Research progress of single-cell RNA sequencing in the immune microenvironment analysis of non-small cell lung cancer_Chinese Journal of Clinical Thoracic and Cardiovascular Surgery

Authors：

YANG Wenwen ¹ , HE Li ¹ , ZHANG Min ¹ , SUN Shuo ¹ , WANG Feng ¹ , MA Minjie ^2,3 ,  HAN Biao ^2,3

1. The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, P. R. China;
2. Department of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000, P. R. China;
3. Gansu Province International Cooperation Base for Research and Application of Key Technology of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000, P. R. China;

Corresponding author：

HAN Biao, Email: hanbiao66@163.com

Keywords：

Non-small cell lung cancer; single-cell RNA sequencing; tumor immune microenvironment; immunotherapy; drug resistance; review

DOI：

10.7507/1007-4848.202206064

Video：

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Non-small cell lung cancer (NSCLC) is one of the most common types of cancer in the world and is an important cause for cancer death. Although the application of immunotherapy in recent years has greatly improved the prognosis of NSCLC, there are still huge challenges in the treatment of NSCLC. The immune microenvironment plays an important role in the process of NSCLC development, infiltration and metastasis, and they can interact and influence each other, forming a vicious circle. Notably, single-cell RNA sequencing enables high-resolution analysis of individual cells and is of great value in revealing cell types, cell evolution trajectories, molecular mechanisms of cell differentiation, and intercellular regulation within the immune microenvironment. Single-cell RNA sequencing is expected to uncover more promising immunotherapies. This article reviews the important researches and latest achievements of single-cell RNA sequencing in the immune microenvironment of NSCLC, and aims to explore the significance of applying single-cell RNA sequencing to analyze the immune microenvironment of NSCLC.

Citation： YANG Wenwen, HE Li, ZHANG Min, SUN Shuo, WANG Feng, MA Minjie, HAN Biao. Research progress of single-cell RNA sequencing in the immune microenvironment analysis of non-small cell lung cancer. Chinese Journal of Clinical Thoracic and Cardiovascular Surgery, 2024, 31(3): 467-472. doi: 10.7507/1007-4848.202206064 Copy

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17.	Zhou X, Xu Y, Zhu L, et al. Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in limited DNA sequencing based on tube and droplet. Micromachines (Basel), 2020, 11(7): 645.
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21.	Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform, 2013, 14(2): 178-192.
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24.	Lavin Y, Kobayashi S, Leader A, et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell, 2017, 169(4): 750-765.
25.	Kim N, Kim HK, Lee K, et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat Commun, 2020, 11(1): 2285.
26.	Song Q, Hawkins GA, Wudel L, et al. Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Cancer Med, 2019, 8(6): 3072-3085.
27.	Galbraith LCA, Mui E, Nixon C, et al. PPAR-gamma induced Akt3 expression increases levels of mitochondrial biogenesis driving prostate cancer. Oncogene, 2021, 40(13): 2355-2366.
28.	Wu F, Fan J, He Y, et al. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nat Commun, 2021, 12(1): 2540.
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30.	Wang Z, Li Z, Zhou K, et al. Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing. Nat Commun, 2021, 12(1): 6500.
31.	Huang ZY, Shao MM, Zhang JC, et al. Single-cell analysis of diverse immune phenotypes in malignant pleural effusion. Nat Commun, 2021, 12(1): 6690.
32.	Kim KT, Lee HW, Lee HO, et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol, 2015, 16(1): 127.
33.	Xiong D, Pan J, Yin Y, et al. Novel mutational landscapes and expression signatures of lung squamous cell carcinoma. Oncotarget, 2017, 9(7): 7424-7441.
34.	Min JW, Kim WJ, Han JA, et al. Identification of distinct tumor subpopulations in lung adenocarcinoma via single-cell RNA-seq. PLoS One, 2015, 10(8): e0135817.
35.	Suber TL, Nikolli I, O'Brien ME, et al. FBXO17 promotes cell proliferation through activation of Akt in lung adenocarcinoma cells. Respir Res, 2018, 19(1): 206.
36.	Ma KY, Schonnesen AA, Brock A, et al. Single-cell RNA sequencing of lung adenocarcinoma reveals heterogeneity of immune response-related genes. JCI Insight, 2019, 4(4): e121387.
37.	Hu Y, Xu C, Ren J, et al. Exposure to tobacco smoking induces a subset of activated tumor-resident Tregs in non-small cell lung cancer. Transl Oncol, 2022, 15(1): 101261.
38.	Ren X, Zhang Z. Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing. Adv Immunol, 2019, 144: 217-245.
39.	Jiang A, Wang J, Liu N, et al. Integration of single-cell RNA sequencing and bulk RNA sequencing data to establish and validate a prognostic model for patients with lung adenocarcinoma. Front Genet, 2022, 13: 833797.
40.	Ruan H, Zhou Y, Shen J, et al. Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single-cell transcriptome analysis. Clin Transl Med, 2020, 10(8): e246.
41.	Van Damme H, Dombrecht B, Kiss M, et al. Therapeutic depletion of CCR8⁺ tumor-infiltrating regulatory T cells elicits antitumor immunity and synergizes with anti-PD-1 therapy. J Immunother Cancer, 2021, 9(2): e001749.
42.	Maroni G, Bassal MA, Krishnan I, et al. Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer. Commun Biol, 2021, 4(1): 370.
43.	Pan J, Chen Y, Zhang Q, et al. Inhibition of lung tumorigenesis by a small molecule CA170 targeting the immune checkpoint protein VISTA. Commun Biol, 2021, 4(1): 906.
44.	Leader AM, Grout JA, Maier BB, et al. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell, 2021, 39(12): 1594-1609.
45.	Sharma P, Hu-Lieskovan S, Wargo JA, et al. Primary, adaptive, and acquired resistance to cancer immunotherapy. Cell, 2017, 168(4): 707-723.
46.	Suzuki A, Matsushima K, Makinoshima H, et al. Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. Genome Biol, 2015, 16(1): 66.
47.	Granchi C, Fortunato S, Minutolo F. Anticancer agents interacting with membrane glucose transporters. Medchemcomm, 2016, 7(9): 1716-1729.
48.	Na KJ, Choi H, Oh HR, et al. Reciprocal change in glucose metabolism of cancer and immune cells mediated by different glucose transporters predicts immunotherapy response. Theranostics, 2020, 10(21): 9579-9590.

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): 209-249.
2. Molina JR, Yang P, Cassivi SD, et al. Non-small cell lung cancer: Epidemiology, risk factors, treatment, and survivorship. Mayo Clin Proc, 2008, 83(5): 584-594.
3. Binnewies M, Roberts EW, Kersten K, et al. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med, 2018, 24(5): 541-550.
4. Chen DS, Mellman I. Oncology meets immunology: The cancer-immunity cycle. Immunity, 2013, 39(1): 1-10.
5. Kargl J, Busch SE, Yang GH, et al. Neutrophils dominate the immune cell composition in non-small cell lung cancer. Nat Commun, 2017, 8: 14381.
6. Kim DH, Kim H, Choi YJ, et al. Exosomal PD-L1 promotes tumor growth through immune escape in non-small cell lung cancer. Exp Mol Med, 2019, 51(8): 1-13.
7. Oh MS, Anker JF, Chae YK. High gene expression of estrogen and progesterone receptors is associated with decreased T cell infiltration in patients with NSCLC. Cancer Treat Res Commun, 2021, 27: 100317.
8. Guo W, Liu S, Zhang X, et al. The coexpression of multi-immune inhibitory receptors on T lymphocytes in primary non-small-cell lung cancer. Drug Des Devel Ther, 2017, 11: 3367-3376.
9. Chen R, Huang M, Yang X, et al. CALR-TLR4 complex inhibits non-small cell lung cancer progression by regulating the migration and maturation of dendritic cells. Front Oncol, 2021, 11: 743050.
10. Mantovani A, Bottazzi B, Colotta F, et al. The origin and function of tumor-associated macrophages. Immunol Today, 1992, 13(7): 265-270.
11. Murray PJ, Wynn TA. Protective and pathogenic functions of macrophage subsets. Nat Rev Immunol, 2011, 11(11): 723-737.
12. Chanmee T, Ontong P, Konno K, et al. Tumor-associated macrophages as major players in the tumor microenvironment. Cancers (Basel), 2014, 6(3): 1670-1690.
13. Casanova-Acebes M, Dalla E, Leader AM, et al. Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells. Nature, 2021, 595(7868): 578-584.
14. Aloe C, Wang H, Vlahos R, et al. Emerging and multifaceted role of neutrophils in lung cancer. Transl Lung Cancer Res, 2021, 10(6): 2806-2818.
15. Najafi S, Mirshafiey A. The role of T helper 17 and regulatory T cells in tumor microenvironment. Immunopharmacol Immunotoxicol, 2019, 41(1): 16-24.
16. Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med, 2018, 50(8): 1-14.
17. Zhou X, Xu Y, Zhu L, et al. Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in limited DNA sequencing based on tube and droplet. Micromachines (Basel), 2020, 11(7): 645.
18. Kumar R, Ichihashi Y, Kimura S, et al. A high-throughput method for illumina RNA-Seq library preparation. Front Plant Sci, 2012, 3: 202.
19. Kumar KR, Cowley MJ, Davis RL. Next-generation sequencing and emerging technologies. Semin Thromb Hemost, 2019, 45(7): 661-673.
20. 1000 Genomes Project Consortium, Auton A, Brooks LD, et al. A global reference for human genetic variation. Nature, 2015, 526(7571): 68-74.
21. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform, 2013, 14(2): 178-192.
22. Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol, 2011, 29(1): 24-26.
23. Oliver GR, Hart SN, Klee EW. Bioinformatics for clinical next generation sequencing. Clin Chem, 2015, 61(1): 124-135.
24. Lavin Y, Kobayashi S, Leader A, et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell, 2017, 169(4): 750-765.
25. Kim N, Kim HK, Lee K, et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat Commun, 2020, 11(1): 2285.
26. Song Q, Hawkins GA, Wudel L, et al. Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Cancer Med, 2019, 8(6): 3072-3085.
27. Galbraith LCA, Mui E, Nixon C, et al. PPAR-gamma induced Akt3 expression increases levels of mitochondrial biogenesis driving prostate cancer. Oncogene, 2021, 40(13): 2355-2366.
28. Wu F, Fan J, He Y, et al. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nat Commun, 2021, 12(1): 2540.
29. Inamura K. Clinicopathological characteristics and mutations driving development of early lung adenocarcinoma: Tumor initiation and progression. Int J Mol Sci, 2018, 19(4): 1259.
30. Wang Z, Li Z, Zhou K, et al. Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing. Nat Commun, 2021, 12(1): 6500.
31. Huang ZY, Shao MM, Zhang JC, et al. Single-cell analysis of diverse immune phenotypes in malignant pleural effusion. Nat Commun, 2021, 12(1): 6690.
32. Kim KT, Lee HW, Lee HO, et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol, 2015, 16(1): 127.
33. Xiong D, Pan J, Yin Y, et al. Novel mutational landscapes and expression signatures of lung squamous cell carcinoma. Oncotarget, 2017, 9(7): 7424-7441.
34. Min JW, Kim WJ, Han JA, et al. Identification of distinct tumor subpopulations in lung adenocarcinoma via single-cell RNA-seq. PLoS One, 2015, 10(8): e0135817.
35. Suber TL, Nikolli I, O'Brien ME, et al. FBXO17 promotes cell proliferation through activation of Akt in lung adenocarcinoma cells. Respir Res, 2018, 19(1): 206.
36. Ma KY, Schonnesen AA, Brock A, et al. Single-cell RNA sequencing of lung adenocarcinoma reveals heterogeneity of immune response-related genes. JCI Insight, 2019, 4(4): e121387.
37. Hu Y, Xu C, Ren J, et al. Exposure to tobacco smoking induces a subset of activated tumor-resident Tregs in non-small cell lung cancer. Transl Oncol, 2022, 15(1): 101261.
38. Ren X, Zhang Z. Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing. Adv Immunol, 2019, 144: 217-245.
39. Jiang A, Wang J, Liu N, et al. Integration of single-cell RNA sequencing and bulk RNA sequencing data to establish and validate a prognostic model for patients with lung adenocarcinoma. Front Genet, 2022, 13: 833797.
40. Ruan H, Zhou Y, Shen J, et al. Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single-cell transcriptome analysis. Clin Transl Med, 2020, 10(8): e246.
41. Van Damme H, Dombrecht B, Kiss M, et al. Therapeutic depletion of CCR8⁺ tumor-infiltrating regulatory T cells elicits antitumor immunity and synergizes with anti-PD-1 therapy. J Immunother Cancer, 2021, 9(2): e001749.
42. Maroni G, Bassal MA, Krishnan I, et al. Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer. Commun Biol, 2021, 4(1): 370.
43. Pan J, Chen Y, Zhang Q, et al. Inhibition of lung tumorigenesis by a small molecule CA170 targeting the immune checkpoint protein VISTA. Commun Biol, 2021, 4(1): 906.
44. Leader AM, Grout JA, Maier BB, et al. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell, 2021, 39(12): 1594-1609.
45. Sharma P, Hu-Lieskovan S, Wargo JA, et al. Primary, adaptive, and acquired resistance to cancer immunotherapy. Cell, 2017, 168(4): 707-723.
46. Suzuki A, Matsushima K, Makinoshima H, et al. Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. Genome Biol, 2015, 16(1): 66.
47. Granchi C, Fortunato S, Minutolo F. Anticancer agents interacting with membrane glucose transporters. Medchemcomm, 2016, 7(9): 1716-1729.
48. Na KJ, Choi H, Oh HR, et al. Reciprocal change in glucose metabolism of cancer and immune cells mediated by different glucose transporters predicts immunotherapy response. Theranostics, 2020, 10(21): 9579-9590.

Chinese Journal of Clinical Thoracic and Cardiovascular Surgery

Research progress of single-cell RNA sequencing in the immune microenvironment analysis of non-small cell lung cancer

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