Hora M, Albiges L, Bedke J, Campi R, Capitanio U, Giles RH, Ljungberg B, Marconi L, Klatte T, Volpe A, et al. European Association of Urology Guidelines Panel on Renal Cell Carcinoma Update on the New World Health Organization Classification of Kidney Tumours 2022: The Urologist’s Point of View. Eur Urol. 2023;83:97–100. https://doi.org/10.1016/j.eururo.2022.11.001.

Article  PubMed  Google Scholar 

Moch H, Amin MB, Berney DM, Comperat EM, Gill AJ, Hartmann A, Menon S, Raspollini MR, Rubin MA, Srigley JR, et al. The 2022 World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs-Part A: RENAL, PENILE AND TESTICULAR TUMours. Eur Urol. 2022;82:458–68. https://doi.org/10.1016/j.eururo.2022.06.016.

Article  PubMed  Google Scholar 

Hsieh JJ, Purdue MP, Signoretti S, Swanton C, Albiges L, Schmidinger M, Heng DY, Larkin J, Ficarra V. Renal cell carcinoma. Nat Rev Dis Primers. 2017;3:17009. https://doi.org/10.1038/nrdp.2017.9.

Article  PubMed  PubMed Central  Google Scholar 

Jonasch E, Gao J, Rathmell WK. Renal cell carcinoma. BMJ. 2014;349:g4797. https://doi.org/10.1136/bmj.g4797.

Article  PubMed  PubMed Central  Google Scholar 

Escudier B, Porta C, Schmidinger M, Algaba F, Patard JJ, Khoo V, Eisen T, Horwich A, Group, E.G.W. Renal cell carcinoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2014;25(Suppl 3):iii49-56. https://doi.org/10.1093/annonc/mdu259.

Article  PubMed  Google Scholar 

Raimondi A, Randon G, Sepe P, Claps M, Verzoni E, de Braud F, Procopio G. The evaluation of response to immunotherapy in metastatic renal cell carcinoma: open challenges in the clinical practice. Int J Mol Sci. 2019;20. https://doi.org/10.3390/ijms20174263

Borcherding N, Vishwakarma A, Voigt AP, Bellizzi A, Kaplan J, Nepple K, Salem AK, Jenkins RW, Zakharia Y, Zhang W. Mapping the immune environment in clear cell renal carcinoma by single-cell genomics. Commun Biol. 2021;4:122. https://doi.org/10.1038/s42003-020-01625-6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Galluzzi L, Vitale I, Aaronson SA, Abrams JM, Adam D, Agostinis P, Alnemri ES, Altucci L, Amelio I, Andrews DW, et al. Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018. Cell Death Differ. 2018;25:486–541. https://doi.org/10.1038/s41418-017-0012-4.

Article  PubMed  PubMed Central  Google Scholar 

Krysko DV, Garg AD, Kaczmarek A, Krysko O, Agostinis P, Vandenabeele P. Immunogenic cell death and DAMPs in cancer therapy. Nat Rev Cancer. 2012;12:860–75. https://doi.org/10.1038/nrc3380.

Article  CAS  PubMed  Google Scholar 

Galluzzi L, Vitale I, Warren S, Adjemian S, Agostinis P, Martinez AB, Chan TA, Coukos G, Demaria S, Deutsch E. et al. Consensus guidelines for the definition, detection and interpretation of immunogenic cell death. J Immunother Cancer 2020;8. https://doi.org/10.1136/jitc-2019-000337

Fucikova J, Kepp O, Kasikova L, Petroni G, Yamazaki T, Liu P, Zhao L, Spisek R, Kroemer G, Galluzzi L. Detection of immunogenic cell death and its relevance for cancer therapy. Cell Death Dis. 2020;11:1013. https://doi.org/10.1038/s41419-020-03221-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kroemer G, Galassi C, Zitvogel L, Galluzzi L. Immunogenic cell stress and death. Nat Immunol. 2022;23:487–500. https://doi.org/10.1038/s41590-022-01132-2.

Article  CAS  PubMed  Google Scholar 

Obeid M, Tesniere A, Ghiringhelli F, Fimia GM, Apetoh L, Perfettini JL, Castedo M, Mignot G, Panaretakis T, Casares N, et al. Calreticulin exposure dictates the immunogenicity of cancer cell death. Nat Med. 2007;13:54–61. https://doi.org/10.1038/nm1523.

Article  CAS  PubMed  Google Scholar 

Yu WD, Sun G, Li J, Xu J, Wang X. Mechanisms and therapeutic potentials of cancer immunotherapy in combination with radiotherapy and/or chemotherapy. Cancer Lett. 2019;452:66–70. https://doi.org/10.1016/j.canlet.2019.02.048.

Article  CAS  PubMed  Google Scholar 

Salas-Benito D, Pérez-Gracia JL, Ponz-Sarvisé M, Rodriguez-Ruiz ME, Martínez-Forero I, Castañón E, López-Picazo JM, Sanmamed MF, Melero I. Paradigms on immunotherapy combinations with chemotherapy. Cancer Discov. 2021;11:1353–67. https://doi.org/10.1158/2159-8290.Cd-20-1312.

Article  CAS  PubMed  Google Scholar 

Catanzaro E, Feron O, Skirtach AG, Krysko DV. Immunogenic cell death and role of nanomaterials serving as therapeutic vaccine for personalized cancer immunotherapy. Front Immunol. 2022;13:925290. https://doi.org/10.3389/fimmu.2022.925290.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lu M, Zhan H, Liu B, Li D, Li W, Chen X, Zhou X. N6-methyladenosine-related non-coding RNAs are potential prognostic and immunotherapeutic responsiveness biomarkers for bladder cancer. EPMA J. 2021;12:589–604. https://doi.org/10.1007/s13167-021-00259-w.

Article  PubMed  PubMed Central  Google Scholar 

Cheng T, Zhan X. Pattern recognition for predictive, preventive, and personalized medicine in cancer. EPMA J. 2017;8:51–60. https://doi.org/10.1007/s13167-017-0083-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Golubnitschaja O, Baban B, Boniolo G, Wang W, Bubnov R, Kapalla M, Krapfenbauer K, Mozaffari MS, Costigliola V. Medicine in the early twenty-first century: paradigm and anticipation - EPMA position paper 2016. EPMA J. 2016;7:23. https://doi.org/10.1186/s13167-016-0072-4.

Article  PubMed  PubMed Central  Google Scholar 

Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, KadelIIl EE, Koeppen H, Astarita JL, Cubas R, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554:544–8. https://doi.org/10.1038/nature25501.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Garg AD, De Ruysscher D, Agostinis P. Immunological metagene signatures derived from immunogenic cancer cell death associate with improved survival of patients with lung, breast or ovarian malignancies: A large-scale meta-analysis. Oncoimmunology. 2016;5:e1069938. https://doi.org/10.1080/2162402X.2015.1069938.

Article  CAS  PubMed  Google Scholar 

Wang X, Wu S, Liu F, Ke D, Wang X, Pan D, Xu W, Zhou L, He W. An immunogenic cell death-related classification predicts prognosis and response to immunotherapy in head and neck squamous cell carcinoma. Frontiers in immunology. 2021;12:781466. https://doi.org/10.3389/fimmu.2021.781466.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive integration of single-cell data. Cell. 2019;177:1888-1902.e1821. https://doi.org/10.1016/j.cell.2019.05.031.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using Cell Chat. Nat Commun. 2021;12:1088. https://doi.org/10.1038/s41467-021-21246-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7. https://doi.org/10.1186/1471-2105-14-7.

Article  PubMed  PubMed Central  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. https://doi.org/10.1093/nar/gkv007.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559. https://doi.org/10.1186/1471-2105-9-559.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma D, Jiang YZ, Liu XY, Liu YR, Shao ZM. Clinical and molecular relevance of mutant-allele tumor heterogeneity in breast cancer. Breast Cancer Res Treat. 2017;162:39–48. https://doi.org/10.1007/s10549-017-4113-z.

Article  CAS  PubMed  Google Scholar 

Mroz EA, Rocco JW. MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma. Oral Oncol. 2013;49:211–5. https://doi.org/10.1016/j.oraloncology.2012.09.007.

Article  CAS  PubMed  Google Scholar 

Rajput A, Bocklage T, Greenbaum A, Lee JH, Ness SA. Mutant-allele tumor heterogeneity scores correlate with risk of metastases in colon cancer. Clin Colorectal Cancer. 2017;16:e165–70. https://doi.org/10.1016/j.clcc.2016.11.004.

Article  PubMed  Google Scholar 

Mroz EA, Tward AD, Hammon RJ, Ren Y, Rocco JW. Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas. PLoS Med. 2015;12:e1001786. https://doi.org/10.1371/journal.pmed.1001786.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Geeleher P, Cox N, Huang RS. pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PloS one. 2014;9:e107468. https://doi.org/10.1371/journal.pone.0107468.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang C, Zhang H, Chen M, Wang S, Qian R, Zhang L, Huang X, Wang J, Liu Z, Qin W et al. A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer. Elife 2022;11, https://doi.org/10.7554/eLife.71880.

Bian Z, Fan R, Xie L A novel cuproptosis-related prognostic gene signature and validation of differential expression in clear cell renal cell carcinoma. Genes (Basel) 2022;13 https://doi.org/10.3390/genes13050851.

Gan Y, Zhang Z, Wang X, Li A, Fan Y, Zhang Q. Pyroptosis-related gene signature predicts the prognosis of ccRCC using TCGA and single-cell RNA seq database. J Healthc Eng. 2022;2022:8224618. https://doi.org/10.1155/2022/8224618.

Article  PubMed  PubMed Central  Google Scholar 

He M, Li M, Guan Y, Wan Z, Tian J, Xu F, Zhou H, Gao M, Bi H, Chong T. A new prognostic risk score: based on the analysis of autophagy-related genes and renal cell carcinoma. Front Gene. 2021;12:820154. https://doi.org/10.3389/fgene.2021.820154.