Multiomics integration and machine learning reveal prognostic programmed cell death signatures in gastric cancer

  • Sung, H. et al. International Most cancers Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 International locations. CA Most cancers J. Clin. 71, 209–249 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Smyth, E. C., Nilsson, M., Grabsch, H. I., van Grieken, N. C. & Lordick, F. Gastric most cancers. Lancet. 396, 635–648 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Berlth, F., Bollschweiler, E., Drebber, U., Hoelscher, A. H. & Moenig, S. Pathohistological classification techniques in gastric most cancers: diagnostic relevance and prognostic worth. World J. Gastroenterol. 20, 5679–5684 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nature CGARNJ Complete molecular characterization of gastric adenocarcinoma. 513 (7517), 202 (2014).

  • Cristescu, R. et al. Molecular evaluation of gastric most cancers identifies subtypes related to distinct scientific outcomes. Nat. Med. 21, 449–456 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ricci, A. D., Rizzo, A. & Brandi, G. DNA injury response alterations in gastric most cancers: pulling down a brand new wall. Future Oncol. (London, England). 17(8), 865–868 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Rodriquenz, M. G. et al. MSI and EBV constructive gastric most cancers’s subgroups and their hyperlink with novel immunotherapy. J. Clin. Med. 9(5), 1427 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yan, H. H. N. et al. A complete human gastric most cancers organoid biobank captures tumor subtype heterogeneity and permits therapeutic screening. Cell Stem Cell. 23, 882-897.e811 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rizzo, A. et al. Peripheral neuropathy and headache in most cancers sufferers handled with immunotherapy and immuno-oncology mixtures: the MOUSEION-02 examine. Exp. Opin. Drug Metab. Toxicol. 17(12), 1455–1466 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Guven, D. C. et al. Immune checkpoint inhibitor-related listening to loss: a scientific evaluation and evaluation of particular person affected person knowledge. Help. Care Most cancers. 31(12), 624 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Rihawi, Okay. et al. Tumor-associated macrophages inflammatory microenvironment in gastric most cancers: novel translational implications. Int. J. Mol. Sci. 22(8), 3805 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sahin, T. Okay., Rizzo, A., Aksoy, S. & Guven, D. C. Prognostic Significance of the Royal Marsden Hospital (RMH) Rating in Sufferers with Most cancers: A scientific evaluation and meta-analysis. Cancers. 16(10), 1835 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, D., Kang, R., Berghe, T. V., Vandenabeele, P. & Kroemer, G. The molecular equipment of regulated cell demise. Cell Res. 29, 347–364 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Galluzzi, L. et al. Molecular mechanisms of cell demise: suggestions of the Nomenclature Committee on Cell Dying 2018. Cell Dying Differ. 25, 486–541 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zou, Y. et al. Leveraging various cell-death patterns to foretell the prognosis and drug sensitivity of triple-negative breast most cancers sufferers after surgical procedure. Int. J. Surg. 107, 106936 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Su, Z., Yang, Z., Xu, Y., Chen, Y. & Yu, Q. Apoptosis, autophagy, necroptosis, and most cancers metastasis. Mol. Most cancers 14, 48 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhou, C. B. & Fang, J. Y. The function of pyroptosis in gastrointestinal most cancers and immune responses to intestinal microbial an infection. Biochim. Biophys. Acta Rev. Most cancers. 1872, 1–10 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Tu, R. H. et al. Neurotransmitter receptor HTR2B regulates lipid metabolism to inhibit ferroptosis in gastric most cancers. Most cancers Res. 83, 3868–3885 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Solar, L. et al. Lactylation of METTL16 promotes cuproptosis by way of m(6)A-modification on FDX1 mRNA in gastric most cancers. Nat. Commun. 14, 6523 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen, J. et al. The E3 ubiquitin ligase TRIM17 promotes gastric most cancers survival and development by way of controlling BAX stability and antagonizing apoptosis. Cell Dying Differ. 30, 2322–2335 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Strusi, G., Suelzu, C. M., Horwood, N., Münsterberg, A. E. & Bao, Y. Phenethyl isothiocyanate and dasatinib mixture synergistically reduces hepatocellular carcinoma development by way of cell cycle arrest and oxeiptosis. Entrance Pharmacol. 14, 1264032 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maru, B. et al. PARP-1 improves leukemia outcomes by inducing parthanatos throughout chemotherapy. Cell Rep. Med. 4, 101191 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ooi, C. H. et al. Oncogenic pathway mixtures predict scientific prognosis in gastric most cancers. PLoS Genet. 5, e1000676 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pasini, F. S. et al. A gene expression profile associated to immune dampening within the tumor microenvironment is related to poor prognosis in gastric adenocarcinoma. J. Gastroenterol. 49, 1453–1466 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jiang, H. et al. Revealing the transcriptional heterogeneity of organ-specific metastasis in human gastric most cancers utilizing single-cell RNA Sequencing. Clin. Transl. Med. 12, e730 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hugo, W. et al. Genomic and transcriptomic options of response to anti-PD-1 remedy in metastatic melanoma. Cell 165, 35–44 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jung, H. et al. DNA methylation loss promotes immune evasion of tumours with excessive mutation and replica quantity load. Nat. Commun. 10, 4278 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Balar, A. V. et al. Atezolizumab as first-line remedy in cisplatin-ineligible sufferers with domestically superior and metastatic urothelial carcinoma: a single-arm, multicentre, section 2 trial. Lancet. 389, 67–76 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package deal for eradicating batch results and different undesirable variation in high-throughput experiments. Bioinformatics. 28, 882–883 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, Okay. KEGG: new views on genomes, pathways, ailments and medicines. Nucleic Acids Res. 45, D353-d361 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Safran, M. et al. GeneCards Model 3: the human gene integrator. Database (Oxford) 2010, baq020 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Zhou, Y. et al. Implications of various cell demise patterns for prognosis and immunity in lung adenocarcinoma. NPJ Summary. Oncol. 7, 121 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, X., Meng, J., Zhou, Y., Jiang, L. & Yan, F. MOVICS: an R package deal for multi-omics integration and visualization in most cancers subtyping. Bioinformatics. 36, 5539–5541 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Chalise, P. & Fridley, B. L. Integrative clustering of multi-level ‘omic knowledge based mostly on non-negative matrix factorization algorithm. PLoS One. 12, e0176278 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barbie, D. A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 462, 108–112 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sohn, B. H. et al. Scientific significance of 4 molecular subtypes of gastric most cancers recognized by the most cancers genome atlas venture. Clin. Most cancers Res. 23, 4441–4449 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Y. et al. Proteomic characterization of gastric most cancers response to chemotherapy and focused remedy reveals new therapeutic methods. Nat. Commun. 13, 5723 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, X. et al. Multi-omics consensus ensemble refines the classification of muscle-invasive bladder most cancers with stratified prognosis, tumour microenvironment and distinct sensitivity to frontline therapies. Clin. Transl. Med. 11, e601 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Audia, J. E. & Campbell, R. M. Histone modifications and most cancers. Chilly Spring Harb. Perspect. Biol. 8, a019521 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zeng, D. et al. IOBR: Multi-omics immuno-oncology organic analysis to decode tumor microenvironment and signatures. Entrance. Immunol. 12, 687975 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xu, L. et al. TIP: An internet server for resolving tumor immunophenotype profiling. Most cancers Res. 78, 6575–6580 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Subramanian, A. et al. Gene set enrichment evaluation: a knowledge-based method for deciphering genome-wide expression profiles. Proc. Natl. Acad. Sci. U S A. 102, 15545–15550 (2005).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stuart, T. et al. Complete integration of single-cell knowledge. Cell. 177, 1888-1902.e1821 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jin, S. et al. Inference and evaluation of cell-cell communication utilizing Cell Chat. Nat. Commun. 12, 1088 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Uhlén, M. et al. Proteomics. Tissue-based map of the human proteome. Science. 347, 1260419 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Wang, S. F. et al. Development differentiation issue 15 induces cisplatin resistance via upregulation of xCT expression and glutathione synthesis in gastric most cancers. Most cancers Sci. 114, 3301–3317 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, C. et al. The NR_109/FUBP1/c-Myc axis regulates TAM polarization and remodels the tumor microenvironment to advertise most cancers growth. J. Immunother. Most cancers. 11, e006230 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, J. X. et al. Neoadjuvant camrelizumab and apatinib mixed with chemotherapy versus chemotherapy alone for domestically superior gastric most cancers: a multicenter randomized section 2 trial. Nat. Commun. 15, 41 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lei, Z. N. et al. Signaling pathways and therapeutic interventions in gastric most cancers. Sign. Transduct. Goal Ther. 7, 358 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, J. Z. et al. BDH2 triggers ROS-induced cell demise and autophagy by selling Nrf2 ubiquitination in gastric most cancers. J. Exp. Clin. Most cancers Res. 39, 123 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rizzo, A. et al. Third- and later-line remedy in superior or metastatic gastric most cancers: a scientific evaluation and meta-analysis. Future Oncol. 16, 4409–4418 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vitale, E., Rizzo, A., Santa, Okay. & Jirillo, E. Associations between “Most cancers Danger”, “Irritation” and “Metabolic Syndrome”: A Scoping Overview. Biology (Basel). 13(5), 352 (2024).

    CAS 
    PubMed 

    Google Scholar
     

  • Viscardi, G. et al. Comparative evaluation of early mortality danger upon immune checkpoint inhibitors alone or together with different brokers throughout strong malignancies: a scientific evaluation and meta-analysis. Eur. J. Most cancers. 177, 175–185 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meng, Q. et al. DNA methylation regulator-mediated modification patterns and tumor microenvironment characterization in gastric most cancers. Mol. Ther. Nucleic Acids. 24, 695–710 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peng, Y., Shi, R., Yang, S. & Zhu, J. Cuproptosis-related gene DLAT is a biomarker of the prognosis and immune microenvironment of gastric most cancers and impacts the invasion and migration of cells. Most cancers Med. 13, e70012 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, S. et al. PTBP1 knockdown impairs autophagy flux and inhibits gastric most cancers development via TXNIP-mediated oxidative stress. Cell Mol. Biol. Lett. 29, 110 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, X. et al. Atlas of metastatic gastric most cancers hyperlinks ferroptosis to illness development and immunotherapy response. Gastroenterology. https://doi.org/10.1053/j.gastro.2024.07.038 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guo, D. et al. Celastrol induces necroptosis and ameliorates irritation by way of concentrating on biglycan in human gastric carcinoma. Int. J. Mol. Sci. 20(22), 5716 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, W. et al. CXCR4 induces cell autophagy and maintains EBV latent an infection in EBVaGC. Theranostics. 10, 11549–11561 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, Q., Xu, X. Y., Hou, X. X. & Chen, S. C. The upregulation of proteins mild chain 3 and autophagy-related 5 and the occurence of intestinal-type gastric most cancers. J. Physiol. Pharmacol. 72(6), 8 (2021).


    Google Scholar
     

  • Minikes, A. M. et al. E-cadherin is a biomarker for ferroptosis sensitivity in diffuse gastric most cancers. Oncogene. 42, 848–857 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, J. et al. FABP4 in macrophages facilitates obesity-associated pancreatic most cancers development by way of the NLRP3/IL-1β axis. Most cancers Lett. 575, 216403 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mónaco, A., Chilibroste, S., Yim, L., Chabalgoity, J. A. & Moreno, M. Inflammasome activation, NLRP3 engagement and macrophage recruitment to tumor microenvironment are all required for Salmonella antitumor impact. Most cancers Immunol. Immunother. 71, 2141–2150 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Galluzzi, L., Buqué, A., Kepp, O., Zitvogel, L. & Kroemer, G. Immunogenic cell demise in most cancers and infectious illness. Nat. Rev. Immunol. 17, 97–111 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tang, D., Chen, X., Kang, R. & Kroemer, G. Ferroptosis: molecular mechanisms and well being implications. Cell Res. 31, 107–125 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jung, Y. J. et al. Impact of IL-10-producing B cells in peripheral blood and tumor tissue on gastric most cancers. Cell Commun. Sign. 21, 320 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yousefi, B. et al. Epigenetic adjustments in gastric most cancers induction by Helicobacter pylori. J Cell Physiol. 234, 21770–21784 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Farasati Far, B. et al. The function of microRNA-21 (miR-21) in pathogenesis, analysis, and prognosis of gastrointestinal cancers: A evaluation. Life Sci. 316, 121340 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Perillo, B. et al. ROS in most cancers remedy: the intense aspect of the moon. Exp. Mol. Med. 52, 192–203 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Timmerman, D. M., Remmers, T. L., Hillenius, S. & Looijenga, L. H. J. Mechanisms of TP53 Pathway Inactivation in Embryonic and Somatic Cells-Relevance for Understanding (Germ Cell) Tumorigenesis. Int. Mol. Sci. 22(10), 5377 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Nam, D., Chapiro, J., Paradis, V., Seraphin, T. P. & Kather, J. N. Synthetic intelligence in liver ailments: Enhancing diagnostics, prognostics and response prediction. JHEP Rep. 4, 100443 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, J. et al. A novel pyroptosis gene expression-based danger rating for survival in gastric most cancers. Entrance Endocrinol. (Lausanne). 14, 1120216 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Shen, Y. et al. Cross-talk between cuproptosis and ferroptosis regulators defines the tumor microenvironment for the prediction of prognosis and therapies in lung adenocarcinoma. Entrance Immunol. 13, 1029092 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, X. Z. et al. Single-cell sequencing of ascites fluid illustrates heterogeneity and therapy-induced evolution throughout gastric most cancers peritoneal metastasis. Nat. Commun. 14, 822 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zulibiya, A. et al. Single-cell RNA sequencing reveals potential for endothelial-to-mesenchymal transition in tetralogy of fallot. Congenit. Coronary heart Dis. 18, 611–625 (2023).

    Article 

    Google Scholar
     

  • Qu, X. et al. Lack of cancer-associated fibroblast-derived exosomal DACT3-AS1 promotes malignant transformation and ferroptosis-mediated oxaliplatin resistance in gastric most cancers. Drug Resist. Updat. 68, 100936 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, X. et al. Single-cell RNA sequencing reveals a pro-invasive cancer-associated fibroblast subgroup related to poor scientific outcomes in sufferers with gastric most cancers. Theranostics. 12, 620–638 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maeda, M. et al. Most cancers cell area of interest elements secreted from cancer-associated fibroblast by lack of H3K27me3. Intestine. 69, 243–251 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Foote, H.-P. et al. Utilizing pharmacokinetic modeling and digital well being file knowledge to foretell scientific and security outcomes after methylprednisolone publicity throughout cardiopulmonary bypass in neonates. Congenit. Coronary heart Dis. 18, 295–313 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hui, Y., Tu, C., Liu, D., Zhang, H. & Gong, X. Danger elements for gastric most cancers: A complete evaluation of observational research. Entrance. Public Well being. 10, 892468 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Mohseni, S. et al. Impact of nutritional vitamins C and E on most cancers survival; a scientific evaluation. Daru. 30, 427–441 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Usui, Y. et al. Helicobacter pylori, homologous-recombination genes, and gastric most cancers. N. Engl. J. Med. 388, 1181–1190 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

    Sensi Tech Hub
    Logo