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Original Research

Identification and Development of Subtypes with Poor Prognosis in Gastric Cancer Based on Both Hypoxia and Immune Cell Infiltration

, , , , &
Pages 9379-9399 | Published online: 06 Dec 2021

References

  • Fitzmaurice C, Akinyemiju TF, Al Lami FH, et al.; Global Burden of Disease Cancer Collaboration. Global, regional, and national cancer incidence, mortality, years of life lost, years lived with disability, and disability-adjusted life-years for 29 cancer groups, 1990 to 2016: a systematic analysis for the global burden of disease study. JAMA Oncol. 2018;4(11):1553–1568. doi:10.1001/jamaoncol.2018.2706
  • Smyth EC, Nilsson M, Grabsch HI, et al. Gastric cancer. Lancet (London, England). 2020;396(10251):635–648. doi:10.1016/S0140-6736(20)31288-5
  • Petrelli F, Berenato R, Turati L, et al. Prognostic value of diffuse versus intestinal histotype in patients with gastric cancer: a systematic review and meta-analysis. J Gastrointest Oncol. 2017;8(1):148–163. doi:10.21037/jgo.2017.01.10
  • Tang C-T, Zeng L, Yang J, et al. Analysis of the incidence and survival of gastric cancer based on the Lauren classification: a large population-based study using SEER. Front Oncol. 2020;10:1212. doi:10.3389/fonc.2020.01212
  • Roy P, Piard F, Dusserre-Guion L, et al. Prognostic comparison of the pathological classifications of gastric cancer: a population-based study. Histopathology. 1998;33(4):304–310. doi:10.1046/j.1365-2559.1998.00534.x
  • Li Z-Y, Zhang Q-W, Teng L-M, et al. Comparable rates of lymph node metastasis and survival between diffuse type and intestinal type early gastric cancer patients: a large population-based study. Gastrointest Endosc. 2019;90(1):84–95.e10. doi:10.1016/j.gie.2019.03.002
  • Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513(7517):202–209. doi:10.1038/nature13480
  • Oh SC, Sohn BH, Cheong J-H, et al. Clinical and genomic landscape of gastric cancer with a mesenchymal phenotype. Nat Commun. 2018;9(1):1777. doi:10.1038/s41467-018-04179-8
  • Fu Z, Mowday AM, Smaill JB, Hermans IF, Patterson AV. Tumour hypoxia-mediated immunosuppression: mechanisms and therapeutic approaches to improve cancer immunotherapy. Cells. 2021;10(5):1006. doi:10.3390/cells10051006
  • Folkman J. Tumor angiogenesis: therapeutic implications. N Engl J Med. 1971;285(21):1182–1186. doi:10.1056/NEJM197111182852108
  • Goel S, Duda DG, Xu L, et al. Normalization of the vasculature for treatment of cancer and other diseases [published correction appears in Physiol Rev. 2014 Apr;94(2):707]. Physiol Rev. 2011;91(3):1071–1121. doi:10.1152/physrev.00038.2010
  • Mantovani A, Sozzani S, Locati M, Allavena P, Sica A. Macrophage polarization: tumor-associated macrophages as a paradigm for polarized M2 mononuclear phagocytes. Trends Immunol. 2002;23(11):549–555. doi:10.1016/s1471-4906(02)02302-5
  • Noman MZ, Desantis G, Janji B, et al. PD-L1 is a novel direct target of HIF-1α, and its blockade under hypoxia enhanced MDSC-mediated T cell activation. J Exp Med. 2014;211(5):781–790. doi:10.1084/jem.20131916
  • Zhang B, Tang B, Gao J, et al. A hypoxia-related signature for clinically predicting diagnosis, prognosis and immune microenvironment of hepatocellular carcinoma patients. J Transl Med. 2020;18(1):342. doi:10.1186/s12967-020-02492-9
  • Cao R, Yuan L, Ma B, et al. Tumour microenvironment (TME) characterization identified prognosis and immunotherapy response in muscle-invasive bladder cancer (MIBC). Cancer Immunol Immunother. 2021;70(1):1–18. doi:10.1007/s00262-020-02649-x
  • Walsh JC, Lebedev A, Aten E, et al. The clinical importance of assessing tumor hypoxia: relationship of tumor hypoxia to prognosis and therapeutic opportunities. Antioxid Redox Signal. 2014;21(10):1516–1554. doi:10.1089/ars.2013.5378
  • Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013;41(Database issue):D991–D995. doi:10.1093/nar/gks1193
  • Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19(1A):A68–A77. doi:10.5114/wo.2014.47136
  • Zhao S, Ye Z, Stanton R. Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. RNA. 2020;26(8):903–909. doi:10.1261/rna.074922.120
  • Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–883. doi:10.1093/bioinformatics/bts034
  • Charoentong P, Finotello F, Angelova M, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18(1):248–262. doi:10.1016/j.celrep.2016.12.019
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi:10.1016/j.cels.2015.12.004
  • Ferreira MR, Santos GA, Biagi CA, Silva Junior WA, Zambuzzi WF. GSVA score reveals molecular signatures from transcriptomes for biomaterials comparison. J Biomed Mater Res A. 2021;109(6):1004–1014. doi:10.1002/jbm.a.37090
  • Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573. doi:10.1093/bioinformatics/btq170
  • Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612. doi:10.1038/ncomms3612
  • Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–259. doi:10.1007/978-1-4939-7493-1_12
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
  • Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523. doi:10.1038/s41467-019-09234-6
  • Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929–1935. doi:10.1126/science.1132939
  • Mariathasan S, Turley SJ, Nickles D, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554(7693):544–548. doi:10.1038/nature25501
  • Hazra A, Gogtay N. Biostatistics series module 6: correlation and linear regression. Indian J Dermatol. 2016;61(6):593–601. doi:10.4103/0019-5154.193662
  • Ritterhouse LL. Tumor mutational burden. Cancer Cytopathol. 2019;127(12):735–736. doi:10.1002/cncy.22174
  • Bao S, Zhao H, Yuan J, et al. Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer. Brief Bioinform. 2020;21(5):1742–1755. doi:10.1093/bib/bbz118
  • Tilford CA, Siemers NO. Gene set enrichment analysis. Methods Mol Biol. 2009;563:99–121. doi:10.1007/978-1-60761-175-2_6
  • Sjölander A. A cautionary note on extended Kaplan-Meier curves for time-varying covariates. Epidemiology. 2020;31(4):517–522. doi:10.1097/EDE.0000000000001188
  • Yu SC, Qi X, Hu YH, Zheng WJ, Wang QQ, Yao HY. Overview of multivariate regression model analysis and application. Zhonghua Yu Fang Yi Xue Za Zhi. 2019;53(3):334–336. doi:10.3760/cma.j.issn.0253-9624.2019.03.020
  • Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28(11):1747–1756. doi:10.1101/gr.239244.118
  • Shi R, Liao C, Zhang Q. Hypoxia-driven effects in cancer: characterization, mechanisms, and therapeutic implications. Cells. 2021;10(3):678. doi:10.3390/cells10030678
  • Gajewski TF, Schreiber H, Fu YX. Innate and adaptive immune cells in the tumor microenvironment. Nat Immunol. 2013;14(10):1014–1022. doi:10.1038/ni.2703
  • Li Q, He W, Wan G. Methyladenosine modification in RNAs: classification and roles in gastrointestinal cancers. Front Oncol. 2021;10:586789. doi:10.3389/fonc.2020.586789
  • Zhou Z, Zhang J, Xu C, et al. An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer. EBioMedicine. 2021;65:103271. doi:10.1016/j.ebiom.2021.103271
  • Shen Y, Peng X, Shen C. Identification and validation of immune-related lncRNA prognostic signature for breast cancer. Genomics. 2020;112(3):2640–2646. doi:10.1016/j.ygeno.2020.02.015
  • Li J, Liu C, Chen Y, et al. Tumor characterization in breast cancer identifies immune-relevant gene signatures associated with prognosis. Front Genet. 2019;10:1119. doi:10.3389/fgene.2019.01119
  • Xie Y, Shi X, Sheng K, et al. PI3K/Akt signaling transduction pathway, erythropoiesis and glycolysis in hypoxia (Review). Mol Med Rep. 2019;19(2):783–791. doi:10.3892/mmr.2018.9713
  • Lee M, Yoon J-H. Metabolic interplay between glycolysis and mitochondrial oxidation: the reverse Warburg effect and its therapeutic implication. World J Biol Chem. 2015;6(3):148–161. doi:10.4331/wjbc.v6.i3.148
  • Calcinotto A, Filipazzi P, Grioni M, et al. Modulation of microenvironment acidity reverses anergy in human and murine tumor-infiltrating T lymphocytes. Cancer Res. 2012;72(11):2746–2756. doi:10.1158/0008-5472.CAN-11-1272
  • Goetze K, Walenta S, Ksiazkiewicz M, et al. Lactate enhances motility of tumor cells and inhibits monocyte migration and cytokine release. Int J Oncol. 2011;39(2):453–463. doi:10.3892/ijo.2011.1055
  • Walenta S, Mueller-Klieser WF. Lactate: mirror and motor of tumor malignancy. Semin Radiat Oncol. 2004;14(3):267–274. doi:10.1016/j.semradonc.2004.04.004
  • Wei L, Sun -J-J, Cui Y-C, et al. Twist may be associated with invasion and metastasis of hypoxic NSCLC cells. Tumour Biol. 2016;37(7):9979–9987. doi:10.1007/s13277-016-4896-2
  • Schito L. Hypoxia-dependent angiogenesis and lymphangiogenesis in cancer. Adv Exp Med Biol. 2019;1136:71–85. doi:10.1007/978-3-030-12734-3_5
  • Ohta A, Diwanji R, Kini R, Subramanian M, Ohta A, Sitkovsky M. In vivo T cell activation in lymphoid tissues is inhibited in the oxygen-poor microenvironment. Front Immunol. 2011;2:27. doi:10.3389/fimmu.2011.00027
  • Yang M, Ma C, Liu S, et al. Hypoxia skews dendritic cells to a T helper type 2-stimulating phenotype and promotes tumour cell migration by dendritic cell-derived osteopontin. Immunology. 2009;128(1 Suppl):e237–e249. doi:10.1111/j.1365-2567.2008.02954.x
  • Foster JG, Wong SC, Sharp TV. The hypoxic tumor microenvironment: driving the tumorigenesis of non-small-cell lung cancer. Future Oncol. 2014;10(16):2659–2674. doi:10.2217/fon.14.201
  • Burrows N, Bashford-Rogers RJM, Bhute VJ, et al. Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development. Nat Immunol. 2020;21(11):1408–1420. doi:10.1038/s41590-020-0772-8
  • Jain RK. Antiangiogenesis strategies revisited: from starving tumors to alleviating hypoxia. Cancer Cell. 2014;26(5):605–622. doi:10.1016/j.ccell.2014.10.006
  • Whatcott CJ, Han H, Von Hoff DD. Orchestrating the tumor microenvironment to improve survival for patients with pancreatic cancer: normalization, not destruction. Cancer J. 2015;21(4):299–306. doi:10.1097/PPO.0000000000000140
  • Thiery JP, Acloque H, Huang RY, Nieto MA. Epithelial-mesenchymal transitions in development and disease. Cell. 2009;139(5):871–890. doi:10.1016/j.cell.2009.11.007
  • Zhang C, Shen L, Qi F, Wang J, Luo J. Multi-omics analysis of tumor mutation burden combined with immune infiltrates in bladder urothelial carcinoma. J Cell Physiol. 2020;235(4):3849–3863. doi:10.1002/jcp.29279
  • Kim SS, Shen S, Miyauchi S, et al. B cells improve overall survival in HPV-associated squamous cell carcinomas and are activated by radiation and PD-1 blockade. Clin Cancer Res. 2020;26(13):3345–3359. doi:10.1158/1078-0432.CCR-19-3211
  • Havel JJ, Chowell D, Chan TA. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat Rev Cancer. 2019;19(3):133–150. doi:10.1038/s41568-019-0116-x
  • Topalian SL, Hodi FS, Brahmer JR, et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med. 2012;366(26):2443–2454. doi:10.1056/NEJMoa1200690
  • Rosenberg JE, Hoffman-Censits J, Powles T, et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, Phase 2 trial. Lancet. 2016;387(10031):1909–1920. doi:10.1016/S0140-6736(16)00561-4
  • Ge S, Xia X, Ding C, et al. A proteomic landscape of diffuse-type gastric cancer [published correction appears in Nat Commun. 2018 May 8;9(1):1850]. Nat Commun. 2018;9(1):1012. doi:10.1038/s41467-018-03121-2
  • Cristescu R, Lee J, Nebozhyn M, et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes. Nat Med. 2015;21(5):449–456. doi:10.1038/nm.3850
  • Lamouille S, Xu J, Derynck R. Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol. 2014;15(3):178–196. doi:10.1038/nrm3758
  • Spaderna S, Schmalhofer O, Hlubek F, et al. A transient, EMT-linked loss of basement membranes indicates metastasis and poor survival in colorectal cancer. Gastroenterology. 2006;131(3):830–840. doi:10.1053/j.gastro.2006.06.016
  • Sun HF, Yang XL, Zhao Y, et al. Loss of TMEM126A promotes extracellular matrix remodeling, epithelial-to-mesenchymal transition, and breast cancer metastasis by regulating mitochondrial retrograde signaling. Cancer Lett. 2019;440–441:189–201. doi:10.1016/j.canlet.2018.10.018
  • Zhao XW, Zhou JP, Bi YL, et al. The role of MAPK signaling pathway in formation of EMT in oral squamous carcinoma cells induced by TNF-α. Mol Biol Rep. 2019;46(3):3149–3156. doi:10.1007/s11033-019-04772-0
  • Xu W, Yang Z, Lu N. A new role for the PI3K/Akt signaling pathway in the epithelial-mesenchymal transition. Cell Adh Migr. 2015;9(4):317–324. doi:10.1080/19336918.2015.1016686
  • Syed V. TGF-β signaling in cancer. J Cell Biochem. 2016;117(6):1279–1287. doi:10.1002/jcb.25496
  • Arend RC, Londoño-Joshi AI, Straughn JM Jr, Buchsbaum DJ. The Wnt/β-catenin pathway in ovarian cancer: a review. Gynecol Oncol. 2013;131(3):772–779. doi:10.1016/j.ygyno.2013.09.034
  • Spivak G. Nucleotide excision repair in humans. DNA Repair (Amst). 2015;36:13–18. doi:10.1016/j.dnarep.2015.09.003
  • Sanderson RJ, Lindahl T. Down-regulation of DNA repair synthesis at DNA single-strand interruptions in poly(ADP-ribose) polymerase-1 deficient murine cell extracts. DNA Repair (Amst). 2002;1(7):547–558. doi:10.1016/s1568-7864(02)00054-x
  • Li Z, Pearlman AH, Hsieh P. DNA mismatch repair and the DNA damage response. DNA Repair (Amst). 2016;38:94–101. doi:10.1016/j.dnarep.2015.11.019
  • Tubbs A, Nussenzweig A. Endogenous DNA damage as a source of genomic instability in cancer. Cell. 2017;168(4):644–656. doi:10.1016/j.cell.2017.01.002
  • Mladenov E, Magin S, Soni A, Iliakis G. DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: cell cycle and proliferation-dependent regulation. Semin Cancer Biol. 2016;37–38:51–64. doi:10.1016/j.semcancer.2016.03.003
  • Maya-Mendoza A, Moudry P, Merchut-Maya JM, Lee M, Strauss R, Bartek J. High speed of fork progression induces DNA replication stress and genomic instability. Nature. 2018;559(7713):279–284. doi:10.1038/s41586-018-0261-5
  • Collura A, Lefevre JH, Svrcek M, Tougeron D, Zaanan A, Duval A. Instabilité des microsatellites et cancer - De l’instabilité du génome à la médecine personnalisée [Microsatellite instability and cancer: from genomic instability to personalized medicine]. Med Sci (Paris). 2019;35(6–7):535–543. doi:10.1051/medsci/2019093
  • Chalmers ZR, Connelly CF, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9(1):34. doi:10.1186/s13073-017-0424-2
  • Lee JK, Ha GH, Kim HS, Lee CW. Oncogenic potential of BEX4 is conferred by Polo-like kinase 1-mediated phosphorylation. Exp Mol Med. 2018;50(10):1–12. doi:10.1038/s12276-018-0168-0
  • Galjart N, Perez F. A plus-end raft to control microtubule dynamics and function. Curr Opin Cell Biol. 2003;15(1):48–53. doi:10.1016/s0955-0674(02)00007-8
  • Akhmanova A, Hoogenraad CC. Microtubule plus-end-tracking proteins: mechanisms and functions. Curr Opin Cell Biol. 2005;17(1):47–54. doi:10.1016/j.ceb.2004.11.001
  • Cirillo L, Gotta M, Meraldi P. The elephant in the room: the role of microtubules in cancer. Adv Exp Med Biol. 2017;1002:93–124. doi:10.1007/978-3-319-57127-0_5
  • Parvin S, Ramirez-Labrada A, Aumann S, et al. LMO2 confers synthetic lethality to PARP inhibition in DLBCL. Cancer Cell. 2019;36(3):237–249.e6. doi:10.1016/j.ccell.2019.07.007
  • Andrade C. The P value and statistical significance: misunderstandings, explanations, challenges, and alternatives. Indian J Psychol Med. 2019;41(3):210–215. doi:10.4103/IJPSYM.IJPSYM_193_19
  • Concato J, Hartigan JA. P values: from suggestion to superstition. J Investig Med. 2016;64(7):1166–1171. doi:10.1136/jim-2016-000206
  • Rocha CRR, Silva MM, Quinet A, Cabral-Neto JB, Menck CFM. DNA repair pathways and cisplatin resistance: an intimate relationship. Clinics (Sao Paulo). 2018;73(suppl1):e478s. doi:10.6061/clinics/2018/e478s
  • Hailan WAQ, Abou-Tarboush FM, Al-Anazi KM, Ahmad A, Qasem A, Farah MA. Gemcitabine induced cytotoxicity, DNA damage and hepatic injury in laboratory mice. Drug Chem Toxicol. 2020;43(2):158–164. doi:10.1080/01480545.2018.1504957
  • Samstein RM, Lee CH, Shoushtari AN, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019;51(2):202–206. doi:10.1038/s41588-018-0312-8