Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2021 Nov 15

PMID 34777377

Citations 8

Authors

Jingni Wu

Zhixiao Fang

Teng Liu

Wei Hu

Yangjun Wu

Shengli Li

Affiliations

Soon will be listed here.

Abstract

Inflammatory skin diseases are induced by disorders of the host defense system of the skin, which is composed of a barrier, innate and acquired immunity, as well as the cutaneous microbiome. These disorders are characterized by recurrent cutaneous lesions and intense itch, which seriously affecting life quality of people across all ages and ethnicities. To elucidate molecular factors for typical inflammatory skin diseases (such as psoriasis and atopic dermatitis), transcriptomic profiling assays have been largely performed. Additionally, single-cell RNA sequencing (scRNA-seq) as well as spatial transcriptomic profiling have revealed multiple potential translational targets and offered guides to improve diagnosis and treatment strategies for inflammatory skin diseases. High-throughput transcriptomics data has shown unprecedented power to disclose the complex pathophysiology of inflammatory skin diseases. Here, we will summarize discoveries from transcriptomics data and discuss how to maximize the transcriptomics data to propel the development of diagnostic biomarkers and therapeutic targets in inflammatory skin diseases.

Citing Articles

Pharmacological Effects of Antioxidant Mycosporine-Glycine in Alleviating Ultraviolet B-Induced Skin Photodamage: Insights from Metabolomic and Transcriptomic Analyses.

Wang K, Qin L, Lin H, Yao M, Cao J, Zhang Q Antioxidants (Basel). 2025; 14(1).

PMID: 39857364 PMC: 11763201. DOI: 10.3390/antiox14010030.

Overexpression of RBM15 modulated the effect of trophoblast cells by promoting the binding ability between YTHDF2 and the CD82 3'UTR to decrease the expression of CD82.

You G, Li Z, Li L, Xu C Heliyon. 2024; 10(9):e30702.

PMID: 38765115 PMC: 11098837. DOI: 10.1016/j.heliyon.2024.e30702.

Identification of Genes Associated with Decreasing Abundance of Monocytes in Long-Term Peritoneal Dialysis Patients.

Zhang Y, Jin Y, Wang H, He L, Zhang Y, Liu Q Int J Gen Med. 2023; 16:5017-5030.

PMID: 37942472 PMC: 10629397. DOI: 10.2147/IJGM.S435041.

Identification of diagnostic molecules and potential therapeutic agents for atopic dermatitis by single-cell RNA sequencing combined with a systematic computing framework that integrates network pharmacology.

Zhang X, Ding C, Zhao Z Funct Integr Genomics. 2023; 23(2):95.

PMID: 36944896 DOI: 10.1007/s10142-023-01005-3.

Potential targets and mechanisms of photobiomodulation for spinal cord injury.

Ju C, Ma Y, Zuo X, Wang X, Song Z, Zhang Z Neural Regen Res. 2023; 18(8):1782-1788.

PMID: 36751806 PMC: 10154481. DOI: 10.4103/1673-5374.361534.

References

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Zaba L, Suarez-Farinas M, Fuentes-Duculan J, Nograles K, Guttman-Yassky E, Cardinale I . Effective treatment of psoriasis with etanercept is linked to suppression of IL-17 signaling, not immediate response TNF genes. J Allergy Clin Immunol. 2009; 124(5):1022-10.e1-395. PMC: 2852188. DOI: 10.1016/j.jaci.2009.08.046. View

Street K, Risso D, Fletcher R, Das D, Ngai J, Yosef N . Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics. 2018; 19(1):477. PMC: 6007078. DOI: 10.1186/s12864-018-4772-0. View

Crone S, Jacobsen A, Federspiel B, Bardram L, Krogh A, Lund A . microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer. Mol Cancer. 2012; 11:71. PMC: 3515505. DOI: 10.1186/1476-4598-11-71. View

Komiya E, Tominaga M, Kamata Y, Suga Y, Takamori K . Molecular and Cellular Mechanisms of Itch in Psoriasis. Int J Mol Sci. 2020; 21(21). PMC: 7664892. DOI: 10.3390/ijms21218406. View

Xu X, Wang Y, Liang H . The role of A-to-I RNA editing in cancer development. Curr Opin Genet Dev. 2017; 48:51-56. PMC: 5869101. DOI: 10.1016/j.gde.2017.10.009. View

Reynolds G, Vegh P, Fletcher J, Poyner E, Stephenson E, Goh I . Developmental cell programs are co-opted in inflammatory skin disease. Science. 2021; 371(6527). PMC: 7611557. DOI: 10.1126/science.aba6500. View

Kirby B . Langerhans cells in psoriasis: getting to the core of the disease. Br J Dermatol. 2018; 178(6):1240. DOI: 10.1111/bjd.16596. View

Goleva E, Berdyshev E, Leung D . Epithelial barrier repair and prevention of allergy. J Clin Invest. 2019; 129(4):1463-1474. PMC: 6436854. DOI: 10.1172/JCI124608. View

10.

Aran D, Looney A, Liu L, Wu E, Fong V, Hsu A . Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019; 20(2):163-172. PMC: 6340744. DOI: 10.1038/s41590-018-0276-y. View

11.

Wang L, Wang S, Li W . RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012; 28(16):2184-5. DOI: 10.1093/bioinformatics/bts356. View

12.

Cevikbas F, Wang X, Akiyama T, Kempkes C, Savinko T, Antal A . A sensory neuron-expressed IL-31 receptor mediates T helper cell-dependent itch: Involvement of TRPV1 and TRPA1. J Allergy Clin Immunol. 2013; 133(2):448-60. PMC: 3960328. DOI: 10.1016/j.jaci.2013.10.048. View

13.

Feldman S, Thaci D, Gooderham M, Augustin M, de la Cruz C, Mallbris L . Tofacitinib improves pruritus and health-related quality of life up to 52 weeks: Results from 2 randomized phase III trials in patients with moderate to severe plaque psoriasis. J Am Acad Dermatol. 2016; 75(6):1162-1170.e3. DOI: 10.1016/j.jaad.2016.07.040. View

14.

Pan Q, Shai O, Lee L, Frey B, Blencowe B . Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12):1413-5. DOI: 10.1038/ng.259. View

15.

Zhao L, Wang J, Li Y, Song T, Wu Y, Fang S . NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res. 2020; 49(D1):D165-D171. PMC: 7779048. DOI: 10.1093/nar/gkaa1046. View

16.

Xiao Y, Wang H, Wang C, Zeng B, Tang X, Zhang Y . miR-203 promotes HaCaT cell overproliferation through targeting LXR-α and PPAR-γ. Cell Cycle. 2020; 19(15):1928-1940. PMC: 7469443. DOI: 10.1080/15384101.2020.1783934. View

17.

Bushmakin A, Mamolo C, Cappelleri J, Stewart M . The relationship between pruritus and the clinical signs of psoriasis in patients receiving tofacitinib. J Dermatolog Treat. 2013; 26(1):19-22. DOI: 10.3109/09546634.2013.861891. View

18.

Nattkemper L, Tey H, Valdes-Rodriguez R, Lee H, Mollanazar N, Albornoz C . The Genetics of Chronic Itch: Gene Expression in the Skin of Patients with Atopic Dermatitis and Psoriasis with Severe Itch. J Invest Dermatol. 2018; 138(6):1311-1317. DOI: 10.1016/j.jid.2017.12.029. View

19.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C . JACUSA: site-specific identification of RNA editing events from replicate sequencing data. BMC Bioinformatics. 2017; 18(1):7. PMC: 5210316. DOI: 10.1186/s12859-016-1432-8. View

20.

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View