Abstract
Background: Cancer stem cells (CSCs) contribute to metastasis and drug resistance to immunotherapy in lung adenocarcinoma (LUAD), so the stemness evaluation of cancer cells is of great significance.
Method: The single-cell RNA sequencing (scRNA-seq) data of the GSE149655 dataset were collected and analyzed. Malignant cells were distinguished by CopyKAT. CytoTRACE score of marker genes in malignant cells was counted by CytoTRACE to construct the stemness score formula. Sample stemness score in TCGA was determined by the formula and divided into high-, medium- and low-stemness score groups. LASSO and COX regression analyses were carried out to screen the key genes related to the prognosis of LUAD from the differentially expressed genes (DEGs) in high- and low-stemness score groups and a risk score model was constructed.
Result: Seven types of cells were identified from a total of 4 samples, and 193 marker genes of 3455 malignant cells were identified. There were 1098 DEGs between low- and high-stemness score groups of TCGA, of which CPS1, CENPK, GJB3, and TPSB2 constituted gene signatures. The 4-gene signature could independently evaluate LUAD survival in the training and validation sets and showed an acceptable area under the receiver operator characteristic (ROC) curves (AUCs).
Conclusion: This study provides insights into the cellular heterogeneity of LUAD and develops a new cancer stemness evaluation indicator and a 4-gene signature as a potential tool for evaluating the response of LUAD to immune checkpoint blockade (ICB) therapy or antineoplastic therapy.
Graphical Abstract
[1]
Sung H, Ferlay J, Siegel RL, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin 2021; 71(3): 209-49.
[http://dx.doi.org/10.3322/caac.21660] [PMID: 33538338]
[http://dx.doi.org/10.3322/caac.21660] [PMID: 33538338]
[2]
Travis WD, Brambilla E, Noguchi M, et al. International association for the study of lung cancer/american thoracic society/european respiratory society international multidisciplinary classification of lung adenocarcinoma. J Thorac Oncol 2011; 6(2): 244-85.
[http://dx.doi.org/10.1097/JTO.0b013e318206a221] [PMID: 21252716]
[http://dx.doi.org/10.1097/JTO.0b013e318206a221] [PMID: 21252716]
[3]
Denisenko TV, Budkevich IN, Zhivotovsky B. Cell death-based treatment of lung adenocarcinoma. Cell Death Dis 2018; 9(2): 117.
[http://dx.doi.org/10.1038/s41419-017-0063-y] [PMID: 29371589]
[http://dx.doi.org/10.1038/s41419-017-0063-y] [PMID: 29371589]
[4]
Hirsch FR, Scagliotti GV, Mulshine JL, et al. Lung cancer: Current therapies and new targeted treatments. Lancet 2017; 389(10066): 299-311.
[http://dx.doi.org/10.1016/S0140-6736(16)30958-8] [PMID: 27574741]
[http://dx.doi.org/10.1016/S0140-6736(16)30958-8] [PMID: 27574741]
[5]
Tsui YM, Chan LK, Ng IOL. Cancer stemness in hepatocellular carcinoma: Mechanisms and translational potential. Br J Cancer 2020; 122(10): 1428-40.
[http://dx.doi.org/10.1038/s41416-020-0823-9] [PMID: 32231294]
[http://dx.doi.org/10.1038/s41416-020-0823-9] [PMID: 32231294]
[6]
Ghatak D, Das Ghosh D, Roychoudhury S. Cancer Stemness: p53 at the Wheel. Front Oncol 2021; 10: 604124.
[http://dx.doi.org/10.3389/fonc.2020.604124] [PMID: 33505918]
[http://dx.doi.org/10.3389/fonc.2020.604124] [PMID: 33505918]
[7]
Glinsky GV. “Stemness” genomics law governs clinical behavior of human cancer: Implications for decision making in disease management. J Clin Oncol 2008; 26(17): 2846-53.
[http://dx.doi.org/10.1200/JCO.2008.17.0266] [PMID: 18539963]
[http://dx.doi.org/10.1200/JCO.2008.17.0266] [PMID: 18539963]
[8]
Li X, Li Y, Yu X, Jin F. Identification and validation of stemness-related lncRNA prognostic signature for breast cancer. J Transl Med 2020; 18(1): 331.
[http://dx.doi.org/10.1186/s12967-020-02497-4] [PMID: 32867770]
[http://dx.doi.org/10.1186/s12967-020-02497-4] [PMID: 32867770]
[9]
Chen X, Zhang D, Jiang F, et al. Prognostic prediction using a stemness index-related signature in a cohort of gastric cancer. Front Mol Biosci 2020; 7: 570702.
[http://dx.doi.org/10.3389/fmolb.2020.570702] [PMID: 33134315]
[http://dx.doi.org/10.3389/fmolb.2020.570702] [PMID: 33134315]
[10]
Zhang M, Wang X, Chen X, Guo F, Hong J. Prognostic value of a stemness index-associated signature in primary lower-grade glioma. Front Genet 2020; 11: 441.
[http://dx.doi.org/10.3389/fgene.2020.00441] [PMID: 32431729]
[http://dx.doi.org/10.3389/fgene.2020.00441] [PMID: 32431729]
[11]
Yi L, Huang P, Zou X, et al. Integrative stemness characteristics associated with prognosis and the immune microenvironment in esophageal cancer. Pharmacol Res 2020; 161: 105144.
[http://dx.doi.org/10.1016/j.phrs.2020.105144] [PMID: 32810627]
[http://dx.doi.org/10.1016/j.phrs.2020.105144] [PMID: 32810627]
[12]
Davis-Marcisak EF, Deshpande A, Stein-O’Brien GL, et al. From bench to bedside: Single-cell analysis for cancer immunotherapy. Cancer Cell 2021; 39(8): 1062-80.
[http://dx.doi.org/10.1016/j.ccell.2021.07.004] [PMID: 34329587]
[http://dx.doi.org/10.1016/j.ccell.2021.07.004] [PMID: 34329587]
[13]
Gulati GS, Sikandar SS, Wesche DJ, et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 2020; 367(6476): 405-11.
[http://dx.doi.org/10.1126/science.aax0249] [PMID: 31974247]
[http://dx.doi.org/10.1126/science.aax0249] [PMID: 31974247]
[14]
Yu G, Wang LG, Han Y, He QY. clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 2012; 16(5): 284-7.
[http://dx.doi.org/10.1089/omi.2011.0118] [PMID: 22455463]
[http://dx.doi.org/10.1089/omi.2011.0118] [PMID: 22455463]
[15]
Gao R, Bai S, Henderson YC, et al. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol 2021; 39(5): 599-608.
[http://dx.doi.org/10.1038/s41587-020-00795-2] [PMID: 33462507]
[http://dx.doi.org/10.1038/s41587-020-00795-2] [PMID: 33462507]
[16]
Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 2015; 12(5): 453-7.
[http://dx.doi.org/10.1038/nmeth.3337] [PMID: 25822800]
[http://dx.doi.org/10.1038/nmeth.3337] [PMID: 25822800]
[17]
Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun 2013; 4(1): 2612.
[http://dx.doi.org/10.1038/ncomms3612] [PMID: 24113773]
[http://dx.doi.org/10.1038/ncomms3612] [PMID: 24113773]
[18]
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): 886-95.
[http://dx.doi.org/10.1158/2326-6066.CIR-18-0822] [PMID: 31043417]
[http://dx.doi.org/10.1158/2326-6066.CIR-18-0822] [PMID: 31043417]
[19]
Jiang P, Gu S, Pan D, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med 2018; 24(10): 1550-8.
[http://dx.doi.org/10.1038/s41591-018-0136-1] [PMID: 30127393]
[http://dx.doi.org/10.1038/s41591-018-0136-1] [PMID: 30127393]
[20]
Hugo W, Zaretsky JM, Sun L, et al. Genomic and transcriptomic features of response to Anti-PD-1 therapy in metastatic melanoma. Cell 2016; 165(1): 35-44.
[http://dx.doi.org/10.1016/j.cell.2016.02.065] [PMID: 26997480]
[http://dx.doi.org/10.1016/j.cell.2016.02.065] [PMID: 26997480]
[21]
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): 544-8.
[http://dx.doi.org/10.1038/nature25501] [PMID: 29443960]
[http://dx.doi.org/10.1038/nature25501] [PMID: 29443960]
[22]
Tirosh I, Venteicher AS, Hebert C, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature 2016; 539(7628): 309-13.
[http://dx.doi.org/10.1038/nature20123] [PMID: 27806376]
[http://dx.doi.org/10.1038/nature20123] [PMID: 27806376]
[23]
Pece S, Tosoni D, Confalonieri S, et al. Biological and molecular heterogeneity of breast cancers correlates with their cancer stem cell content. Cell 2010; 140(1): 62-73.
[http://dx.doi.org/10.1016/j.cell.2009.12.007] [PMID: 20074520]
[http://dx.doi.org/10.1016/j.cell.2009.12.007] [PMID: 20074520]
[24]
Chen P, Hsu WH, Han J, Xia Y, DePinho RA. Cancer stemness meets immunity: From mechanism to therapy. Cell Rep 2021; 34(1): 108597.
[http://dx.doi.org/10.1016/j.celrep.2020.108597] [PMID: 33406434]
[http://dx.doi.org/10.1016/j.celrep.2020.108597] [PMID: 33406434]
[25]
Pastò A, Consonni FM, Sica A. Influence of innate immunity on cancer cell stemness. Int J Mol Sci 2020; 21(9): 3352.
[http://dx.doi.org/10.3390/ijms21093352] [PMID: 32397392]
[http://dx.doi.org/10.3390/ijms21093352] [PMID: 32397392]
[26]
Malta TM, Sokolov A, Gentles AJ, et al. Machine learning identifies stemness features associated with oncogenic dedifferentiation. Cell 2018; 173(2): 338-354.e15.
[http://dx.doi.org/10.1016/j.cell.2018.03.034] [PMID: 29625051]
[http://dx.doi.org/10.1016/j.cell.2018.03.034] [PMID: 29625051]
[27]
Bian J, Fu J, Wang X, et al. Characterization of immunogenicity of malignant cells with stemness in intrahepatic cholangiocarcinoma by single-cell RNA sequencing. Stem Cells Int 2022; 2022: 1-14.
[http://dx.doi.org/10.1155/2022/3558200] [PMID: 35530414]
[http://dx.doi.org/10.1155/2022/3558200] [PMID: 35530414]
[28]
Wu G, Zhao Z, Yan Y, et al. CPS1 expression and its prognostic significance in lung adenocarcinoma. Ann Transl Med 2020; 8(6): 341.
[http://dx.doi.org/10.21037/atm.2020.02.146] [PMID: 32355785]
[http://dx.doi.org/10.21037/atm.2020.02.146] [PMID: 32355785]
[29]
Zeng H, Shen Y, Hirachan S, Bhandari A, Zhang X. Pan-cancer investigation of CENPK gene: Clinical significance and oncogenic immunology. Am J Transl Res 2021; 13(12): 13336-55.
[PMID: 35035680]
[PMID: 35035680]
[30]
Zhang D, Chen C, Li Y, et al. Cx31.1 acts as a tumour suppressor in non-small cell lung cancer (NSCLC) cell lines through inhibition of cell proliferation and metastasis. J Cell Mol Med 2012; 16(5): 1047-59.
[http://dx.doi.org/10.1111/j.1582-4934.2011.01389.x] [PMID: 21777377]
[http://dx.doi.org/10.1111/j.1582-4934.2011.01389.x] [PMID: 21777377]
[31]
Wang X, Li Y, Fu J, Zhou K, Wang T. ARNTL2 is a prognostic biomarker and correlates with immune cell infiltration in triple-negative breast cancer. Pharm Genomics Pers Med 2021; 14: 1425-40.
[http://dx.doi.org/10.2147/PGPM.S331431] [PMID: 34785930]
[http://dx.doi.org/10.2147/PGPM.S331431] [PMID: 34785930]
