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2018 ; 8
(1
): 7967
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English Wikipedia
Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular
Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and
sno/mt-RNAs
#MMPMID29789629
Koduru SV
; Leberfinger AN
; Kawasawa YI
; Mahajan M
; Gusani NJ
; Sanyal AJ
; Ravnic DJ
Sci Rep
2018[May]; 8
(1
): 7967
PMID29789629
show ga
Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men
and eighth leading cause of death in women in the United States in 2017. In our
study, we sought to identify sncRNAs in various stages of development of HCC. We
obtained publicly available small RNA-seq data derived from patients with
cirrhosis (n?=?14), low-grade dysplastic nodules (LGDN, n?=?9), high grade
dysplastic nodules (HGDN, n?=?6), early hepatocellular carcinoma (eHCC, n?=?6),
and advanced hepatocellular carcinoma (HCC, n?=?20), along with healthy liver
tissue samples (n?=?9). All samples were analyzed for various types of non-coding
RNAs using PartekFlow software. We remapped small RNA-seq to miRBase to obtain
differential expressions of miRNAs and found 87 in cirrhosis, 106 in LGDN, 59 in
HGDN, 80 in eHCC, and 133 in HCC. Pathway analysis of miRNAs obtained from
diseased samples compared to normal samples showed signaling pathways in the
microRNA dependent EMT, CD44, and others. Additionally, we analyzed the data sets
for piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. We validated the in silico data
using human HCC samples with NanoString miRNA global expression. Our results
suggest that publically available data is a valuable resource for sncRNA
identification in HCC progression (FDR set to <0.05 for all samples) and that a
data mining approach is useful for biomarker development.