Dynamic gene screening enabled identification of a 10-gene panel for early detection and progression assessment of gastric cancer

Computational and Structural Biotechnology Journal - Tập 21 - Trang 677-687 - 2023
Fei Long1,2, Shuo Li1,2, Yaqi Xu1, Min Liu1, Xuan Zhang1, Junting Zhou1, Yiyi Chen1, Yuan Rong2,3, Xiangyu Meng2,4, Fubing Wang1,2,4
1Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
2Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, China
3Forensic Center of Justice, Zhongnan Hospital of Wuhan University, Wuhan, China
4Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China

Tài liệu tham khảo

Rao, 2012, Increased intratumoral neutrophil in colorectal carcinomas correlates closely with malignant phenotype and predicts patients' adverse prognosis, PLoS One, 7, 10.1371/journal.pone.0030806 Yuasa, 2005, Survival after surgical treatment of early gastric cancer, surgical techniques, and long-term survival, Langenbeck's Arch Surg, 390, 286, 10.1007/s00423-004-0482-y Park, 2006, Prognostic factors for advanced gastric cancer: stage-stratified analysis of patients who underwent curative resection, Cancer Res Treatment: Off J Korean Cancer Assoc, 38, 13, 10.4143/crt.2006.38.1.13 Lauren, 1965, The two histological main types of gastric carcinoma: diffuse and so‐called intestinal‐type carcinoma: an attempt at a histo‐clinical classification, Acta Pathol Microbiol Scand, 64, 31, 10.1111/apm.1965.64.1.31 Correa, 1975, A model for gastric cancer epidemiology, The Lancet, 306, 58, 10.1016/S0140-6736(75)90498-5 Zhang, 2019, Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer, Cell Rep, 27, 1934, 10.1016/j.celrep.2019.04.052 Balkwill, 2001, Inflammation and cancer: back to Virchow?, The Lancet, 357, 539, 10.1016/S0140-6736(00)04046-0 Coussens, 2002, Inflammation and cancer, Nature, 420, 860, 10.1038/nature01322 Kim, 2022, Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity, NPJ Prec Oncol, 6, 1 Xu, 2014, Differential gene expression profiling of gastric intraepithelial neoplasia and early-stage adenocarcinoma, World J Gastroenterology: WJG, 20, 17883, 10.3748/wjg.v20.i47.17883 Hanada, 2014, Helicobacter pylori infection introduces DNA double-strand breaks in host cells, Infect Immun, 82, 4182, 10.1128/IAI.02368-14 Oh, 2018, Clinical and genomic landscape of gastric cancer with a mesenchymal phenotype, Nat Commun, 9, 1, 10.1038/s41467-018-04179-8 Zhang, 2015, Overexpression of E2F mRNAs associated with gastric cancer progression identified by the transcription factor and miRNA co-regulatory network analysis, PLoS One, 10 Yoon, 2020, Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model, BMC Cancer, 20, 1, 10.1186/s12885-020-06814-4 Smyth, 2005, 397 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinform, 26, 139, 10.1093/bioinformatics/btp616 Bardou P, Mariette J, Escudié F, Djemiel C, Klopp CJBb. jvenn: an interactive Venn diagram viewer, 15(1); 2014, p. 1–7. Tang Z., Li C., Kang B., Gao G., Li C., Zhang Z.J.Nar GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. 45(W1); 2017. p. W98–W102. Robin, 2011, pROC: an open-source package for R and S+ to analyze and compare ROC curves, BMC Bioinform, 12, 1, 10.1186/1471-2105-12-77 Liberzon, 2011, Molecular signatures database (MSigDB) 3.0, Bioinform, 27, 1739, 10.1093/bioinformatics/btr260 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci USA, 102, 15545, 10.1073/pnas.0506580102 Wu, 2021, clusterProfiler 4.0: A universal enrichment tool for interpreting omics data, The Innov, 2 Wilkerson, 2010, ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking, Bioinform, 26, 1572, 10.1093/bioinformatics/btq170 Mayakonda, 2018, Maftools: efficient and comprehensive analysis of somatic variants in cancer, Genome Res, 28, 1747, 10.1101/gr.239244.118 Gao, 2013, Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal, Sci Signal, 6, pl1, 10.1126/scisignal.2004088 Hänzelmann, 2013, GSVA: gene set variation analysis for microarray and RNA-seq data, BMC Bioinform, 14, 1, 10.1186/1471-2105-14-7 Charoentong, 2017, Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade, Cell Rep, 18, 248, 10.1016/j.celrep.2016.12.019 Chen, 2018, Profiling tumor infiltrating immune cells with CIBERSORT, Cancer Syst Biol: Springer, 243, 10.1007/978-1-4939-7493-1_12 Racle, 2020, EPIC: a tool to estimate the proportions of different cell types from bulk gene expression data, Bioinform Cancer Immunotherapy: Springer, 233, 10.1007/978-1-0716-0327-7_17 Yoshihara, 2013, Inferring tumour purity and stromal and immune cell admixture from expression data, Nat Commun, 4, 1, 10.1038/ncomms3612 Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat Biotechnol, 36, 10.1038/nbt.4096 Zhang, 2019, CellMarker: a manually curated resource of cell markers in human and mouse, Nucleic Acids Res, 47, D721, 10.1093/nar/gky900 Necula, 2019, Recent advances in gastric cancer early diagnosis, World J Gastroenterol, 25, 2029, 10.3748/wjg.v25.i17.2029 Yasui, 2009, Transcriptome dissection of gastric cancer: identification of novel diagnostic and therapeutic targets from pathology specimens, Pathol Int, 59, 121, 10.1111/j.1440-1827.2009.02329.x Yap, 2007, Molecular gene expression signature patterns for gastric cancer diagnosis, Comput Biol Chem, 31, 275, 10.1016/j.compbiolchem.2007.06.001 Cui, 2011, An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer, Nucleic Acids Res, 39, 1197, 10.1093/nar/gkq960 Puliga, 2021, Microsatellite instability in Gastric Cancer: Between lights and shadows, Cancer Treat Rev, 95, 10.1016/j.ctrv.2021.102175 Liu, 2018, Comparative molecular analysis of gastrointestinal adenocarcinomas, Cancer Cell, 33, 721, 10.1016/j.ccell.2018.03.010 Joyce, 2015, T cell exclusion, immune privilege, and the tumor microenvironment, Science, 348, 74, 10.1126/science.aaa6204 Chen, 2021, Identification and characterization of robust hepatocellular carcinoma prognostic subtypes based on an integrative metabolite‐protein interaction network, Adv Sci, 8, 2100311, 10.1002/advs.202100311 Herrera, 2018, Endothelial cell activation on 3D-matrices derived from PDGF-BB-stimulated fibroblasts is mediated by Snail1, Oncogen, 7, 1 Li, 2018, Association of MUC16 mutation with tumor mutation load and outcomes in patients with gastric cancer, JAMA Oncol, 4, 1691, 10.1001/jamaoncol.2018.2805 Yang, 2020, MUC4, MUC16, and TTN genes mutation correlated with prognosis, and predicted tumor mutation burden and immunotherapy efficacy in gastric cancer and pan‐cancer, Clin Transl Med, 10, 4, 10.1002/ctm2.155 Tahara, 2016, Mutation spectrum of TP53 gene predicts clinicopathological features and survival of gastric cancer, Oncotarget, 7, 42252, 10.18632/oncotarget.9770 Jiang, 2018, Immunogenomics analysis reveals that TP53 mutations inhibit tumor immunity in gastric cancer, Transl Oncol, 11, 1171, 10.1016/j.tranon.2018.07.012 Dong, 2021, Epigenetic regulation and post-translational modifications of SNAI1 in cancer metastasis, Int J Mol Sci, 22, 11062, 10.3390/ijms222011062 Klein, 2018, The tumor vascular endothelium as decision maker in cancer therapy, Front Oncol, 8, 367, 10.3389/fonc.2018.00367 Mhaidly, 2020, Fibroblast heterogeneity in tumor micro-environment: role in immunosuppression and new therapies Burchett, 2019, Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells, J Biol Chem, 294, 1173, 10.1074/jbc.RA118.004787 Benetti, 2005, The calpain system is involved in the constitutive regulation of β-catenin signaling functions, J Biol Chem, 280, 22070, 10.1074/jbc.M501810200 Yang, 2022, CAST as a potential oncogene, identified by machine search, in gastric cancer infiltrated with macrophages and associated with Lgr5, Biomol, 12, 670 Ferrand, 2006, Gastrin and cancer: a review, Cancer Lett, 238, 15, 10.1016/j.canlet.2005.06.025 Dehez, 2001, Gastrin-induced DNA synthesis requires p38-MAPK activation via PKC/Ca2+ and Src-dependent mechanisms, FEBS Lett, 496, 25, 10.1016/S0014-5793(01)02396-1 Ferrand, 2004, Involvement of JAK2 upstream of the PI 3-kinase in cell–cell adhesion regulation by gastrin, Exp Cell Res, 301, 128, 10.1016/j.yexcr.2004.07.037 Miyazaki, 1999, Gastrin induces heparin-binding epidermal growth factor–like growth factor in rat gastric epithelial cells transfected with gastrin receptor, Gastroenterol, 116, 78, 10.1016/S0016-5085(99)70231-3 Mayayo-Peralta, 2021, Duality of glucocorticoid action in cancer: tumor-suppressor or oncogene?, Endocrine-related Cancer, 28, R157, 10.1530/ERC-20-0489 de Vries, 2008, Gastric cancer risk in patients with premalignant gastric lesions: a nationwide cohort study in the Netherlands, Gastroenterol, 134, 945, 10.1053/j.gastro.2008.01.071