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


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Abstract

Background:RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis.

Methods:RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package.

Results:Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy.

Conclusion:The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.

About the authors

Jiajing Wang

Department of Clinical Laboratory, Beilun People's Hospital

Email: info@benthamscience.net

Jianfeng Shu

Huamei Hospital, University of Chinese Academy of Sciences

Author for correspondence.
Email: info@benthamscience.net

References

  1. 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. doi: 10.3322/caac.21660 PMID: 33538338
  2. Wu, F.; Wang, L.; Zhou, C. Lung cancer in China: Current and prospect. Curr. Opin. Oncol., 2021, 33(1), 40-46. doi: 10.1097/CCO.0000000000000703 PMID: 33165004
  3. 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.
  4. Wang, M.; Herbst, R.S.; Boshoff, C. Toward personalized treatment approaches for non-small-cell lung cancer. Nat. Med., 2021, 27(8), 1345-1356. doi: 10.1038/s41591-021-01450-2 PMID: 34385702
  5. Jones, P.A.; Baylin, S.B. The epigenomics of cancer. Cell, 2007, 128(4), 683-692. doi: 10.1016/j.cell.2007.01.029 PMID: 17320506
  6. Flavahan, W.A.; Gaskell, E.; Bernstein, B.E. Epigenetic plasticity and the hallmarks of cancer. Science, 2017, 357(6348), eaal2380. doi: 10.1126/science.aal2380 PMID: 28729483
  7. 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. doi: 10.1002/jcp.30847 PMID: 35908197
  8. 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. doi: 10.1126/science.1083558 PMID: 12702876
  9. 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. doi: 10.1158/0008-5472.CAN-08-3351 PMID: 19276365
  10. 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. doi: 10.1038/ni.3688 PMID: 28218746
  11. 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. doi: 10.1186/s12935-020-01679-w PMID: 33372610
  12. 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. doi: 10.1186/s13046-021-02200-5 PMID: 35078505
  13. 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. doi: 10.1038/s41417-022-00533-7 PMID: 36123390
  14. 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. doi: 10.3389/fgene.2022.996950 PMID: 36246663
  15. 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. doi: 10.3389/fcell.2021.758777 PMID: 35141229
  16. 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. doi: 10.3389/fimmu.2021.641507 PMID: 33777035
  17. 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. doi: 10.1158/0008-5472.CAN-11-1403 PMID: 22080568
  18. 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. doi: 10.1038/onc.2015.375 PMID: 26477306
  19. 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. doi: 10.1002/imt2.36
  20. 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. doi: 10.1093/nar/gkac1071 PMID: 36420896
  21. 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. doi: 10.3389/fonc.2019.01314 PMID: 31921619
  22. 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. doi: 10.3389/fgene.2022.870945 PMID: 35464855
  23. 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. doi: 10.1016/j.ccell.2021.04.014 PMID: 34019806
  24. 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. doi: 10.1101/gr.239244.118 PMID: 30341162
  25. Wilkerson, M.D.; Hayes, D.N. ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking. Bioinformatics, 2010, 26(12), 1572-1573. doi: 10.1093/bioinformatics/btq170 PMID: 20427518
  26. 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. doi: 10.1038/nature08822 PMID: 20164920
  27. 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. doi: 10.1016/j.immuni.2018.03.023 PMID: 29628290
  28. Ishwaran, H.; Lu, M.; Kogalur, U.B. Random Forest SRC: Variable importance (VIMP) with subsampling inference vignette. 2021. Available from: doi: 10.13140/RG.2.2.23799.75680
  29. 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. doi: 10.1002/sim.5958 PMID: 24027076
  30. 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. doi: 10.1038/ncomms3612 PMID: 24113773
  31. 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. doi: 10.1007/978-1-4939-7493-1_12 PMID: 29344893
  32. Hänzelmann, S.; Castelo, R.; Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 2013, 14(1), 7. doi: 10.1186/1471-2105-14-7 PMID: 23323831
  33. 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. doi: 10.1038/nature08460 PMID: 19847166
  34. 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. doi: 10.1158/0008-5472.CAN-18-0689 PMID: 30154154
  35. 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. doi: 10.1172/JCI91190 PMID: 28650338
  36. 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. doi: 10.1158/2326-6066.CIR-18-0822 PMID: 31043417
  37. 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. doi: 10.1016/j.cell.2014.12.033 PMID: 25594174
  38. 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. doi: 10.1038/s41591-018-0157-9 PMID: 30127394
  39. 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. doi: 10.1089/omi.2011.0118 PMID: 22455463
  40. 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. doi: 10.3389/fcell.2021.736298 PMID: 34616742
  41. 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. doi: 10.1038/s41573-018-0007-y PMID: 30610226
  42. 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. doi: 10.3389/fcell.2021.767668 PMID: 34917614
  43. 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. doi: 10.1038/s41388-020-01475-w PMID: 32978516
  44. 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. doi: 10.1038/nature23450 PMID: 28792938
  45. Wu, M.; Fu, P.; Qu, L.; Liu, J.; Lin, A. Long noncoding RNAs, New critical regulators in cancer immunity. Front. Oncol., 2020, 10, 550987. doi: 10.3389/fonc.2020.550987 PMID: 33194608
  46. 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. doi: 10.3390/cells10123313 PMID: 34943820
  47. 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. doi: 10.1093/bib/bbu002 PMID: 24562872
  48. 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. doi: 10.1042/BSR20200980 PMID: 33015704
  49. 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. doi: 10.1002/cam4.3505 PMID: 33030278
  50. 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. doi: 10.3389/fmed.2022.843749 PMID: 35280857
  51. Wei, W.; Ji, S. Cellular senescence: Molecular mechanisms and pathogenicity. J. Cell. Physiol., 2018, 233(12), 9121-9135. doi: 10.1002/jcp.26956 PMID: 30078211
  52. 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. doi: 10.1002/pbc.26960 PMID: 29350470
  53. Kythreotou, A.; Siddique, A.; Mauri, F.A.; Bower, M.; Pinato, D.J. Pd-L1. J. Clin. Pathol., 2018, 71(3), 189-194. doi: 10.1136/jclinpath-2017-204853 PMID: 29097600
  54. 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. doi: 10.1007/s12094-022-02943-3 PMID: 36088513
  55. 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. doi: 10.1111/1759-7714.14042 PMID: 34061456
  56. Ding, Y.; Liu, J.H. The signature lncRNAs associated with the lung adenocarcinoma patients prognosis. Math. Biosci. Eng., 2020, 17(2), 1593-1603. doi: 10.3934/mbe.2020083 PMID: 32233597
  57. 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. doi: 10.1002/jcla.23951 PMID: 34558724
  58. 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. doi: 10.1080/21655979.2021.1951522 PMID: 34338158

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