Genome‑wide profiling of lncRNA and mRNA expression in CRSwNP

  • Authors:
    • Minglei Liu
    • Ping Guo
    • Jun An
    • Chao Guo
    • Fengxiang Lu
    • Yanhua Lei
  • View Affiliations

  • Published online on: March 5, 2019     https://doi.org/10.3892/mmr.2019.10005
  • Pages: 3855-3863
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )


Abstract

Chronic rhinosinusitis with nasal polyps (CRSwNP) is one of the most prevalent chronic diseases. In patients with CRSwNP, the present study performed comprehensive bioinformatics analyses to characterize the transcriptome profiles of mRNAs and long non‑coding RNAs (lncRNAs). A total of 265 differentially expressed lncRNAs and 994 mRNAs were identified. The majority of up‑ and downregulated differentially expressed genes were significantly enriched in the biological process of ‘signal transduction’. The most significantly enriched molecular function was ‘protein binding’ and the most significantly enriched cellular component was ‘membrane’. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis led to identification of several significantly enriched pathways [false discovery rate (FDR)<0.05], including ‘cytokine‑cytokine receptor interaction’ (FDR=3.94x1016) and ‘cell adhesion molecules’ (CAMs) (FDR=1.28x10‑5). Key differentially expressed lncRNAs were identified, including lncRNA XLOC_010280, which regulates chemokine (C‑C motif) ligand 18 (CCL18) and inflammation, and RP11‑798M19.6, which regulates polypeptide N‑acetylgalactosaminyltransferase 7 (GALNT7) and cell proliferation. Based on the results of reverse transcription‑quantitative polymerase chain reaction, except for CCL8, neural precursor cell expressed developmentally downregulated gene 4‑like and GALNT7, the expression of 3 other selected genes was consistent with the results of integrated analysis. The results of the present study provide a foundation for future investigations into mRNAs and lncRNAs as diagnostic and therapeutic targets in CRSwNP.

References

1 

Beule A: Epidemiology of chronic rhinosinusitis, selected risk factors, comorbidities, and economic burden. GMS Curr Top Otorhinolaryngol Head Neck Surg. 14:Doc112015.PubMed/NCBI

2 

Ma Z, Shen Y, Zeng Q, Liu J, Yang L, Fu R and Hu G: miR-150-5p regulates EGR2 to promote the development of chronic rhinosinusitis via the DC-Th axis. Int Immunopharmacol. 54:188–197. 2017. View Article : Google Scholar : PubMed/NCBI

3 

Bohman A, Juodakis J, Oscarsson M, Bacelis J, Bende M and Torinsson Naluai Å: A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis. PLoS One. 12:e01852442017. View Article : Google Scholar : PubMed/NCBI

4 

Chaaban MR, Walsh EM and Woodworth BA: Epidemiology and differential diagnosis of nasal polyps. Am J Rhinol Allergy. 27:473–478. 2013. View Article : Google Scholar : PubMed/NCBI

5 

Lin H, Li Z, Lin D, Zheng C and Zhang W: Role of NLRP3 inflammasome in eosinophilic and non-eosinophilic chronic rhinosinusitis with nasal polyps. Inflammation. 39:2045–2052. 2016. View Article : Google Scholar : PubMed/NCBI

6 

Kim JY, Kim DK, Yu MS, Cha MJ, Yu SL and Kang J: Role of epigenetics in the pathogenesis of chronic rhinosinusitis with nasal polyps. Mol Med Rep. 17:1219–1227. 2018.PubMed/NCBI

7 

Cava C, Bertoli G and Castiglioni I: Integrating genetics and epigenetics in breast cancer: Biological insights, experimental, computational methods and therapeutic potential. BMC Syst Biol. 9:622015. View Article : Google Scholar : PubMed/NCBI

8 

Saris CG, Horvath S, van Vught PW, van Es MA, Blauw HM, Fuller TF, Langfelder P, DeYoung J, Wokke JH, Veldink JH, et al: Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics. 10:4052009. View Article : Google Scholar : PubMed/NCBI

9 

Li WB, Zhou J, Xu L, Su XL, Liu Q and Pang H: Identification of genes associated with papillary thyroid carcinoma (PTC) for diagnosis by integrated analysis. Horm Metab Res. 48:226–231. 2016. View Article : Google Scholar : PubMed/NCBI

10 

Huang QX, Cui JY, Ma H, Jia XM, Huang FL and Jiang LX: Screening of potential biomarkers for cholangiocarcinoma by integrated analysis of microarray data sets. Cancer Gene Ther. 23:48–53. 2016. View Article : Google Scholar : PubMed/NCBI

11 

Zhang L, Zhang J, Yang G, Wu D, Jiang L, Wen Z and Li M: Investigating the concordance of gene ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis. BMC Bioinformatics. 14:1432013. View Article : Google Scholar : PubMed/NCBI

12 

Yang L, Feng S and Yang Y: Identification of transcription factors (TFs) and targets involved in the cholangiocarcinoma (CCA) by integrated analysis. Cancer Gene Ther. 23:439–445. 2016. View Article : Google Scholar : PubMed/NCBI

13 

Zhang H, Zhang C, Feng R, Zhang H, Gao M and Ye L: Investigating the microRNA-mRNA regulatory network in acute myeloid leukemia. Oncol Lett. 14:3981–3988. 2017. View Article : Google Scholar : PubMed/NCBI

14 

Wang F, Wang R, Li Q, Qu X, Hao Y, Yang J, Zhao H, Wang Q, Li G, Zhang F, et al: A transcriptome profile in hepatocellular carcinomas based on integrated analysis of microarray studies. Diagn Pathol. 12:42017. View Article : Google Scholar : PubMed/NCBI

15 

Wang J, Qu D, An J, Yuan G and Liu Y: Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma. Mol Med Rep. 16:8735–8746. 2017. View Article : Google Scholar : PubMed/NCBI

16 

Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 25:402–408. 2001. View Article : Google Scholar : PubMed/NCBI

17 

Wu T, Wu HD, Xu ZX, Han F, Zhang BQ, Sun J and Hu SJ: Abnormal expression of long non-coding RNAs in myocardial infarction. Heart Vessels. 32:1253–1261. 2017. View Article : Google Scholar : PubMed/NCBI

18 

Zhao B, Wang M, Xu J, Li M and Yu Y: Identification of pathogenic genes and upstream regulators in age-related macular degeneration. BMC Ophthalmol. 17:1022017. View Article : Google Scholar : PubMed/NCBI

19 

Okada N, Nakayama T, Asaka D, Inoue N, Tsurumoto T, Takaishi S, Otori N, Kojima H, Matsuda A, Oboki K, et al: Distinct gene expression profiles and regulation networks of nasal polyps in eosinophilic and non-eosinophilic chronic rhinosinusitis. Int Forum Allergy Rhinol. 8:592–604. 2018. View Article : Google Scholar : PubMed/NCBI

20 

Charo IF and Ransohoff RM: The many roles of chemokines and chemokine receptors in inflammation. N Engl J Med. 354:610–621. 2006. View Article : Google Scholar : PubMed/NCBI

21 

Viola A and Luster AD: Chemokines and their receptors: Drug targets in immunity and inflammation. Annu Rev Pharmacol Toxicol. 48:171–197. 2008. View Article : Google Scholar : PubMed/NCBI

22 

Peterson S, Poposki JA, Nagarkar DR, Chustz RT, Peters AT, Suh LA, Carter R, Norton J, Harris KE, Grammer LC, et al: Increased expression of CC chemokine ligand 18 in patients with chronic rhinosinusitis with nasal polyps. J Allergy Clin Immunol. 129:119–127.e1-9. 2012. View Article : Google Scholar : PubMed/NCBI

23 

Hieshima K, Imai T, Baba M, Shoudai K, Ishizuka K, Nakagawa T, Tsuruta J, Takeya M, Sakaki Y, Takatsuki K, et al: A novel human CC chemokine PARC that is most homologous to macrophage-inflammatory protein-1 alpha/LD78 alpha and chemotactic for T lymphocytes, but not for monocytes. J Immunol. 159:1140–1149. 1997.PubMed/NCBI

24 

Wang W, Gao Z, Wang H, Li T, He W, Lv W and Zhang J: Transcriptome analysis reveals distinct gene expression profiles in eosinophilic and noneosinophilic chronic rhinosinusitis with nasal polyps. Sci Rep. 6:266042016. View Article : Google Scholar : PubMed/NCBI

25 

Nie GH, Luo L, Duan HF, Li XQ, Yin MJ, Li Z and Zhang W: GALNT7, a target of miR-494, participates in the oncogenesis of nasopharyngeal carcinoma. Tumour Biol. 37:4559–4567. 2016. View Article : Google Scholar : PubMed/NCBI

Related Articles

Journal Cover

May 2019
Volume 19 Issue 5

Print ISSN: 1791-2997
Online ISSN:1791-3004

Sign up for eToc alerts

Recommend to Library

Copy and paste a formatted citation
APA
Liu, M., Guo, P., An, J., Guo, C., Lu, F., & Lei, Y. (2019). Genome‑wide profiling of lncRNA and mRNA expression in CRSwNP. Molecular Medicine Reports, 19, 3855-3863. https://doi.org/10.3892/mmr.2019.10005
MLA
Liu, M., Guo, P., An, J., Guo, C., Lu, F., Lei, Y."Genome‑wide profiling of lncRNA and mRNA expression in CRSwNP". Molecular Medicine Reports 19.5 (2019): 3855-3863.
Chicago
Liu, M., Guo, P., An, J., Guo, C., Lu, F., Lei, Y."Genome‑wide profiling of lncRNA and mRNA expression in CRSwNP". Molecular Medicine Reports 19, no. 5 (2019): 3855-3863. https://doi.org/10.3892/mmr.2019.10005