The intra-class heterogeneity of immunophenotyping and immune landscape in oesophageal cancer and clinical implications

References

• Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424.
   PubMed Web of Science ®Google Scholar
• Henry MA, Lerco MM, Ribeiro PW, et al. Epidemiological features of esophageal cancer. Squamous cell carcinoma versus adenocarcinoma. Acta Cir Bras. 2014;29(6):389–393.
   PubMed Web of Science ®Google Scholar
• He Y, Liang D, Du L, et al. Clinical characteristics and survival of 5283 esophageal cancer patients: a multicenter study from eighteen hospitals across six regions in China. Cancer Commun (Lond). 2020;40(10):531–544.
   PubMed Web of Science ®Google Scholar
• Schizas D, Charalampakis N, Kole C, et al. Immunotherapy for esophageal cancer: a 2019 update. Immunotherapy. 2020;12(3):203–218.
   PubMed Web of Science ®Google Scholar
• Zeng H, Chen W, Zheng R, et al. Changing cancer survival in China during 2003–15: a pooled analysis of 17 population-based cancer registries. Lancet Glob Health. 2018;6(5):e555–e567.
   PubMed Web of Science ®Google Scholar
• Zarean E, Azizmohammad Looha M, Amini P, et al. Factors affecting long-survival of patients with esophageal cancer using non-mixture cure fraction model. Asian Pac J Cancer Prev. 2018;19(6):1677–1683.
   PubMedGoogle Scholar
• Allemani C, Matsuda T, Di Carlo V, et al. Global surveillance of trends in cancer survival 2000–14 (CONCORD-3): analysis of individual records for 37 513 025 patients diagnosed with one of 18 cancers from 322 population-based registries in 71 countries. Lancet. 2018;391(10125):1023–1075.
   PubMed Web of Science ®Google Scholar
• Ohigashi Y, Sho M, Yamada Y, et al. Clinical significance of programmed death-1 ligand-1 and programmed death-1 ligand-2 expression in human esophageal cancer. Clin Cancer Res. 2005;11(8):2947–2953.
   PubMed Web of Science ®Google Scholar
• Goel G, Sun W. Advances in the management of gastrointestinal cancers—an upcoming role of immune checkpoint blockade. J Hematol Oncol. 2015;8:86.
   PubMed Web of Science ®Google Scholar
• Joyce JA, Fearon DT. T cell exclusion, immune privilege, and the tumor microenvironment. Science. 2015;348(6230):74–80.
   PubMed Web of Science ®Google Scholar
• Vinay DS, Ryan EP, Pawelec G, et al. Immune evasion in cancer: mechanistic basis and therapeutic strategies. Semin Cancer Biol. 2015;35 Suppl:S185–S198.
   PubMed Web of Science ®Google Scholar
• Li J, Chen Z, Tian L, et al. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut. 2014;63(11):1700–1710.
   PubMed Web of Science ®Google Scholar
• Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573.
   PubMed Web of Science ®Google Scholar
• Breuer K, Foroushani AK, Laird MR, et al. InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res. 2013;41(Database issue):D1228–D1233.
   PubMed Web of Science ®Google Scholar
• Thorsson V, Gibbs DL, Brown SD, et al. The immune landscape of cancer. Immunity. 2018;48(4):812–830.e814.
   PubMed Web of Science ®Google Scholar
• Jiang P, Gu S, Pan D, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018;24(10):1550–1558.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Cacchiarelli D, Grimsby J, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32(4):381–386.
   PubMed Web of Science ®Google Scholar
• Sun Y, Yao J, Nowak NJ, et al. Cancer progression modeling using static sample data. Genome Biol. 2014;15(8):440.
   PubMed Web of Science ®Google Scholar
• Horvath S, Dong J. Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol. 2008;4(8):e1000117.
   PubMed Web of Science ®Google Scholar
• Ponsuksili S, Du Y, Hadlich F, et al. Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties. BMC Genomics. 2013;14:533.
   PubMed Web of Science ®Google Scholar
• Cui Y, Chen H, Xi R, et al. Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma. Cell Res. 2020;30(10):902–913.
   PubMed Web of Science ®Google Scholar
• Danilova L, Ho WJ, Zhu Q, et al. Programmed cell death ligand-1 (PD-L1) and CD8 expression profiling identify an immunologic subtype of pancreatic ductal adenocarcinomas with favorable survival. Cancer Immunol Res. 2019;7(6):886–895.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–674.
   PubMed Web of Science ®Google Scholar
• Miyashita M, Sasano H, Tamaki K, et al. Prognostic significance of tumor-infiltrating CD8+ and FOXP3+ lymphocytes in residual tumors and alterations in these parameters after neoadjuvant chemotherapy in triple-negative breast cancer: a retrospective multicenter study. Breast Cancer Res. 2015;17:124.
   PubMed Web of Science ®Google Scholar
• Feng W, Li Y, Shen L, et al. Prognostic value of tumor-infiltrating lymphocytes for patients with completely resected stage IIIA(N2) non-small cell lung cancer. Oncotarget. 2016;7(6):7227–7240.
   PubMedGoogle Scholar
• Mahmoud SM, Paish EC, Powe DG, et al. Tumor-infiltrating CD8+ lymphocytes predict clinical outcome in breast cancer. J Clin Oncol. 2011;29(15):1949–1955.
   PubMed Web of Science ®Google Scholar
• Jensen HK, Donskov F, Nordsmark M, et al. Increased intratumoral FOXP3-positive regulatory immune cells during interleukin-2 treatment in metastatic renal cell carcinoma. Clin Cancer Res. 2009;15(3):1052–1058.
   PubMed Web of Science ®Google Scholar
• Chen J, Yao Y, Gong C, et al. CCL18 from tumor-associated macrophages promotes breast cancer metastasis via PITPNM3. Cancer Cell. 2011;19(4):541–555.
   PubMed Web of Science ®Google Scholar
• Su S, Liu Q, Chen J, et al. A positive feedback loop between mesenchymal-like cancer cells and macrophages is essential to breast cancer metastasis. Cancer Cell. 2014;25(5):605–620.
   PubMed Web of Science ®Google Scholar
• Gerlinger M, Rowan AJ, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366(10):883–892.
   PubMed Web of Science ®Google Scholar
• Suzuki Y, Ng SB, Chua C, et al. Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer. Mol Oncol. 2017;11(2):124–139.
   PubMed Web of Science ®Google Scholar
• Tseng RC, Chang JM, Chen JH, et al. Deregulation of SLIT2-mediated Cdc42 activity is associated with esophageal cancer metastasis and poor prognosis. J Thorac Oncol. 2015;10(1):189–198.
   PubMed Web of Science ®Google Scholar
• Jiang L, Wang Y, Rong Y, et al. miR-1179 promotes cell invasion through SLIT2/ROBO1 axis in esophageal squamous cell carcinoma. Int J Clin Exp Pathol. 2015;8(1):319–327.
   PubMed Web of Science ®Google Scholar
• Chang H, Dong T, Ma X, et al. Spondin 1 promotes metastatic progression through Fak and Src dependent pathway in human osteosarcoma. Biochem Biophys Res Commun. 2015;464(1):45–50.
   PubMed Web of Science ®Google Scholar
• Huang RL, Su PH, Liao YP, et al. Integrated epigenomics analysis reveals a DNA methylation panel for endometrial cancer detection using cervical scrapings. Clin Cancer Res. 2017;23(1):263–272.
   PubMed Web of Science ®Google Scholar