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Functional & Integrative Genomics

, Volume 19, Issue 1, pp 109–121 | Cite as

Comprehensive analysis of the whole coding and non-coding RNA transcriptome expression profiles and construction of the circRNA–lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma

  • Rui Zhao
  • Feng-Qing Li
  • Lin-Li Tian
  • De-Si Shang
  • Yan Guo
  • Jia-Rui Zhang
  • Ming LiuEmail author
Original Article

Abstract

Recently, accumulating evidence has demonstrated that non-coding RNAs (ncRNAs) play a vital role in oncogenicity. Nevertheless, the regulatory mechanisms and functions remain poorly understood, especially for lncRNAs and circRNAs. In this study, we simultaneously detected, for the first time, the expression profiles of the whole transcriptome, including miRNA, circRNA and lncRNA + mRNA, in five pairs of laryngeal squamous cell carcinoma (LSCC) and matched non-carcinoma tissues by microarrays. Five miRNAs, four circRNAs, three lncRNAs and five mRNAs that were dysregulated were selected to confirm the verification of the microarray data by quantitative real-time PCR (qRT-PCR) in 20 pairs of LSCC samples. We constructed LSCC-related competing endogenous RNA (ceRNA) networks of lncRNAs and circRNAs (circRNA or lncRNA–miRNA–mRNA) respectively. Functional annotation revealed the lncRNA-mediated ceRNA network were enriched for genes involved in the tumor-associated pathways. Hsa_circ_0033988 with the highest degree in the circRNA-mediated ceRNA network was associated with fatty acid degradation, which was responsible for the depletion of fat in tumor-associated cachexia. Finally, to clarify the ncRNA co-regulation mechanism, we constructed a circRNA–lncRNA co-regulated network by integrating the above two networks and identified 9 modules for further study. A subnetwork of module 2 with the most dysregulated microRNAs was extracted to establish the ncRNA-involved TGF-β-associated pathway. In conclusion, our findings provide a high-throughput microarray data of the coding and non-coding RNAs and establish the foundation for further functional research on the ceRNA regulatory mechanism of non-coding RNAs in LSCC.

Keywords

circRNA lncRNA Co-regulation ceRNA network Microarray Laryngeal squamous cell carcinoma 

Notes

Funding

This study was supported by the National Natural Science Foundation of China (No. 81572647).

Compliance with ethical standards

This study was approved by the Human Research Ethics Committee from Harbin Medical University. Informed consent was obtained from all individual participants included in the study.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human tissues were in accordance with the ethical standards of the institutional committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Supplementary material

10142_2018_631_MOESM1_ESM.xlsx (30.9 mb)
Online Resource 1: The microarray original data of miRNA, circRNA and lncRNA+mRNA in five pairs of LSCC and matched non-carcinoma tissues (XLSX 31608 kb)
10142_2018_631_MOESM2_ESM.pdf (82 kb)
Online Resource 2: Primers used for qRT-PCR. (PDF 82 kb)
10142_2018_631_MOESM3_ESM.pdf (489 kb)
Online Resource 3: The top 30 significant terms by GO and KEGG pathway analysis for differential expressed mRNAs in the LSCC microarray. (PDF 489 kb)
10142_2018_631_MOESM4_ESM.pdf (828 kb)
Online Resource 4: Volcano plots for the expression profiles of miRNAs(A), lncRNAs(B), mRNAs(C) and circRNAs(D-F). (PDF 827 kb)
10142_2018_631_MOESM5_ESM.pdf (968 kb)
Online Resource 5: The expression correlation between microarray and PCR. (PDF 967 kb)
10142_2018_631_MOESM6_ESM.pdf (159 kb)
Online Resource 6: The top 10 ranked lncRNAs according to degree in the lncRNA-miRNA-mRNA ceRNA network. (PDF 158 kb)
10142_2018_631_MOESM7_ESM.pdf (256 kb)
Online Resource 7: The sub-ceRNA-network of LINC00657. (PDF 256 kb)
10142_2018_631_MOESM8_ESM.pdf (183 kb)
Online Resource 8: KEGG pathway analysis of the differentially expressed mRNAs in the LINC00657 subnetwork (PDF 182 kb)
10142_2018_631_MOESM9_ESM.pdf (406 kb)
Online Resource 9: GO and KEGG pathway enrichment analysis of the differentially expressed mRNAs in the circRNA-miRNA-mRNA ceRNA network. (PDF 406 kb)
10142_2018_631_MOESM10_ESM.pdf (86 kb)
Online Resource 10: The top 10 circRNAs sorted by degree in the circRNA-miRNA-mRNA ceRNA network (PDF 85 kb)
10142_2018_631_MOESM11_ESM.pdf (191 kb)
Online Resource 11: KEGG pathway enrichment analysis of the differentially expressed mRNAs in the circRNA-lncRNA co-regulated ceRNA network. (PDF 191 kb)
10142_2018_631_MOESM12_ESM.pdf (432 kb)
Online Resource 12: The detailed information of nine modules in the circRNA-lncRNA co-regulated ceRNA network. (PDF 432 kb)
10142_2018_631_MOESM13_ESM.pdf (909 kb)
Online Resource 13: KEGG pathway enrichment analysis of the differentially expressed mRNAs in module 2. (PDF 909 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Otolaryngology-Head and Neck SurgeryThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
  2. 2.Department of GerontologyThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
  3. 3.College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina

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