A genomic instability-derived risk index predicts clinical outcome and immunotherapy response for clear cell renal cell carcinoma

References

• VasudevNS, SelbyPJ, BanksRE. Renal cancer biomarkers: the promise of personalized care. BMC Med. 2012;10(1):112.
   PubMedGoogle Scholar
• HsiehJJ, PurdueMP, SignorettiS, etal. Renal cell carcinoma. Nat Rev Dis Primers. 2017;3(1):17009..
   PubMed Web of Science ®Google Scholar
• HuangJJ, HsiehJJ. The therapeutic landscape of renal cell carcinoma: from the dark age to the golden age. Semin Nephrol. 2020;40(1):28–41.
   PubMed Web of Science ®Google Scholar
• CorreaAF, RuthKJ, Al-Saleem T, etal. Overall tumor genomic instability: an important predictor of recurrence-free survival in patients with localized clear cell renal cell carcinoma. Cancer Biol Ther. 2020;21(5):424–431..
   PubMed Web of Science ®Google Scholar
• DuensingS, HohenfellnerM. Adjuvant therapy for renal-cell carcinoma: settled for now. Lancet. 2016;387(10032):1973–1974.
   PubMed Web of Science ®Google Scholar
• XuW, AtkinsMB, McDermottDF. Checkpoint inhibitor immunotherapy in kidney cancer. Nat Rev Urol. 2020;17(3):137–150.
   PubMed Web of Science ®Google Scholar
• McDermottDF, HuseniMA, AtkinsMB, etal. Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma. Nat Med. 2018;24(6):749–757..
   PubMed Web of Science ®Google Scholar
• CassidyLD, VenkitaramanAR. Genome instability mechanisms and the structure of cancer genomes. Curr Opin Genet Dev. 2012;22(1):10–13.
   PubMed Web of Science ®Google Scholar
• CarterSL, EklundAC, KohaneIS, etal. Asignature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006;38(9):1043–1048.
   PubMed Web of Science ®Google Scholar
• HieronymusH, MuraliR, TinA, etal. Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death. Elife. 2018;7. DOI:10.7554/eLife.37294.
   PubMed Web of Science ®Google Scholar
• HanahanD, WeinbergRA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–674.
   PubMed Web of Science ®Google Scholar
• KunkelTA, ErieDA. Eukaryotic mismatch repair in relation to DNA replication. Annu Rev Genet. 2015;49(1):291–313.
   PubMedGoogle Scholar
• DeguchiM, ShiinaH, IgawaM, etal. DNA mismatch repair genes in renal cell carcinoma. JUrol. 2003;169(6):2365–2371.
   Google Scholar
• HellMP, DudaM, WeberTC, etal. Tumor suppressor VHL functions in the control of mitotic fidelity. Cancer Res. 2014;74(9):2422–2431.
   PubMed Web of Science ®Google Scholar
• MetcalfJL, BradshawPS, KomosaM, etal. K63-ubiquitylation of VHL by SOCS1 mediates DNA double-strand break repair. Oncogene. 2014;33(8):1055–1065.
   PubMed Web of Science ®Google Scholar
• PuC, TaoS, XuJ, etal. Harnessing genomic stress for antitumor immunity. Antioxid Redox Signal. 2020. DOI:10.1089/ars.2020.8221
   PubMed Web of Science ®Google Scholar
• GrivennikovSI, GretenFR, KarinM. Immunity, inflammation, and cancer. Cell. 2010;140(6):883–899.
   PubMed Web of Science ®Google Scholar
• TurajlicS, LitchfieldK, XuH, etal. Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis. Lancet Oncol. 2017;18(8):1009–1021..
   PubMed Web of Science ®Google Scholar
• ShollLM, HirschFR, HwangD, etal. The promises and challenges of tumor mutation burden as an immunotherapy biomarker: aperspective from the international association for the study of lung cancer pathology committee. JThorac Oncol. 2020;15(9):1409–1424.
   PubMed Web of Science ®Google Scholar
• MiaoYR, ZhangQ, LeiQ, etal. ImmuCellAI: aunique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Adv Sci (Weinh). 2020;7(7):1902880.
   PubMedGoogle Scholar
• JiangP, GuS, PanD, etal. Signatures of Tcell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018;24(10):1550–1558.
   PubMed Web of Science ®Google Scholar
• BarataPC, RiniBI. Treatment of renal cell carcinoma: current status and future directions. CA Cancer JClin. 2017;67(6):507–524.
   PubMed Web of Science ®Google Scholar
• TysnesBB. Tumor-initiating and -propagating cells: cells that we would like to identify and control. Neoplasia. 2010;12(7):506–515.
   PubMed Web of Science ®Google Scholar
• SieberOM, HeinimannK, TomlinsonIP. Genomic instability–the engine of tumorigenesis? Nat Rev Cancer. 2003;3(9):701–708.
   PubMed Web of Science ®Google Scholar
• MatsudaM, TsutsumiK, KanematsuT, etal. Involvement of phospholipase C-related inactive protein in the mouse reproductive system through the regulation of gonadotropin levels. Biol Reprod. 2009;81(4):681–689.
   PubMed Web of Science ®Google Scholar
• UmebayashiH, MizokamiA, MatsudaM, etal. Phospholipase C-related catalytically inactive protein, anovel microtubule-associated protein 1 light chain 3-binding protein, negatively regulates autophagosome formation. Biochem Biophys Res Commun. 2013;432(2):268–274.
   PubMed Web of Science ®Google Scholar
• OnoratiAV, DyczynskiM, OjhaR, etal. Targeting autophagy in cancer. Cancer. 2018;124(16):3307–3318.
   PubMed Web of Science ®Google Scholar
• BuW, HaoX, YangT, etal. Autophagy contributes to the maintenance of genomic integrity by reducing oxidative stress. Oxid Med Cell Longev. 2020;2020:2015920.
   PubMed Web of Science ®Google Scholar
• BhutiaSK, MukhopadhyayS, SinhaN, etal. Autophagy: cancer’s friend or foe? Adv Cancer Res. 2013;118:61–95.
   PubMed Web of Science ®Google Scholar
• LevyJ, TowersCG, ThorburnA. Targeting autophagy in cancer. Nat Rev Cancer. 2017;17(9):528–542.
   PubMed Web of Science ®Google Scholar
• RybsteinMD, Bravo-San PJ, KroemerG, etal. The autophagic network and cancer. Nat Cell Biol. 2018;20(3):243–251.
   PubMed Web of Science ®Google Scholar
• EvanGI, VousdenKH. Proliferation, cell cycle and apoptosis in cancer. Nature. 2001;411(6835):342–348.
   PubMed Web of Science ®Google Scholar
• XiongZ, XiaoW, BaoL, etal. Tumor Cell “Slimming” regulates tumor progression through PLCL1/UCP1-mediated lipid browning. Adv Sci (Weinh). 2019;6(10):1801862..
   PubMedGoogle Scholar
• KosfeldA, KreuzerM, DanielC, etal. Whole-exome sequencing identifies mutations of TBC1D1 encoding a Rab-GTPase-activating protein in patients with congenital anomalies of the kidneys and urinary tract (CAKUT). Hum Genet. 2016;135(1):69–87..
   PubMed Web of Science ®Google Scholar
• StoneS, AbkevichV, RussellDL, etal. TBC1D1 is acandidate for asevere obesity gene and evidence for agene/gene interaction in obesity predisposition. Hum Mol Genet. 2006;15(18):2709–2720.
   PubMed Web of Science ®Google Scholar
• DizmanN, PhilipEJ, PalSK. Genomic profiling in renal cell carcinoma. Nat Rev Nephrol. 2020;16(8):435–451.
   PubMed Web of Science ®Google Scholar
• NiuX, ZhangT, LiaoL, etal. The von Hippel-Lindau tumor suppressor protein regulates gene expression and tumor growth through histone demethylase JARID1C. Oncogene. 2012;31(6):776–786..
   PubMed Web of Science ®Google Scholar
• DaCW, DaCI, FaresAF, etal. Prognostic impact of concomitant loss of PBRM1 and BAP1 protein expression in early stages of clear cell renal cell carcinoma. Urol Oncol. 2018;36(5):243.e1–243.e8.
   Web of Science ®Google Scholar
• HognerA, KrauseH, JandrigB, etal. PBRM1 and VHL expression correlate in human clear cell renal cell carcinoma with differential association with patient’s overall survival. Urol Oncol. 2018;36(3):94.e1–94.e14.
   PubMed Web of Science ®Google Scholar
• YusimI, MermershtainW, NeulanderE, etal. Influence of age on the prognosis of patients with renal cell carcinoma (RCC). Onkologie. 2002;25(6):548–550.
   PubMedGoogle Scholar
• SakaiI, MiyakeH, MuramakiM, etal. Significant impact of age at diagnosis on the prognosis of Japanese patients with pT1 renal cell carcinoma following surgical resection. BJU Int. 2012;109(5):695–699.
   PubMed Web of Science ®Google Scholar
• KucukU, PalaEE, SezerO, etal. Significance of TNM staging, demographic and histologic features in predicting the prognosis of renal cell carcinoma. Acta Chir Belg. 2015;115(3):202–207.
   PubMed Web of Science ®Google Scholar
• KeZB, ChenSH, ChenYH, etal. Risk factors for brain metastases in patients with renal cell carcinoma. Biomed Res Int. 2020;2020:6836234.
   PubMedGoogle Scholar
• VeselyMD, KershawMH, SchreiberRD, etal. Natural innate and adaptive immunity to cancer. Annu Rev Immunol. 2011;29(1):235–271.
   PubMed Web of Science ®Google Scholar
• NishikawaH, SakaguchiS. Regulatory Tcells in tumor immunity. IntJCancer. 2010;127(4):759–767.
   Google Scholar
• FridmanWH, ZitvogelL, Sautes-Fridman C, etal. The immune contexture in cancer prognosis and treatment. Nat Rev Clin Oncol. 2017;14(12):717–734.
   PubMed Web of Science ®Google Scholar
• ZhangS, ZhangE, LongJ, etal. Immune infiltration in renal cell carcinoma. Cancer Sci. 2019;110(5):1564–1572..
   PubMed Web of Science ®Google Scholar
• DrakeCG, SteinMN. The immunobiology of kidney cancer. Jclin oncol. 2018;36(36):3547-+.
   Web of Science ®Google Scholar
• SiskaPJ, BeckermannKE, MasonFM, etal. Mitochondrial dysregulation and glycolytic insufficiency functionally impair CD8 Tcells infiltrating human renal cell carcinoma. JCI Insight. 2017;2(12). DOI:10.1172/jci.insight.93411.
   PubMed Web of Science ®Google Scholar
• PaluckaK, BanchereauJ. Cancer immunotherapy via dendritic cells. Nat Rev Cancer. 2012;12(4):265–277.
   PubMed Web of Science ®Google Scholar
• FucikovaJ, Palova-Jelinkova L, BartunkovaJ, etal. Induction of tolerance and immunity by dendritic cells: mechanisms and clinical applications. Front Immunol. 2019;10(2393). DOI:10.3389/fimmu.2019.02393
   PubMedGoogle Scholar
• AsadzadehZ, MohammadiH, SafarzadehE, etal. The paradox of Th17 cell functions in tumor immunity. Cell Immunol. 2017;322:15–25.
   PubMed Web of Science ®Google Scholar
• ShisslerSC, LeeMS, WebbTJ. Mixed signals: co-stimulation in invariant natural Killer T cell-mediated cancer immunotherapy. Front Immunol. 2017;8:1447.
   PubMed Web of Science ®Google Scholar
• MiaoD, MargolisCA, GaoW, etal. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018;359(6377):801–806.
   PubMed Web of Science ®Google Scholar
• FifeBT, PaukenKE, EagarTN, etal. Interactions between PD-1 and PD-L1 promote tolerance by blocking the TCR-induced stop signal. Nat Immunol. 2009;10(11):1185–1192.
   PubMed Web of Science ®Google Scholar
• KeirME, LiangSC, GuleriaI, etal. Tissue expression of PD-L1 mediates peripheral Tcell tolerance. JExp Med. 2006;203(4):883–895..
   Google Scholar
• BuchbinderEI, DesaiA. CTLA-4 and PD-1 pathways: similarities, differences, and implications of their inhibition. Am JClin Oncol. 2016;39(1):98–106.
   PubMed Web of Science ®Google Scholar
• MotzerRJ, EscudierB, McDermottDF, etal. Survival outcomes and independent response assessment with nivolumab plus ipilimumab versus sunitinib in patients with advanced renal cell carcinoma: 42-month follow-up of arandomized phase 3 clinical trial. JImmunother Cancer. 2020;8(2). DOI:10.1136/jitc-2020-000891.
   Google Scholar
• HarfeBD, Jinks-Robertson S. DNA mismatch repair and genetic instability. Annu Rev Genet. 2000;34:359–399.
   PubMed Web of Science ®Google Scholar
• MiyagawaK. Genetic instability and cancer. IntJHematol. 1998;67(1):3–14.
   Google Scholar
• Dominguez-Brauer C, ThuKL, MasonJM, etal. Targeting Mitosis in Cancer: emerging Strategies. Mol Cell. 2015;60(4):524–536.
   PubMed Web of Science ®Google Scholar
• WangG, VasquezKM. Effects of replication and transcription on DNA structure-related genetic instability. Genes (Basel). 2017;8:1.
   Web of Science ®Google Scholar
• MassagueJ. G1 cell-cycle control and cancer. Nature. 2004;432(7015):298–306.
   PubMed Web of Science ®Google Scholar
• LaGoryEL, WuC, TaniguchiCM, etal. Suppression of PGC-1alpha is critical for reprogramming oxidative metabolism in renal cell carcinoma. Cell Rep. 2015;12(1):116–127..
   PubMed Web of Science ®Google Scholar
• ZhangYP, ChengYB, LiS, etal. An epithelial-mesenchymal transition-related long non-coding RNA signature to predict overall survival and immune microenvironment in kidney renal clear cell carcinoma. Bioengineered. 2021;12(1):555–564.
   PubMed Web of Science ®Google Scholar
• ZhangJ, YanA, CaoW, etal. Development and validation of a VHL-associated immune prognostic signature for clear cell renal cell carcinoma. Cancer Cell Int. 2020;20(1):584.
   PubMed Web of Science ®Google Scholar