Review for 10.1186/s12876-020-01596-2 (2021)

Reviewer’s report
Title: 
Alterations in MicroRNA Gene Expression Profile in Liver Transplant
Patients with Hepatocellular Carcinoma
Version: 
1 
Date: 
31 Oct 2020
Reviewer's report:
Dear Editor,
BMC Gastroenterology.
The manuscript "Alterations in microRNA gene expression profile in liver
transplant patients with hepatocellular Carcinoma" by Afshari A, et al is a nice
effort to grasp the molecular basis of transplant rejection in HCC patients. Novel
and easily accessible biomarkers of acute rejection could facilitate early
detection and effective clinical management in LT rejected patients. Authors
report the down-regulation of two miRNAs (miR194-5p, miR584as-3p) and
upregulation of 
miR4449 and miR-3158-5p in liver transplant rejected patients
and claim these to be candidate biomarkers for LT rejection in HCC patients.
However, authors need to address some serious concerns. I am asking for a
Revision.
1. To be consistent with the conclusions authors are drawing, the essential
microarray data representing 14 transplant patients need to be represented in Fig.
3. Fig. 3 shows profiles of just 2 individuals as mentioned in the figure legend.
This data is the foundation of the entire data.
2. It would be useful authors 
refer to a 2017 manuscript by Miyaaki Hisamitsu,
et al, Annals of Transplantation, reporting the intrahepatic miRNA profiles in
liver 
transplant patients with viral co-infections. Miyaki et al report fold changes
in expression from 2 to 44 fold using same miRNA microarray techniques. 
3. Authors in table 2 show fold and log2-fold change in differentially expressing
miRNA candidates. It is not clear how the fold change was calculated. Due to the
biological heterogeneity and experimental variabilities, generally fold change < 2
is not considered significant. All values in table 2 represent < 2 fold changes.
4. Figure 4 shows the real time qPCR validation of the microarray data. Again it
is not clear how the fold change was calculated in qPCR assays. Compared to <2
microarray fold changes, authors report 8 and 70 fold up-regulation in miR 4449
and miR 
3158-5p, respectively and 2 and 40 fold down regulation in miR 194-5p
and miR 548as-3p. Authors need to explain why are relative changes not
consistent.
5. The layout of the figures need to be modified for effective representation of
data. For example Fig. 2 could be combined with modified Figure 3, etc. Fig 2,
showing matrix plot is not clear. Two rows are labeled and one is left to wonder
what the middle two rows are.
6. Small grammer/typos like line 50 pg1, line 4, page 2 need to be fixed. What is
Simple Expressed analysis?
7. Reference 31 lacks the journal info.
In summary, It is an interesting study but needs to be reviewed before it is
deemed fit for publication.
Thanks,
Aejaz 
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Is the study design appropriate to answer the research question (including the use
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