Zhang, J.; Wang, Y. An immune-related signature predicts survival in patients with lung adenocarcinoma. Front. Oncol., 2019, 9, 1314.
[http://dx.doi.org/10.3389/fonc.2019.01314] [PMID: 31921619]

He, R.; Man, C.; Huang, J.; He, L.; Wang, X.; Lang, Y.; Fan, Y. Identification of RNA methylation-related lncrnas signature for predicting hot and cold tumors and prognosis in colon cancer. Front. Genet., 2022, 13, 870945.
[http://dx.doi.org/10.3389/fgene.2022.870945] [PMID: 35464855]

Bagaev, A.; Kotlov, N.; Nomie, K.; Svekolkin, V.; Gafurov, A.; Isaeva, O.; Osokin, N.; Kozlov, I.; Frenkel, F.; Gancharova, O.; Almog, N.; Tsiper, M.; Ataullakhanov, R.; Fowler, N. Conserved pan-cancer microenvironment subtypes predict response to immunotherapy. Cancer Cell, 2021, 39(6), 845-865.e7.
[http://dx.doi.org/10.1016/j.ccell.2021.04.014] [PMID: 34019806]

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]

Wilkerson, M.D.; Hayes, D.N. ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking. Bioinformatics, 2010, 26(12), 1572-1573.
[http://dx.doi.org/10.1093/bioinformatics/btq170] [PMID: 20427518]

Beroukhim, R.; Mermel, C.H.; Porter, D.; Wei, G.; Raychaudhuri, S.; Donovan, J.; Barretina, J.; Boehm, J.S.; Dobson, J.; Urashima, M.; Mc Henry, K.T.; Pinchback, R.M.; Ligon, A.H.; Cho, Y.J.; Haery, L.; Greulich, H.; Reich, M.; Winckler, W.; Lawrence, M.S.; Weir, B.A.; Tanaka, K.E.; Chiang, D.Y.; Bass, A.J.; Loo, A.; Hoffman, C.; Prensner, J.; Liefeld, T.; Gao, Q.; Yecies, D.; Signoretti, S.; Maher, E.; Kaye, F.J.; Sasaki, H.; Tepper, J.E.; Fletcher, J.A.; Tabernero, J.; Baselga, J.; Tsao, M.S.; Demichelis, F.; Rubin, M.A.; Janne, P.A.; Daly, M.J.; Nucera, C.; Levine, R.L.; Ebert, B.L.; Gabriel, S.; Rustgi, A.K.; Antonescu, C.R.; Ladanyi, M.; Letai, A.; Garraway, L.A.; Loda, M.; Beer, D.G.; True, L.D.; Okamoto, A.; Pomeroy, S.L.; Singer, S.; Golub, T.R.; Lander, E.S.; Getz, G.; Sellers, W.R.; Meyerson, M. The landscape of somatic copy-number alteration across human cancers. Nature, 2010, 463(7283), 899-905.
[http://dx.doi.org/10.1038/nature08822] [PMID: 20164920]

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]

Ishwaran, H.; Lu, M.; Kogalur, U.B. Random Forest SRC: Variable importance (VIMP) with subsampling inference vignette. 2021. Available from:
[http://dx.doi.org/10.13140/RG.2.2.23799.75680]

Blanche, P.; Dartigues, J.F.; Jacqmin-Gadda, H. Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks. Stat. Med., 2013, 32(30), 5381-5397.
[http://dx.doi.org/10.1002/sim.5958] [PMID: 24027076]

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]

Chen, B.; Khodadoust, M.S.; Liu, C.L.; Newman, A.M.; Alizadeh, A.A. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol. Biol., 2018, 1711, 243-259.
[http://dx.doi.org/10.1007/978-1-4939-7493-1_12] [PMID: 29344893]

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]

Barbie, D.A.; Tamayo, P.; Boehm, J.S.; Kim, S.Y.; Moody, S.E.; Dunn, I.F.; Schinzel, A.C.; Sandy, P.; Meylan, E.; Scholl, C.; Fröhling, S.; Chan, E.M.; Sos, M.L.; Michel, K.; Mermel, C.; Silver, S.J.; Weir, B.A.; Reiling, J.H.; Sheng, Q.; Gupta, P.B.; Wadlow, R.C.; Le, H.; Hoersch, S.; Wittner, B.S.; Ramaswamy, S.; Livingston, D.M.; Sabatini, D.M.; Meyerson, M.; Thomas, R.K.; Lander, E.S.; Mesirov, J.P.; Root, D.E.; Gilliland, D.G.; Jacks, T.; Hahn, W.C. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature, 2009, 462(7269), 108-112.
[http://dx.doi.org/10.1038/nature08460] [PMID: 19847166]

Xu, L.; Deng, C.; Pang, B.; Zhang, X.; Liu, W.; Liao, G.; Yuan, H.; Cheng, P.; Li, F.; Long, Z.; Yan, M.; Zhao, T.; Xiao, Y.; Li, X. TIP: A web server for resolving tumor immunophenotype profiling. Cancer Res., 2018, 78(23), 6575-6580.
[http://dx.doi.org/10.1158/0008-5472.CAN-18-0689] [PMID: 30154154]

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]

Danilova, L.; Ho, W.J.; Zhu, Q.; Vithayathil, T.; De Jesus-Acosta, A.; Azad, N.S.; Laheru, D.A.; Fertig, E.J.; Anders, R.; Jaffee, E.M.; Yarchoan, M. Programmed cell death ligand-1 (PD-L1) and CD8 expression profiling identify an immunologic subtype of pancreatic ductal adenocarcinomas with favorable survival. Cancer Immunol. Res., 2019, 7(6), 886-895.
[http://dx.doi.org/10.1158/2326-6066.CIR-18-0822] [PMID: 31043417]

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, 2015, 160(1-2), 48-61.
[http://dx.doi.org/10.1016/j.cell.2014.12.033] [PMID: 25594174]

Auslander, N.; Zhang, G.; Lee, J.S.; Frederick, D.T.; Miao, B.; Moll, T.; Tian, T.; Wei, Z.; Madan, S.; Sullivan, R.J.; Boland, G.; Flaherty, K.; Herlyn, M.; Ruppin, E. Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Nat. Med., 2018, 24(10), 1545-1549.
[http://dx.doi.org/10.1038/s41591-018-0157-9] [PMID: 30127394]

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]

Zhan, L.; Zhang, J.; Zhu, S.; Liu, X.; Zhang, J.; Wang, W.; Fan, Y.; Sun, S.; Wei, B.; Cao, Y. N⁶-Methyladenosine RNA Modification: An emerging immunotherapeutic approach to turning up cold tumors. Front. Cell Dev. Biol., 2021, 9, 736298.
[http://dx.doi.org/10.3389/fcell.2021.736298] [PMID: 34616742]

Galon, J.; Bruni, D. Approaches to treat immune hot, altered and cold tumours with combination immunotherapies. Nat. Rev. Drug Discov., 2019, 18(3), 197-218.
[http://dx.doi.org/10.1038/s41573-018-0007-y] [PMID: 30610226]

Xu, Y.; Zhang, M.; Zhang, Q.; Yu, X.; Sun, Z.; He, Y.; Guo, W. Role of Main RNA Methylation in hepatocellular carcinoma: N6-Methyladenosine, 5-Methylcytosine, and N1-Methyladenosine. Front. Cell Dev. Biol., 2021, 9, 767668.
[http://dx.doi.org/10.3389/fcell.2021.767668] [PMID: 34917614]

Sun, Z.; Xue, S.; Zhang, M.; Xu, H.; Hu, X.; Chen, S.; Liu, Y.; Guo, M.; Cui, H. Aberrant NSUN2-mediated m⁵C modification of H19 lncRNA is associated with poor differentiation of hepatocellular carcinoma. Oncogene, 2020, 39(45), 6906-6919.
[http://dx.doi.org/10.1038/s41388-020-01475-w] [PMID: 32978516]

Li, H.B.; Tong, J.; Zhu, S.; Batista, P.J.; Duffy, E.E.; Zhao, J.; Bailis, W.; Cao, G.; Kroehling, L.; Chen, Y.; Wang, G.; Broughton, J.P.; Chen, Y.G.; Kluger, Y.; Simon, M.D.; Chang, H.Y.; Yin, Z.; Flavell, R.A. m⁶A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature, 2017, 548(7667), 338-342.
[http://dx.doi.org/10.1038/nature23450] [PMID: 28792938]

Wu, M.; Fu, P.; Qu, L.; Liu, J.; Lin, A. Long noncoding RNAs, New critical regulators in cancer immunity. Front. Oncol., 2020, 10, 550987.
[http://dx.doi.org/10.3389/fonc.2020.550987] [PMID: 33194608]

Eptaminitaki, G.C.; Wolff, N.; Stellas, D.; Sifakis, K.; Baritaki, S. Long non-coding RNAs (lncRNAs) in response and resistance to cancer immunosurveillance and immunotherapy. Cells, 2021, 10(12), 3313.
[http://dx.doi.org/10.3390/cells10123313] [PMID: 34943820]

Yadav, V.K.; De, S. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief. Bioinform., 2015, 16(2), 232-241.
[http://dx.doi.org/10.1093/bib/bbu002] [PMID: 24562872]

Ren, N.; Liang, B.; Li, Y. Identification of prognosis-related genes in the tumor microenvironment of stomach adenocarcinoma by TCGA and GEO datasets. Biosci. Rep., 2020, 40(10), BSR20200980.
[http://dx.doi.org/10.1042/BSR20200980] [PMID: 33015704]

Gong, Z.; Zhang, J.; Guo, W. Tumor purity as a prognosis and immunotherapy relevant feature in gastric cancer. Cancer Med., 2020, 9(23), 9052-9063.
[http://dx.doi.org/10.1002/cam4.3505] [PMID: 33030278]

Feng, H.; Zhao, Y.; Yan, W.; Wei, X.; Lin, J.; Jiang, P.; Wang, C.; Li, B. Identification of signature genes and characterizations of tumor immune microenvironment and tumor purity in lung adenocarcinoma based on machine learning. Front. Med., 2022, 9, 843749.
[http://dx.doi.org/10.3389/fmed.2022.843749] [PMID: 35280857]

Wei, W.; Ji, S. Cellular senescence: Molecular mechanisms and pathogenicity. J. Cell. Physiol., 2018, 233(12), 9121-9135.
[http://dx.doi.org/10.1002/jcp.26956] [PMID: 30078211]

Witt, D.A.; Donson, A.M.; Amani, V.; Moreira, D.C.; Sanford, B.; Hoffman, L.M.; Handler, M.H.; Levy, J.M.M.; Jones, K.L.; Nellan, A.; Foreman, N.K.; Griesinger, A.M. Specific expression of PD-L1 in RELA-fusion supratentorial ependymoma: Implications for PD-1-targeted therapy. Pediatr. Blood Cancer, 2018, 65(5), e26960.
[http://dx.doi.org/10.1002/pbc.26960] [PMID: 29350470]

Kythreotou, A.; Siddique, A.; Mauri, F.A.; Bower, M.; Pinato, D.J. Pd-L1. J. Clin. Pathol., 2018, 71(3), 189-194.
[http://dx.doi.org/10.1136/jclinpath-2017-204853] [PMID: 29097600]

Lu, J.; Zhu, D.; Zhang, X.; Wang, J.; Cao, H.; Li, L. The crucial role of LncRNA MIR210HG involved in the regulation of human cancer and other disease. Clin. Transl. Oncol., 2022, 25(1), 137-150.
[http://dx.doi.org/10.1007/s12094-022-02943-3] [PMID: 36088513]

Shang, B.; Li, Z.; Li, M.; Jiang, S.; Feng, Z.; Cao, Z.; Wang, H. Silencing LINC01116 suppresses the development of lung adenocarcinoma via the AKT signaling pathway. Thorac. Cancer, 2021, 12(14), 2093-2103.
[http://dx.doi.org/10.1111/1759-7714.14042] [PMID: 34061456]

Ding, Y.; Liu, J.H. The signature lncRNAs associated with the lung adenocarcinoma patients prognosis. Math. Biosci. Eng., 2020, 17(2), 1593-1603.
[http://dx.doi.org/10.3934/mbe.2020083] [PMID: 32233597]

Zheng, J.; Zhao, Z.; Wan, J.; Guo, M.; Wang, Y.; Yang, Z.; Li, Z.; Ming, L.; Qin, Z. N-6 methylation-related lncRNA is potential signature in lung adenocarcinoma and influences tumor microenvironment. J. Clin. Lab. Anal., 2021, 35(11), e23951.
[http://dx.doi.org/10.1002/jcla.23951] [PMID: 34558724]

Ren, J.; Wang, A.; Liu, J.; Yuan, Q. Identification and validation of a novel redox-related lncRNA prognostic signature in lung adenocarcinoma. Bioengineered, 2021, 12(1), 4331-4348.
[http://dx.doi.org/10.1080/21655979.2021.1951522] [PMID: 34338158]