197
Views
2
CrossRef citations to date
0
Altmetric
Original Research

Identification of Immunological Biomarkers of Atopic Dermatitis by Integrated Analysis to Determine Molecular Targets for Diagnosis and Therapy

, , , , &
Pages 8193-8209 | Published online: 15 Nov 2021

References

  • Langan SM, Irvine AD, Weidinger S. Atopic dermatitis. Lancet. 2020;396(10247):345–360. doi:10.1016/S0140-6736(20)31286-1
  • Asher MI, Montefort S, Björkstén B, et al. Worldwide time trends in the prevalence of symptoms of asthma, allergic rhinoconjunctivitis, and eczema in childhood: ISAAC phases one and three repeat multicountry cross-sectional surveys. Lancet. 2006;368(9537):733–743. doi:10.1016/S0140-6736(06)69283-0
  • Nettis E, Ortoncelli M, Pellacani G, et al. A Multicenter Study on the prevalence of clinical patterns and clinical phenotypes in adult atopic dermatitis. J Investig Allergol Clin Immunol. 2020;30:448–450. doi:10.18176/jiaci.0519
  • Dattola A, Bennardo L, Silvestri M, Nisticò SP. What’s new in the treatment of atopic dermatitis? Dermatol Ther. 2019;32:e12787. doi:10.1111/dth.12787
  • Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–259.
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12:453–457.
  • Ge P, Wang W, Li L, et al. Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of colorectal cancer. Biomed Pharmacother. 2019;118:109228. doi:10.1016/j.biopha.2019.109228
  • Zhu G, Pei L, Yin H, et al. Profiles of tumor-infiltrating immune cells in renal cell carcinoma and their clinical implications. Oncol Lett. 2019;18:5235–5242.
  • Czarnowicki T, Krueger JG, Guttman-Yassky E. Novel concepts of prevention and treatment of atopic dermatitis through barrier and immune manipulations with implications for the atopic march. J Allergy Clin Immunol. 2017;139(6):1723–1734. doi:10.1016/j.jaci.2017.04.004
  • Klonowska J, Gleń J, Nowicki R, Trzeciak M. New cytokines in the pathogenesis of atopic dermatitis—new therapeutic targets. Int J Mol Sci. 2018;19(10):3086. doi:10.3390/ijms19103086
  • Khattri S, Brunner PM, Garcet S, et al. Efficacy and safety of ustekinumab treatment in adults with moderate-to-severe atopic dermatitis. Exp Dermatol. 2017;26(1):28–35. doi:10.1111/exd.13112
  • Brunner PM, Pavel AB, Khattri S, et al. Baseline IL-22 expression in patients with atopic dermatitis stratifies tissue responses to fezakinumab. J Allergy Clin Immunol. 2019;143(1):142–154. doi:10.1016/j.jaci.2018.07.028
  • Khattri S, Shemer A, Rozenblit M, et al. Cyclosporine in patients with atopic dermatitis modulates activated inflammatory pathways and reverses epidermal pathology. J Allergy Clin Immunol. 2014;133(6):1626–1634. doi:10.1016/j.jaci.2014.03.003
  • Esaki H, Ewald DA, Ungar B, et al. Identification of novel immune and barrier genes in atopic dermatitis by means of laser capture microdissection. J Allergy Clin Immunol. 2015;135(1):153–163. doi:10.1016/j.jaci.2014.10.037
  • Gittler JK, Shemer A, Suárez-Fariñas M, et al. Progressive activation of TH2/TH22 cytokines and selective epidermal proteins characterizes acute and chronic atopic dermatitis. J Allergy Clin Immunol. 2012;130(6):1344–1354. doi:10.1016/j.jaci.2012.07.012
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
  • Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–1202. doi:10.1016/j.molp.2020.06.009
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • Franceschini A, Szklarczyk D, Frankild S, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2012;41(D1):D808–D815. doi:10.1093/nar/gks1094
  • Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432. doi:10.1093/bioinformatics/btq675
  • Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11. doi:10.1186/1752-0509-8-S4-S11
  • Khan A, Fornes O, Stigliani A, et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018;46:D260–D266. doi:10.1093/nar/gkx1126
  • Chou CH, Shrestha S, Yang CD, et al. miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res. 2018;46:D296–D302. doi:10.1093/nar/gkx1067
  • Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92–D97. doi:10.1093/nar/gkt1248
  • Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48:D845–D855.
  • Bhattacharya S, Dunn P, Thomas CG, et al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data. 2018;5:180015. doi:10.1038/sdata.2018.15
  • Wishart DS, Feunang YD, Guo AC, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018;46(D1):D1074–D1082. doi:10.1093/nar/gkx1037
  • Xia J, Gill EE, Hancock RE. NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nat Protoc. 2015;10:823–844. doi:10.1038/nprot.2015.052
  • Chou KC, Shen HB. Cell-PLoc: a package of web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc. 2008;3:153–162. doi:10.1038/nprot.2007.494
  • Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33:1–22. doi:10.18637/jss.v033.i01
  • Fujita H, Shemer A, Suárez-Fariñas M, et al. Lesional dendritic cells in patients with chronic atopic dermatitis and psoriasis exhibit parallel ability to activate T-cell subsets. J Allergy Clin Immunol. 2011;128:574–582. doi:10.1016/j.jaci.2011.05.016
  • Esaki H, Brunner PM, Renert-Yuval Y, et al. Early-onset pediatric atopic dermatitis is T(H)2 but also T(H)17 polarized in skin. J Allergy Clin Immunol. 2016;138:1639–1651. doi:10.1016/j.jaci.2016.07.013
  • Liu F, Goodarzi H, Chen H, Misery L. IgE, mast cells, and eosinophils in atopic dermatitis. Clin Rev Allerg Immu. 2011;41:298–310. doi:10.1007/s12016-011-8252-4
  • Ragusa M, Barbagallo C, Brex D, et al. Molecular crosstalking among noncoding RNAs: a new network layer of genome regulation in cancer. Int J Genomics. 2017;2017:4723193. doi:10.1155/2017/4723193
  • Morelli P, Gaspari M, Gabriele C, et al. Proteomic analysis from skin swabs reveals a new set of proteins identifying skin impairment in atopic dermatitis. Exp Dermatol. 2021;30:811–819. doi:10.1111/exd.14276
  • Harper JI, Godwin H, Green A, et al. A study of matrix metalloproteinase expression and activity in atopic dermatitis using a novel skin wash sampling assay for functional biomarker analysis. Br J Dermatol. 2010;162:397–403. doi:10.1111/j.1365-2133.2009.09467.x
  • Kato Y, Pawankar R, Kimura Y, Kawana S. Increased expression of RANTES, CCR3 and CCR5 in the lesional skin of patients with atopic eczema. Int Arch Allergy Immunol. 2006;139(3):245–257. doi:10.1159/000091170
  • Ma L, Xue HB, Wang F, Shu CM, Zhang JH. MicroRNA-155 may be involved in the pathogenesis of atopic dermatitis by modulating the differentiation and function of T helper type 17 (Th17) cells. Clin Exp Immunol. 2015;181:142–149. doi:10.1111/cei.12624
  • He H, Suryawanshi H, Morozov P, et al. Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. J Allergy Clin Immunol. 2020;145:1615–1628. doi:10.1016/j.jaci.2020.01.042
  • Hsu YL, Chen YJ, Chang WA, et al. Interaction between tumor-associated dendritic cells and colon cancer cells contributes to tumor progression via CXCL1. Int J Mol Sci. 2018;19;2427.
  • Gianello V, Salvi V, Parola C, et al. The PDE4 inhibitor CHF6001 modulates pro-inflammatory cytokines, chemokines and Th1- and Th17-polarizing cytokines in human dendritic cells. Biochem Pharmacol. 2019;163:371–380. doi:10.1016/j.bcp.2019.03.006
  • Sallusto F, Cassotta A, Hoces D, Foglierini M, Lanzavecchia A. Do memory CD4 T cells keep their cell-type programming: plasticity versus fate commitment? T-cell heterogeneity, plasticity, and selection in humans. Cold Spring Harb Perspect Biol. 2018;10:a029421. doi:10.1101/cshperspect.a029421
  • Dooms H, Wolslegel K, Lin P, Abbas AK. Interleukin-2 enhances CD4+ T cell memory by promoting the generation of IL-7R alpha-expressing cells. J Exp Med. 2007;204:547–557. doi:10.1084/jem.20062381
  • Woodward DA, Roozen HN, Dufort MJ, et al. The human tissue-resident CCR5(+) T cell compartment maintains protective and functional properties during inflammation. Sci Transl Med. 2019;11:eaaw8718.
  • Colantonio L, Recalde H, Sinigaglia F, D’Ambrosio D. Modulation of chemokine receptor expression and chemotactic responsiveness during differentiation of human naive T cells into Th1 or Th2 cells. Eur J Immunol. 2002;32:1264–1273.
  • Furue M, Furue K, Tsuji G, Nakahara T. Interleukin-17A and keratinocytes in psoriasis. Int J Mol Sci. 2020;21:1275.
  • Schreiner D, King CG. CD4+ memory T cells at home in the tissue: mechanisms for health and disease. Front Immunol. 2018;9. doi:10.3389/fimmu.2018.02394
  • Bin L, Deng L, Yang H, et al. Forkhead box C1 regulates human primary keratinocyte terminal differentiation. PLoS One. 2016;11:e167392. doi:10.1371/journal.pone.0167392