Gene Expression Profiling of MicroRNAs in Small-Bowel Transplantation Paraffin-Embedded Mucosal Biopsy Tissue

Identification of Candidate Biomarkers for Transplant Rejection from Transcriptome Data: A Systematic Review

BACKGROUND

Traditional methods for rejection control in transplanted patients are considered invasive, risky, and prone to sampling errors. Using molecular biomarkers as an alternative protocol to biopsies, for monitoring rejection may help to mitigate some of these problems, increasing the survival rates and well-being of patients. Recent advances in omics technologies provide an opportunity for screening new molecular biomarkers to identify those with clinical utility.

OBJECTIVE

This systematic literature review (SLR) aimed to summarize existing evidence derived from large-scale expression profiling regarding differentially expressed mRNA and miRNA in graft rejection, highlighting potential molecular biomarkers in transplantation.

METHODS

The study was conducted following PRISMA methodology and the BiSLR guide for performing SLR in bioinformatics. PubMed, ScienceDirect, and EMBASE were searched for publications from January 2001 to January 2018, and studies (i) aiming at the identification of transplant rejection biomarkers, (ii) including human subjects, and (iii) applying methodologies for differential expression analysis from large-scale expression profiling were considered eligible. Differential expression patterns reported for genes and miRNAs in rejection were summarized from both cross-organ and organ-specific perspectives, and pathways enrichment analysis was performed for candidate biomarkers to interrogate their functional role in transplant rejection.

RESULTS

A total of 821 references were collected, resulting in 604 studies after removal of duplicates. After application of inclusion and exclusion criteria, 33 studies were included in our analysis. Among the 1517 genes and 174 miRNAs identifed, CXCL9, CXCL10, STAT1, hsa-miR-142-3p, and hsa-miR-155 appeared to be particularly promising as biomarkers in transplantation, with an increased expression associated with transplant rejection in multiple organs. In addition, hsa-miR-28-5p was consistently decreased in samples taken from rejected organs.

CONCLUSION

Despite the need for further research to fill existing knowledge gaps, transcriptomic technologies have a relevant role in the discovery of accurate biomarkers for transplant rejection diagnostics. Studies have reported consistent evidence of differential expression associated with transplant rejection, although issues such as experimental heterogeneity hinder a more systematic characterization of observed molecular changes. Special attention has been giving to large-scale mRNA expression profiling in rejection, whereas there is still room for improvements in the characterization of miRnome in this condition.

PROSPERO REGISTRATION NUMBER

CRD42018083321.

Effect of miR-146a and miR-155 on cardiac xenotransplantation

The aim of the present study was to investigate the expression levels of miR-146a and miR-155 in a cardiac xenograft model treated with the immunosuppressant FK506, and to construct lentiviral vectors to further study the roles of miR-146a and miR-155 in cardiac xenotransplantation. Expression levels of miR-146a and miR-155 were examined by quantitative polymerase chain reaction analysis and protein expression of RelA, which is a member of the nuclear factor-κB family, was examined by western blot analysis. Pre-miR-146a and pre-miR-155 fragments were designed and synthesized according to MiRBase and were cloned into the plasmid pCDH1-MCS1-EF1-copGFP. Recombinant plasmids were identified by enzyme digestion and sequencing. Survival time of cardiac grafts in the FK506 treatment group was significantly increased in comparison with the control group (P<0.05). In addition, the histopathological grading results were significantly decreased in the treatment group (P<0.05). A significant decrease in RelA protein expression levels was observed in the treatment group (P<0.05), along with a significant increase in miR-146a expression levels (P<0.05) and a significant decrease in miR-155 expression levels (P<0.05). Digestion and sequencing findings demonstrated that the insertion of miRNA into the plasmid pCDH1-MCS1-EF1-copGFP conformed with the pre-miRNAs, and the lentiviral vectors were concentrated to a titer of 5×10⁷ IFU/ml. These findings demonstrated that FK506 is able to inhibit the rejection effect in a mouse-to-rat cardiac xenotransplantation model. FK506 treatment altered the expression levels of miR-146a and miR-155, indicating that they may have an important role in regulating the immune response to the rejection effect. miR-146a and miR-155 lentiviral vectors were successfully constructed for further experiments both in vitro and in vivo.

RNA Profiling in Human and Murine Transplanted Hearts: Identification and Validation of Therapeutic Targets for Acute Cardiac and Renal Allograft Rejection

Acute cellular rejection (ACR) is the adverse response of the recipient's immune system against the allogeneic graft. Using human surveillance endomyocardial biopsies (EMBs) manifesting ACR and murine allogeneic grafts, we profiled implicated microRNAs (miRs) and mRNAs. MiR profiling showed that miR-21, -142-3p, -142-5p, -146a, -146b, -155, -222, -223, and -494 increased during ACR in humans and mice, whereas miR-149-5p decreased. mRNA profiling revealed 70 common differentially regulated transcripts, all involved in immune signaling and immune-related diseases. Interestingly, 33 of 70 transcripts function downstream of IL-6 and its transcription factor spleen focus forming virus proviral integration oncogene (SPI1), an established target of miR-155, the most upregulated miR in human EMBs manifesting rejection. In a mouse model of cardiac transplantation, miR-155 absence and pharmacological inhibition attenuated ACR, demonstrating the causal involvement and therapeutic potential of miRs. Finally, we corroborated our miR signature in acute cellular renal allograft rejection, suggesting a nonorgan specific signature of acute rejection. We concluded that miR and mRNA profiling in human and murine ACR revealed the shared significant dysregulation of immune genes. Inflammatory miRs, for example miR-155, and transcripts, in particular those related to the IL-6 pathway, are promising therapeutic targets to prevent acute allograft rejection.

Evaluation of Immune Profiles and MicroRNA Expression Profiles in Peripheral Blood Mononuclear Cells of Long-Term Stable Liver Transplant Recipients and Recipients With Acute Rejection Episodes

OBJECTIVE

This study aimed to document the difference of immunophenotypes in peripheral blood mononuclear cells (PBMCs) between long-term stable liver transplant recipients and recipients with acute rejection. We also sought to identify whether there is any correlation between microRNA (miRNA) expression profile and the differential immunoprofile in these 2 groups to establish a specific miRNA biomarker to identify potential liver transplant recipients.

METHODS

PBMCs were isolated from 53 stable liver transplant recipients (STA group) and 15 liver transplant recipients with repeated biopsy-proven rejection episodes admitted to our hospital. Immunoprofiles were analyzed by means of flow cytometry. Analysis of miRNA expression in the PBMCs was performed by means of real-time polymerase chain reaction.

RESULTS

The immune profiling analysis showed increased frequency of peripheral natural killer cells and regulatory T cells in stable liver transplant recipients compared with the acute rejection recipients and healthy volunteers (P < .05). There was no significant difference in the immune cell levels (CD19(+) B cells, CD4(+) T cells, and CD8(+) T cells) in PBMCs among the transplant recipient groups and healthy control subjects. Three miRNAs, miR-18b, miR-340, and miR-106b, were up-regulated in the PBMCs of the STA recipients compared with recipients with acute rejection.

CONCLUSIONS

These results suggest that miR-18b, miR-340, and miR-106b, which regulate the expression of specific immunophenotypes, can be used as potential biomarkers to identify long-term stable liver transplant recipients from recipients with acute rejection.

Plasma microRNA, a potential biomarker for acute rejection after liver transplantation

BACKGROUND

Acute rejection (AR) of an organ transplant is a life-threatening complication. Currently, there are few diagnostic biomarkers suitable for clinical application. We aim to determine the potential of plasma microRNAs as biomarkers for AR.

METHODS

Using rat orthotopic liver transplantation model and microarrays, we compared the difference in the spectrum and levels of microRNAs in both plasma and grafts between AR rats and control. AR-related plasma microRNAs were selected and validated using real-time quantification polymerase chain reaction. Plasma from AR rats with or without tacrolimus treatment was used for microRNA dynamic monitoring. To clarify the origin of AR-related plasma microRNAs, drug-induced liver damage rat model were performed and in situ hybridization was used to detect and localize the specific microRNA in allografts.

RESULTS

We found that plasma miR-122, miR-192, and miR-146a was significantly up-regulated when AR occur (fold change>2; P<0.05) and the elevation could be repressed by immunosuppression. In liver injury rat model, up-regulated plasma miR-122 (fold change=22.126; P=0.002) and miR-192 (fold change=8.833; P<0.001) rather than miR-146a (fold change=1.181; P=0.594) were observed. Further study demonstrated that miR-146a was up-regulated by sixfold in microvesicles isolated from AR plasma, whereas miR-122 and miR-192 showed no distinct change. In situ hybridization revealed that the portal areas of the AR graft were brimming with lymphocytes, which showed highly intense staining for miR-146a.

CONCLUSIONS

Our study provides the global fingerprint of plasma microRNAs in AR rats and suggests that plasma miR-122 and miR-192 reflect liver injury, whereas miR-146a may associate with cellular rejection.

MicroRNA expression profiling in archival tissue specimens: methods and data processing

The discovery that the human genome codes for thousands (if not millions) of previously unrecognized non-protein coding RNAs with regulatory functions has changed our understanding of many physiological and pathological processes. A prominent class of non-coding RNAs with important functions in cancer initiation and progression comprised by very short single-stranded, mRNA translation modulating RNAs, termed microRNAs. The determination of microRNA expression profiles is now widely used in biology and pathology, employing a range of methodologies. A steadily growing number of studies describe the analysis of formalin-fixed paraffin-embedded, so-called "archival" specimens. However, procedures for data processing and calculations are far from standardized and differ considerably between published studies, making comparisons and meta-analyses still quite difficult. In this review, we provide a short overview of profiling methods used for archival samples and describe in detail a modified method for normalization and processing of raw data obtained by fluorescence-labeled bead technology from Luminex.Inc.

MicroRNAs: potential biomarker in organ transplantation

MicroRNAs (miRs) are non-coding RNAs that could regulate gene expression at the posttranscriptional level, and have been indicated to be involved in diverse biological processes. They are emerging as master regulator of immune response and may likely play a key role in transplant rejection process. The extensive and comprehensive use of miR microarrays has enabled the identification of miRs as potential biomarkers for transplantation; many miRs have been reported associated with transplant rejection. Here we reviewed the emerging data on transplant recipients' miRs expression pattern, and discussed the possible mechanism of how miRs regulate transplant immune response.