International Journal of Frontiers in Medicine, 2023, 5(10); doi: 10.25236/IJFM.2023.051013.
Tao Yu1, Xuehan Gao2, Jueyi Zhou3, Liping Zhao3, Jihong Feng3
1Department of Respiratory and Critical Care Medicine, People's Hospital of Inner Mongolia Autonomous Region, Hohhot, China
2Department of Immunology, Zunyi Medical University, Zunyi, China
3Department of Oncology, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People's Hospital, Lishui, China
Lung cancer is the most common and aggressive cancer and the leading cause of cancer-related death worldwide, with non-small cell lung cancer (NSCLC) being the most common type. However, the issue of tumor heterogeneity in non-small cell lung cancer has received increasing attention and is not currently addressed at single-cell resolution. In this study, integrated single-cell RNA sequencing (scRNA-seq) samples from Non-Small-Cell Lung Cancer (NSCLC) samples and paracancerous control samples were downloaded from the high-throughput Gene Expression Omnibus (GEO) data and batch RNA-seq data for analysis. Three NSCLC cell subsets in different differentiation states were compared and analyzed. GSEA-GO analysis predicts the biological functions and pathways of differentiation-related genes. The sequencing results of a total of 4320 cells from 11 NSCLC samples and 5 paracancerous lung tissue samples were obtained from the GEO database. After data standardization and data filtering, all cells were subjected to unsupervised clustering to obtain 3 different clusters, which were visualized after dimensionality reduction through T-SNE, and 10 differential marker genes were analyzed and screened, which can be clustered in different clusters. Gene set enrichment analysis found that CDRG was significantly associated with immune regulation and immune response, and 278 NSCLC cell differentiation-related genes (CDRG) were identified. Our study identified NSCLC cells with distinct differentiation characteristics based on single-cell sequencing data from GEO, emphasizing the important role of cell differentiation in predicting the clinical outcome of NSCLC patients and their potential response to immunotherapy.
Non-small cell lung cancer, tumor heterogeneity, immune prognosis, single-cell sequencing, GEO database, GSEA analysis
Tao Yu, Xuehan Gao, Jueyi Zhou, Liping Zhao, Jihong Feng. Dissecting heterogeneity and immune cell populations in non-small cell lung cancer by single-cell RNA sequencing. International Journal of Frontiers in Medicine (2023), Vol. 5, Issue 10: 81-87. https://doi.org/10.25236/IJFM.2023.051013.
[1] Torre LA, Siegel RL, Jemal A. Lung cancer statistics. Adv Exp Med Biol. 2016, 893(1):1–19.
[2] Seow WJ, Matsuo K, Hsiung CA. Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations. Hum Mol Genet, 2017, 26(1): 454–465.
[3] Goveia J, Rohlenova K, Taverna F. An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates. Cancer Cell. 2020, 37(1): 21-36.
[4] Kron A, Scheffler M, Heydt C. Genetic Heterogeneity of MET-Aberrant NSCLC and Its Impact on the Outcome of Immunotherapy. J Thorac Oncol. 2021, 16(4): 572-582.
[5] Jia Q, Wu W, Wang Y. Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer. Nat Commun. 2018, 9(1): 53-61.
[6] Sui H, Ma N, Wang Y. Anti-PD-1/PD-L1 Therapy for Non-Small-Cell Lung Cancer: Toward Personalized Medicine and Combination Strategies. J Immunol Res. 2018, 8(1): 20-69.
[7] Klein AM, Mazutis L, Akartuna I. Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell, 2015, 161(3): 1187–1201.
[8] Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol. Nat Biotechnol, 2016, 34(4): 1145–1160.
[9] Zheng GX, Terry JM, Belgrader P. Massively parallel digital transcriptional profiling of single cells. Cancer Manag Res, 2019, 11(1): 7197-7210.
[10] Azizi E, Carr AJ, Plitas G. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell, 2018, 174(1): 1293–1308.
[11] Peng J, Sun BF, Chen CY. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res, 2019, 29(1): 725–738.
[12] Shalek AK, Satija R, Shuga J. Single-cell RNA-seq reveals dynamic paracrine control cellular variation. Nature. 2014, 510(7): 363-369.
[13] Qiu X, Mao Q, Tang Y. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods, 2017, 14(2): 979–982.
[14] Jonna S, Subramaniam DS. Molecular diagnostics and targeted therapies in non-small cell lung cancer (NSCLC): an update. Discov Med. 2019, 27(148): 167-170.
[15] Pe'er D, Ogawa S, Elhanani O. Tumor heterogeneity. Cancer Cell. 2021, 39(8): 1015-1017.
[16] Ren X, Zhang L, Zhang Y. Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment. Annu Rev Immunol. 2021 Apr 26;39:583-609.
[17] Sun YF, Wu L, Liu SP. Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma. Nat Commun. 2021, 12(1): 40-91.
[18] Cooper LA, Demicco EG, Saltz JH. PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective. J Pathol. 2018, 244(5): 512-524.
[19] Chen YP, Lv JW, Mao YP. Unraveling tumor microenvironment heterogeneity in nasopharyngeal carcinoma identifies biologically distinct immune subtypes predicting prognosis and immunotherapy responses. Mol Cancer. 2021, 20(1): 14-31.
[20] Havel JJ, Chowell D, Chan TA. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat Rev Cancer. 2019, 19(3): 133-150.
[21] Gao S. Data Analysis in Single-Cell Transcriptome Sequencing. Methods Mol Biol. 2018, 1754(1): 311-326.
[22] Stepan H, Hund M, Andraczek T. Combining Biomarkers to Predict Pregnancy Complications and Redefine Preeclampsia: The Angiogenic-Placental Syndrome. Hypertension. 2020 Apr;75(4):918-926.