Comprehensive analysis of single cell and bulk RNA sequencing reveals the heterogeneity of melanoma tumor microenvironment and predicts the response of immunotherapy

Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9(1):34.

Article  Google Scholar 

Pitcovski J, Shahar E, Aizenshtein E, Gorodetsky R. Melanoma antigens and related immunological markers. Crit Rev Oncol Hematol. 2017;115:36–49.

Article  Google Scholar 

Maida I, Zanna P, Guida S, et al. Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. J Transl Med. 2019;17(1):20.

Article  Google Scholar 

Arnold M, Singh D, Laversanne M, Vignat J, Vaccarella S, Meheus F, et al. Global Burden of Cutaneous Melanoma in 2020 and projections to 2040. JAMA Dermatol. 2022;158(5):495–503.

Article  Google Scholar 

Li M, Long X, Bu W, Zhang G, Deng G, Liu Y, et al. Immune-related risk score: an immune-cell-pair-based prognostic model for cutaneous melanoma. Front Immunol. 2023;14:1112181.

Article  CAS  Google Scholar 

Yu L, He R, Cui Y. Characterization of tumor microenvironment and programmed death-related genes to identify molecular subtypes and drug resistance in pancreatic cancer. Front Pharmacol. 2023;14:1146280.

Article  CAS  Google Scholar 

Knackstedt T, Knackstedt RW, Couto R, Gastman B. Malignant melanoma: Diagnostic and Management Update. Plast Reconstr Surg. 2018;142(2):e202–16.

Article  Google Scholar 

Kessenbrock K, Plaks V, Werb Z. Matrix metalloproteinases: regulators of the tumor microenvironment. Cell. 2010;141(1):52–67.

Article  CAS  Google Scholar 

Long GV, Swetter SM, Menzies AM, Gershenwald JE, Scolyer RA. Cutaneous melanoma. Lancet. 2023;402(10400):485–502.

Article  Google Scholar 

Czarnecka AM, Sobczuk P, Rogala P, Świtaj T, Placzke J, Kozak K, et al. Efficacy of immunotherapy beyond RECIST progression in advanced melanoma: a real-world evidence. Cancer Immunol Immunother. 2022;71(8):1949–58.

Article  CAS  Google Scholar 

Sharma P, Hu-Lieskovan S, Wargo JA, Ribas A. Primary, adaptive, and Acquired Resistance to Cancer Immunotherapy. Cell. 2017;168(4):707–23.

Article  CAS  Google Scholar 

Ye D, Desai J, Shi J, Liu SM, Shen W, Liu T, Shi Y, et al. Co-enrichment of CD8-positive T cells and macrophages is associated with clinical benefit of tislelizumab in solid tumors. Biomark Res. 2023;11(1):25.

Article  Google Scholar 

Junttila MR, de Sauvage FJ. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature. 2013;501(7467):346–54.

Article  CAS  Google Scholar 

Ren D, Hua Y, Yu B, Ye X, He Z, Li C, et al. Predictive biomarkers and mechanisms underlying resistance to PD1/PD-L1 blockade cancer immunotherapy. Mol Cancer. 2020;19(1):19.

Article  Google Scholar 

He M, Roussak K, Ma F, Borcherding N, Garin V, White M, et al. CD5 expression by dendritic cells directs T cell immunity and sustains immunotherapy responses. Science. 2023;379(6633):eabg2752.

Article  CAS  Google Scholar 

McDermott DF, Huseni MA, Atkins MB, Motzer RJ, Rini BI, Escudier B, et al. Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma. Nat Med. 2018;24(6):749–57.

Article  CAS  Google Scholar 

Ceci C, Atzori MG, Lacal PM, Graziani G. Targeting Tumor-Associated macrophages to increase the efficacy of Immune Checkpoint inhibitors: a glimpse into Novel Therapeutic approaches for metastatic melanoma. Cancers (Basel). 2020;12(11):3401.

Article  CAS  Google Scholar 

Xiong D, Wang Y, You M. A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response. Nat Commun. 2020;11(1):5084.

Article  CAS  Google Scholar 

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 2013;41(Database issue):D991–5.

CAS  Google Scholar 

Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, et al. Defining T Cell States Associated with response to Checkpoint Immunotherapy in Melanoma. Cell. 2019;176(1–2):404.

Article  CAS  Google Scholar 

Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, et al. A Cancer Cell Program promotes T cell exclusion and resistance to checkpoint blockade. Cell. 2018;175(4):984–e99724.

Article  CAS  Google Scholar 

Riaz N, Havel JJ, Makarov V, Desrichard A, Urba WJ, Sims JS, et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017;171(4):934–e94916.

Article  CAS  Google Scholar 

Gide TN, Quek C, Menzies AM, Tasker AT, Shang P, Holst J, et al. Distinct Immune cell populations define response to Anti-PD-1 monotherapy and Anti-PD-1/Anti-CTLA-4 combined Therapy. Cancer Cell. 2019;35(2):238–e2556.

Article  CAS  Google Scholar 

Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, et al. Genomic and transcriptomic features of response to Anti-PD-1 therapy in metastatic melanoma. Cell. 2016;165(1):35–44.

Article  CAS  Google Scholar 

Lee JH, Shklovskaya E, Lim SY, Carlino MS, Menzies AM, Stewart A, et al. Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition. Nat Commun. 2020;11(1):1897.

Article  CAS  Google Scholar 

Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T, et al. Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Nat Med. 2018;24(10):1545–9.

Article  CAS  Google Scholar 

Du K, Wei S, Wei Z, Frederick DT, Miao B, Moll T, et al. Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma. Nat Commun. 2021;12(1):6023.

Article  CAS  Google Scholar 

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411–20.

Article  CAS  Google Scholar 

Kang B, Camps J, Fan B, Jiang H, Ibrahim MM, Hu X, et al. Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment. Genome Biol. 2022;23(1):265.

Article  CAS  Google Scholar 

Zhang Y, Bai Y, Ma XX, Song JK, Luo Y, Fei XY, et al. Clinical-mediated discovery of pyroptosis in CD8 + T cell and NK cell reveals melanoma heterogeneity by single-cell and bulk sequence. Cell Death Dis. 2023;14(8):553.

Article  CAS  Google Scholar 

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019;566(7745):496–502.

Article  CAS  Google Scholar 

Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun. 2021;12(1):1088.

Article  CAS  Google Scholar 

Sun D, Guan X, Moran AE, Wu LY, Qian DZ, Schedin P, et al. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data. Nat Biotechnol. 2022;40(4):527–38.

Article  CAS  Google Scholar 

Chu T, Wang Z, Pe’er D, Danko CG. Cell type and gene expression deconvolution with BayesPrism enables bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nat Cancer. 2022;3(4):505–17.

Article  CAS  Google Scholar 

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.

Article  Google Scholar 

Wang H, Shao Y, Zhou S, Zhang C, Xiu N. Support Vector Machine Classifier via L0/1 soft-margin loss. IEEE Trans Pattern Anal Mach Intell. 2022;44(10):7253–65.

Article  Google Scholar 

Reinhold WC, Sunshine M, Liu H, Varma S, Kohn KW, Morris J, et al. CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 Cell Line Set. Cancer Res. 2012;72(14):3499–511.

Article  CAS  Google Scholar 

Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352(6282):189–96.

Article  CAS 

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