الفهرس 
Introduction and Aim of the workOnly 14 pages are availabe for public view
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Abstract
Hepatocellular carcinoma is one of the most prevalent gastrointestinal tumors. It is considered the second cause of cancer-related death worldwide, despite the significant advancement in HCC diagnosis and treatment. The precise biology of the tumor is still not fully understood, which has a negative impact on patient’s outcome.
The most often utilized serum marker for detecting and first diagnosing HCC in clinical practice is alpha-fetoprotein (AFP). Nevertheless, AFP has a low specificity and only around 60% sensitivity at a cutoff value of 20 ng/mL. Moreover, high negative and false-positive rates are caused by the fact that AFP levels stay normal in 15–30% of patients with advanced-stage disease and even rise in some patients with chronic hepatitis, liver cirrhosis, and other liver diseases. Therefore, the need for identifying specific biomarkers is urgent.
This study was conducted to identify miRNA profiling in HCC child A Egyptian patient’s tissues, and recommend miRNAs as new promising diagnostic and prognostic markers in this class of patients.
I- Sequencing data and differential expression miRNA analysis
Total RNA was extracted from 21 HCC patients’ tissues who underwent surgery at the National Liver Institute, Menoufia University. A total of 279 miRNAs were discovered as expressed miRNAs. All miRNA expression data were imported into DEseq2 software to identify the differentially expressed miRNAs (DEMs). Thirty-two miRNAs were retrieved as DEMs with 24 being upregulated and 8 down-regulated. A comparison for HCC tissues and HCC adjacent tissues found that has-miR-4488, has-miR-3178, and has-miR-3182 were represented only in the HCC tissues.
II- Prediction of miRNA target genes and enrichment analysis
MiRTarBase was used for functional annotation with selection of validated not predicted targets and this illustrated that the down regulated DEMs targeting 199 genes selected based on the number of interactions, FDR<0.05 and P values < 0.05 represented in 44 pathways. MYC and CALU were found as hub genes and FOXO signaling pathway, cell cycle, and transcriptional dysregulation in cancer as the most relevant pathways. But for the up regulated DEMs, 866 genes were found based on the same previous conditions revealing CDKN1B and BCL2 as the highest down regulated genes and ubiquitin-mediated proteolysis, FOXO signaling pathways, p53 pathway as the most relevant pathways.
III- miRNA regulatory networks and their target genes
IV- miRNA-target genes network
miRNA network comprising 17 DEMs and their targets to focus on has-miR-130a-5p, has-let-7c-5p, has-miR-34a-5p and has-miR-96-5P as hub miRNAs. has-miR-130a-5p was shown as centric miRNA with the largest number of target genes.
V- Protein- protein interaction network (PPI)
To investigate the relationships and interactions between the HCC-related proteins, the PPI network was built. Out of 1069 proteins, 1061 had strong interactions with one another to form a cluster.
VI- ROC curve analysis for DEMs
Normalized counts of unique miRNAs (has-miR-4488, has-miR3178, has-miR-3182, and has-miR-214-3p) were used to investigate diagnostic and prognostic potentials and false Positive values by ROC curve analysis illustrated that the mentioned miRNAs have diagnostic and prognostic values with low false positive values (0 - 33%).
To conclude, miRNA profiling for Egyptian hepatocellular carcinoma (HCC) patients Child A was used to construct a comprehensive miRNA-target genes network and protein-protein interaction network with the illustration of involved significant pathways. 41 differentially expressed miRNAs were identified. Further specificity and sensitivity tests revealed that four miRNAs; hsa-miR-4488, hsa-miR-3178, hsa-miR-3182, and hsa-miR-214 were significantly associated with diagnosis and prognosis of HCC. Therefore, these differentially expressed miRNAs are expected to be potential biomarkers or therapeutic targets for HCC. Further studies are needed for the validation of the identified miRNAs roles in the pathophysiology and diagnosis of HCC on a large cohort group including higher sample size and different HCC stages.