单细胞转录组测序在黑素瘤研究中的应用

doi:10.35541/cjd.20210191

Abstract

Abstract: 【Abstract】 Tumor heterogeneity is one of the important characteristics of melanoma. Single-cell RNA sequencing can not only further reveal the heterogeneity of melanoma cells, but also has unique advantages in analyzing the occurrence and development of melanoma, finding new targets for immunotherapy and uncovering mechanisms of drug resistance. This review summarizes the application of single-cell transcriptome sequencing in melanoma research.

Key words: Melanoma, Sequence analysis, RNA, Transcriptome, Single-cell analysis, Genetic heterogeneity, Tumor microenvironment, Immunotherapy, Drug resistance, neoplasm, Single-cell RNA sequencing

Li Tingting, Guan Mengmeng, Zhao Juan, Kang Xiaojing. Application of single-cell RNA sequencing in melanoma research[J]. Chinese Journal of Dermatology, 2023, 56(10): 977-981.doi:10.35541/cjd.20210191

References ［42］

［1］	Hu X, Hu Y, Wu F, et al. Integration of single⁃cell multi⁃omics for gene regulatory network inference［J］. Comput Struct Biotechnol J, 2020,18:1925⁃1938. doi: 10.1016/j.csbj.2020.06. 033.
［2］	Pratapa A, Jalihal AP, Law JN, et al. Benchmarking algorithms for gene regulatory network inference from single⁃cell transcriptomic data［J］. Nat Methods, 2020,17（2）:147⁃154. doi: 10.1038/s41592⁃019⁃0690⁃6.
［3］	朱容慧, 李巍. 单细胞RNA测序技术及其在皮肤病学研究中的应用［J］. 中华皮肤科杂志, 2019,52（7）:506⁃509. doi: 10. 3760/cma.j.issn.0412⁃4030.2019.07.015.
［4］	Puram SV, Tirosh I, Parikh AS, et al. Single⁃cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer［J］. Cell, 2017,171（7）:1611⁃1624. doi: 10.1016/j.cell.2017.10.044.
［5］	Mereu E, Lafzi A, Moutinho C, et al. Benchmarking single⁃cell RNA⁃sequencing protocols for cell atlas projects［J］. Nat Biotechnol, 2020,38（6）:747⁃755. doi: 10.1038/s41587⁃020⁃0469⁃4.
［6］	Lähnemann D, Köster J, Szczurek E, et al. Eleven grand challenges in single⁃cell data science［J］. Genome Biol, 2020,21（1）:31. doi: 10.1186/s13059⁃020⁃1926⁃6.
［7］	Savas P, Virassamy B, Ye C, et al. Single⁃cell profiling of breast cancer T cells reveals a tissue⁃resident memory subset associated with improved prognosis［J］. Nat Med, 2018,24（7）:986⁃993. doi: 10.1038/s41591⁃018⁃0078⁃7.
［8］	Mustachio LM, Roszik J. Opportunities for single⁃cell sequencing technologies and data science［J］. Cancers （Basel）, 2020,12（11）:3433. doi: 10.3390/cancers12113433.
［9］	Zhang L, Yu X, Zheng L, et al. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer［J］. Nature, 2018,564（7735）:268⁃272. doi: 10.1038/s41586⁃018⁃0694⁃x.
［10］	Guo X, Zhang Y, Zheng L, et al. Global characterization of T cells in non⁃small⁃cell lung cancer by single⁃cell sequencing［J］. Nat Med, 2018,24（7）:978⁃985. doi: 10.1038/s41591⁃018⁃0045⁃3.
［11］	刘慧萍, 崔恒, 昌晓红. 单细胞测序技术在恶性肿瘤研究中的应用进展［J］. 中国肿瘤临床, 2020,47（7）:365⁃368. doi: 10. 3969/j.issn.1000⁃8179.2020.07.323.
［12］	Lin Z, Meng X, Wen J, et al. Intratumor heterogeneity correlates with reduced immune activity and worse survival in melanoma patients［J］. Front Oncol, 2020,10:596493. doi: 10.3389/fonc. 2020.596493.
［13］	Gerber T, Willscher E, Loeffler⁃Wirth H, et al. Mapping heterogeneity in patient⁃derived melanoma cultures by single⁃cell RNA⁃seq［J］. Oncotarget, 2017,8（1）:846⁃862. doi: 10. 18632/oncotarget.13666.
［14］	Tirosh I, Izar B, Prakadan SM, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single⁃cell RNA⁃seq［J］. Science, 2016,352（6282）:189⁃196. doi: 10.1126/science.aad0501.
［15］	Gokuldass A, Draghi A, Papp K, et al. Qualitative analysis of tumor⁃infiltrating lymphocytes across human tumor types reveals a higher proportion of bystander CD8（+） T cells in non⁃melanoma cancers compared to melanoma［J］. Cancers （Basel）, 2020,12（11）:3344. doi: 10.3390/cancers12113344.
［16］	Li H, van der Leun AM, Yofe I, et al. Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma［J］. Cell, 2019,176（4）:775⁃789.e18. doi: 10.1016/j.cell.2018.11.043.
［17］	Carmona SJ, Siddiqui I, Bilous M, et al. Deciphering the transcriptomic landscape of tumor⁃infiltrating CD8 lymphocytes in B16 melanoma tumors with single⁃cell RNA⁃Seq［J］. Oncoimmunology, 2020,9（1）:1737369. doi: 10.1080/2162402X. 2020.1737369.
［18］	Davidson S, Efremova M, Riedel A, et al. Single⁃cell RNA sequencing reveals a dynamic stromal niche that supports tumor growth［J］. Cell Rep, 2020,31（7）:107628. doi: 10.1016/j.celrep.2020.107628.
［19］	Hirata E, Ishibashi K, Kohsaka S, et al. The brain microenvironment induces DNMT1 suppression and indolence of metastatic cancer cells［J］. iScience, 2020,23（9）:101480. doi: 10.1016/j.isci.2020.101480.
［20］	Wouters J, Kalender⁃Atak Z, Minnoye L, et al. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma［J］. Nat Cell Biol, 2020,22（8）:986⁃998. doi: 10.1038/s41556⁃020⁃0547⁃3.
［21］	Li X, Karras P, Torres R, et al. Disseminated melanoma cells transdifferentiate into endothelial cells in intravascular niches at metastatic sites［J］. Cell Rep, 2020,31（11）:107765. doi: 10. 1016/j.celrep.2020.107765.
［22］	Hamid O, Robert C, Daud A, et al. Five⁃year survival outcomes for patients with advanced melanoma treated with pembrolizumab in KEYNOTE⁃001［J］. Ann Oncol, 2019,30（4）:582⁃588. doi: 10.1093/annonc/mdz011.
［23］	Dai WF, Beca JM, Croxford R, et al. Real⁃world comparative effectiveness of second⁃line ipilimumab for metastatic melanoma: a population⁃based cohort study in Ontario, Canada［J］. BMC Cancer, 2020,20（1）:304. doi: 10.1186/s12885⁃020⁃06798⁃1.
［24］	Helmink BA, Reddy SM, Gao J, et al. B cells and tertiary lymphoid structures promote immunotherapy response［J］. Nature, 2020,577（7791）:549⁃555. doi: 10.1038/s41586⁃019⁃1922⁃8.
［25］	Xiong D, Wang Y, You M. A gene expression signature of TREM2（hi） macrophages and γδ T cells predicts immunotherapy response［J］. Nat Commun, 2020,11（1）:5084. doi: 10.1038/s41467⁃020⁃18546⁃x.
［26］	Schetters S, Rodriguez E, Kruijssen L, et al. Monocyte⁃derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy［J］. J Immunother Cancer, 2020,8（2）:e000588. doi: 10.1136/jitc⁃2020⁃000588.
［27］	Kim K, Park S, Park SY, et al. Single⁃cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti⁃PD⁃1 responses in human cancer［J］. Genome Med, 2020,12（1）:22. doi: 10.1186/s13073⁃020⁃00722⁃9.
［28］	Sade⁃Feldman M, Yizhak K, Bjorgaard SL, et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma［J］. Cell, 2018,175（4）:998⁃1013.e20. doi: 10. 1016/j.cell.2018.10.038.
［29］	Singer M, Wang C, Cong L, et al. A distinct gene module for dysfunction uncoupled from activation in tumor⁃infiltrating T cells［J］. Cell, 2016,166（6）:1500⁃1511.e9. doi: 10.1016/j.cell. 2016.08.052.
［30］	Nirschl CJ, Suárez⁃Fariñas M, Izar B, et al. IFNγ⁃dependent tissue⁃immune homeostasis is co⁃opted in the tumor microenvironment［J］. Cell, 2017,170（1）:127⁃141.e15. doi: 10. 1016/j.cell.2017.06.016.
［31］	Jerby⁃Arnon L, Shah P, Cuoco MS, et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade［J］. Cell, 2018,175（4）:984⁃997. doi: 10.1016/j.cell.2018.09.006.
［32］	Shaffer SM, Dunagin MC, Torborg SR, et al. Rare cell variability and drug⁃induced reprogramming as a mode of cancer drug resistance［J］. Nature, 2017,546（7658）:431⁃435. doi: 10.1038/nature22794.
［33］	Rambow F, Rogiers A, Marin⁃Bejar O, et al. Toward minimal residual disease⁃directed therapy in melanoma［J］. Cell, 2018,174（4）:843⁃855.e19. doi: 10.1016/j.cell.2018.06.025.
［34］	Long JE, Wongchenko MJ, Nickles D, et al. Therapeutic resistance and susceptibility is shaped by cooperative multi⁃compartment tumor adaptation［J］. Cell Death Differ, 2019,26（11）:2416⁃2429. doi: 10.1038/s41418⁃019⁃0310⁃0.
［35］	Prieto⁃Fernández E, Egia⁃Mendikute L, Bosch A, et al. Hypoxia promotes syndecan⁃3 expression in the tumor microenvironment［J］. Front Immunol, 2020,11:586977. doi: 10.3389/fimmu.2020. 586977.
［36］	Fairfax BP, Taylor CA, Watson RA, et al. Peripheral CD8（+） T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma［J］. Nat Med, 2020,26（2）:193⁃199. doi: 10.1038/s41591⁃019⁃0734⁃6.
［37］	Peng H, Zeng X, Zhou Y, et al. A component overlapping attribute clustering （COAC） algorithm for single⁃cell RNA sequencing data analysis and potential pathobiological implications［J/OL］. PLoS Comput Biol, 2019,15（2）:e1006772. doi: 10.1371/journal.pcbi.1006772.
［38］	Slyper M, Porter C, Ashenberg O, et al. A single⁃cell and single⁃nucleus RNA⁃Seq toolbox for fresh and frozen human tumors［J］. Nat Med, 2020,26（5）:792⁃802. doi: 10.1038/s41591⁃020⁃0844⁃1.
［39］	Tsoucas D, Dong R, Chen H, et al. Accurate estimation of cell⁃type composition from gene expression data［J］. Nat Commun, 2019,10（1）:2975. doi: 10.1038/s41467⁃019⁃10802⁃z.
［40］	Ho YJ, Anaparthy N, Molik D, et al. Single⁃cell RNA⁃seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations［J］. Genome Res, 2018,28（9）:1353⁃1363. doi: 10.1101/gr.234062.117.
［41］	Cheng C, Easton J, Rosencrance C, et al. Latent cellular analysis robustly reveals subtle diversity in large⁃scale single⁃cell RNA⁃seq data［J］. Nucleic Acids Res, 2019,47（22）:e143. doi: 10. 1093/nar/gkz826.
［42］	Song Y, Xu X, Wang W, et al. Single cell transcriptomics: moving towards multi⁃omics［J］. Analyst, 2019,144（10）:3172⁃3189. doi: 10.1039/c8an01852a.

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Application of single-cell RNA sequencing in melanoma research

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