PMID- 30128795
OWN - NLM
STAT- MEDLINE
DCOM- 20190415
LR  - 20200225
IS  - 1438-7948 (Electronic)
IS  - 1438-793X (Linking)
VI  - 19
IP  - 1
DP  - 2019 Jan
TI  - 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.
PG  - 109-121
LID - 10.1007/s10142-018-0631-y [doi]
AB  - 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-beta-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.
FAU - Zhao, Rui
AU  - Zhao R
AD  - Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated 
      Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
FAU - Li, Feng-Qing
AU  - Li FQ
AD  - Department of Gerontology, The Second Affiliated Hospital of Harbin Medical 
      University, Harbin, China.
FAU - Tian, Lin-Li
AU  - Tian LL
AD  - Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated 
      Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
FAU - Shang, De-Si
AU  - Shang DS
AD  - College of Bioinformatics Science and Technology, Harbin Medical University, 
      Harbin, China.
FAU - Guo, Yan
AU  - Guo Y
AD  - Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated 
      Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
FAU - Zhang, Jia-Rui
AU  - Zhang JR
AD  - Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated 
      Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
FAU - Liu, Ming
AU  - Liu M
AUID- ORCID: 0000-0002-5957-0142
AD  - Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated 
      Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China. 
      liumingent@163.com.
LA  - eng
PT  - Journal Article
DEP - 20180821
PL  - Germany
TA  - Funct Integr Genomics
JT  - Functional & integrative genomics
JID - 100939343
RN  - 0 (MicroRNAs)
RN  - 0 (RNA, Circular)
RN  - 0 (RNA, Long Noncoding)
RN  - 0 (RNA, Messenger)
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - Carcinoma, Squamous Cell/*genetics/metabolism/pathology
MH  - Computational Biology
MH  - Gene Expression Profiling
MH  - *Gene Expression Regulation, Neoplastic
MH  - Gene Ontology
MH  - Gene Regulatory Networks
MH  - Humans
MH  - Laryngeal Neoplasms/*genetics/metabolism/pathology
MH  - MicroRNAs/classification/*genetics/metabolism
MH  - Microarray Analysis
MH  - Molecular Sequence Annotation
MH  - RNA/classification/genetics/metabolism
MH  - RNA, Circular
MH  - RNA, Long Noncoding/classification/*genetics/metabolism
MH  - RNA, Messenger/classification/*genetics/metabolism
MH  - *Transcriptome
OTO - NOTNLM
OT  - Co-regulation
OT  - Laryngeal squamous cell carcinoma
OT  - Microarray
OT  - ceRNA network
OT  - circRNA
OT  - lncRNA
EDAT- 2018/08/22 06:00
MHDA- 2019/04/16 06:00
CRDT- 2018/08/22 06:00
PHST- 2018/02/18 00:00 [received]
PHST- 2018/08/03 00:00 [accepted]
PHST- 2018/07/21 00:00 [revised]
PHST- 2018/08/22 06:00 [pubmed]
PHST- 2019/04/16 06:00 [medline]
PHST- 2018/08/22 06:00 [entrez]
AID - 10.1007/s10142-018-0631-y [pii]
AID - 10.1007/s10142-018-0631-y [doi]
PST - ppublish
SO  - Funct Integr Genomics. 2019 Jan;19(1):109-121. doi: 10.1007/s10142-018-0631-y. 
      Epub 2018 Aug 21.