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RNA sequencing uncovers the key microRNAs potentially contributing to sudden sensorineural hearing loss.

Abstract This study aimed to identify miRNAs that may contribute to the pathogenesis of sudden sensorineural hearing loss (SSNHL) by RNA-seq (RNA-sequencing).RNA was extracted from SSNHL patients and healthy volunteers, respectively. Sequencing was performed on HiSeq4000 platform. After filtering, clean reads were mapped to the human reference genome hg19. Differential expression analysis of miRNAs between the SSNHL samples and the normal samples was performed using DEseq to identify differentially expressed microRNAs (DEMs). The target genes of the DEMs were predicted using the online tool miRWalk, which were then mapped to DAVID (https://david.ncifcrf.gov/) for functional annotation based on GO database and for pathway enrichment analysis based on KEGG. Finally, a miRNA-target-protein-protein interaction (PPIs) network was constructed using the DEMs and their target genes with interaction.Differential expression analysis reveals 24 DEMs between the SSNHL group and control group. A total of 1083 target genes were predicted. GO functional annotation analysis reveals that the target genes in the top 10 terms are mainly related to the development of salivary glands, neurotransmission, dendritic development, and other processes. KEGG pathway enrichment analysis reveals that the target genes were functionally enriched in pathways arachidonic acid metabolism, complement and coagulation cascades, linoleic acid metabolism, and MAPK signaling pathway. In the miRNA-target-PPI network, hsa-miR-34a/548n/15a/143/23a/210/1255a/18b/ /1180/99b had the most target genes; genes YWHAG, GSK3B, CDC42, NR3C1, LCK, UNC119, SIN3A, and NFKB2, interact with most other genes among all the predicted target genes.Hsa-miR-34a/15a/23a/210/18b/548n/143 is likely to have a role in the pathogenesis of SSNHL.
PMID
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Authors

Mayor MeshTerms
Keywords
Journal Title medicine
Publication Year Start




PMID- 29381991
OWN - NLM
STAT- In-Process
LR  - 20180202
IS  - 1536-5964 (Electronic)
IS  - 0025-7974 (Linking)
VI  - 96
IP  - 47
DP  - 2017 Nov
TI  - RNA sequencing uncovers the key microRNAs potentially contributing to sudden
      sensorineural hearing loss.
PG  - e8837
LID - 10.1097/MD.0000000000008837 [doi]
AB  - This study aimed to identify miRNAs that may contribute to the pathogenesis of
      sudden sensorineural hearing loss (SSNHL) by RNA-seq (RNA-sequencing).RNA was
      extracted from SSNHL patients and healthy volunteers, respectively. Sequencing
      was performed on HiSeq4000 platform. After filtering, clean reads were mapped to 
      the human reference genome hg19. Differential expression analysis of miRNAs
      between the SSNHL samples and the normal samples was performed using DEseq to
      identify differentially expressed microRNAs (DEMs). The target genes of the DEMs 
      were predicted using the online tool miRWalk, which were then mapped to DAVID
      (https://david.ncifcrf.gov/) for functional annotation based on GO database and
      for pathway enrichment analysis based on KEGG. Finally, a
      miRNA-target-protein-protein interaction (PPIs) network was constructed using the
      DEMs and their target genes with interaction.Differential expression analysis
      reveals 24 DEMs between the SSNHL group and control group. A total of 1083 target
      genes were predicted. GO functional annotation analysis reveals that the target
      genes in the top 10 terms are mainly related to the development of salivary
      glands, neurotransmission, dendritic development, and other processes. KEGG
      pathway enrichment analysis reveals that the target genes were functionally
      enriched in pathways arachidonic acid metabolism, complement and coagulation
      cascades, linoleic acid metabolism, and MAPK signaling pathway. In the
      miRNA-target-PPI network, hsa-miR-34a/548n/15a/143/23a/210/1255a/18b/ /1180/99b
      had the most target genes; genes YWHAG, GSK3B, CDC42, NR3C1, LCK, UNC119, SIN3A, 
      and NFKB2, interact with most other genes among all the predicted target
      genes.Hsa-miR-34a/15a/23a/210/18b/548n/143 is likely to have a role in the
      pathogenesis of SSNHL.
CI  - Copyright (c) 2017 The Authors. Published by Wolters Kluwer Health, Inc. All
      rights reserved.
FAU - Li, Qi
AU  - Li Q
FAU - Peng, Xiaohong
AU  - Peng X
FAU - Huang, Haoran
AU  - Huang H
FAU - Li, Jingjing
AU  - Li J
FAU - Wang, Fan
AU  - Wang F
FAU - Wang, Jie
AU  - Wang J
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Medicine (Baltimore)
JT  - Medicine
JID - 2985248R
PMC - PMC5708990
EDAT- 2018/02/01 06:00
MHDA- 2018/02/01 06:00
CRDT- 2018/02/01 06:00
PHST- 2018/02/01 06:00 [entrez]
PHST- 2018/02/01 06:00 [pubmed]
PHST- 2018/02/01 06:00 [medline]
AID - 10.1097/MD.0000000000008837 [doi]
AID - 00005792-201711270-00082 [pii]
PST - ppublish
SO  - Medicine (Baltimore). 2017 Nov;96(47):e8837. doi: 10.1097/MD.0000000000008837.