MicroRNAs: small molecules, big effects

Transcriptomic miRNA and mRNA signatures in primary prostate cancer that are associated with lymph-node invasion

BACKGROUND

Nomograms or comparable techniques can be used to determine which patients with prostate cancer (PCa) will benefit from extended pelvic lymph node dissection (ePLND). While nomograms help guide clinical decisions, ∼80% of the patients undergo unnecessary ePLND. This pilot study aims to identify both transcriptomic mRNA and microRNA (miR) signatures in primary PCa tumours that are associated with the presence of lymph node metastasis (LNM).

METHODS

Primary PCa tumours obtained from 88 patients (pathologically diagnosed as N0 [pN0, n = 44] or as N1 [pN1, n = 44]) were profiled using two different probe-based captured direct assays based on next-generation sequencing and targeting 19398 mRNA transcripts (human transcriptome panel [HTP] dataset) and 2083 miRs (miRs whole-transcriptome assay [WTA] dataset). The TCGA-PRAD (pN0 [n = 382] and pN1 [n = 70]) and GSE220095 (pN0 [n = 138] and pN1 [n = 17]) datasets were used for validation using bioinformatic analyses.

RESULTS

A four-mRNA signature (CHRNA2, NPR3, VGLL3 and PAH) was found in primary tumour tissue samples from pN1 PCa patients, and then it was validated using the TCGA-PRAD and GSE220095 datasets. Adding serum prostate-specific antigen (PSA) values to the four-gene signature increased the performance to identify pN1 (HTP [AUC = .8487, p = 2.18e-09], TCGA-PRAD [AUC = .7150, p = 8.66e-08] and GSE220095 datasets [AUC = .8772, p = 4.09e-07]). Paired miR analyses showed that eight miRs were significantly upregulated in primary PCa that were pN1 (p < .01). The eight-miR signature performance increased when adding PSA (WTA dataset [AUC = .8626, p = 4.66e-10]) or Grade group (WTA dataset [AUC = .8689, p = 2e-10]). When combining the miR/mRNA signatures (miR-663b, CHRNA2 and PAH) with PSA levels, it showed the best performance to distinguish pN1 from pN0 PCa patients.

CONCLUSION

This study found miR/mRNA signatures in primary PCa tumours that in combination with serum PSA levels may complement nomograms for better detection of PCa patients with LNM and triage patients into better surgical decision-making.

KEY POINTS

Primary prostate cancer (PCa) tumours from patients pathologically diagnosed as N0 (pN0) or N1 (pN1) were dually assessed for microRNA (miRs) and mRNA levels using an NGS-based assay. A four-mRNA and an eight-miRNA signature were found. The mRNA signatures were further validated using two datasets. The combination of serum prostate-specific antigen (PSA) levels or Grade Group with the miR/mRNA signatures separates pN1 from pN0 PCa patients.

miR-147 Represses NDUFA4, Inducing Mitochondrial Dysfunction and Tubular Damage in Cold Storage Kidney Transplantation

SIGNIFICANCE STATEMENT

Cold storage-associated transplantation (CST) injury occurs in renal transplant from deceased donors, the main organ source. The pathogenesis of CST injury remains poorly understood, and effective therapies are not available. This study has demonstrated an important role of microRNAs in CST injury and revealed the changes in microRNA expression profiles. Specifically, microRNA-147 (miR-147) is consistently elevated during CST injury in mice and in dysfunctional renal grafts in humans. Mechanistically, NDUFA4 (a key component of mitochondrial respiration complex) is identified as a direct target of miR-147. By repressing NDUFA4, miR-147 induces mitochondrial damage and renal tubular cell death. Blockade of miR-147 and overexpression of NDUFA4 reduce CST injury and improve graft function, unveiling miR-147 and NDUFA4 as new therapeutic targets in kidney transplantation.

BACKGROUND

Kidney injury due to cold storage-associated transplantation (CST) is a major factor determining the outcome of renal transplant, for which the role and regulation of microRNAs remain largely unclear.

METHODS

The kidneys of proximal tubule Dicer (an enzyme for microRNA biogenesis) knockout mice and their wild-type littermates were subjected to CST to determine the function of microRNAs. Small RNA sequencing then profiled microRNA expression in mouse kidneys after CST. Anti-microRNA-147 (miR-147) and miR-147 mimic were used to examine the role of miR-147 in CST injury in mouse and renal tubular cell models.

RESULTS

Knockout of Dicer from proximal tubules attenuated CST kidney injury in mice. RNA sequencing identified multiple microRNAs with differential expression in CST kidneys, among which miR-147 was induced consistently in mouse kidney transplants and in dysfunctional human kidney grafts. Anti-miR-147 protected against CST injury in mice and ameliorated mitochondrial dysfunction after ATP depletion injury in renal tubular cells in intro . Mechanistically, miR-147 was shown to target NDUFA4, a key component of the mitochondrial respiration complex. Silencing NDUFA4 aggravated renal tubular cell death, whereas overexpression of NDUFA4 prevented miR-147-induced cell death and mitochondrial dysfunction. Moreover, overexpression of NDUFA4 alleviated CST injury in mice.

CONCLUSIONS

microRNAs, as a class of molecules, are pathogenic in CST injury and graft dysfunction. Specifically, miR-147 induced during CST represses NDUFA4, leading to mitochondrial damage and renal tubular cell death. These results unveil miR-147 and NDUFA4 as new therapeutic targets in kidney transplantation.

A Review of micro RNAs changes in T2DM in animals and humans

Type 2 diabetes mellitus (T2DM) and its associated complications have become a crucial public health concern in the world. According to the literature, chronic inflammation and the progression of T2DM have a close relationship. Accumulated evidence suggests that inflammation enhances the insulin secretion lost by islets of Langerhans and the resistance of target tissues to insulin action, which are two critical features in T2DM development. Based on recently highlighted research that plasma concentration of inflammatory mediators such as tumor necrosis factor α and interleukin-6 are elevated in insulin-resistant and T2DM, and it raises novel question marks about the processes causing inflammation in both situations. Over the past few decades, microRNAs (miRNAs), a class of short, noncoding RNA molecules, have been discovered to be involved in the regulation of inflammation, insulin resistance, and T2DM pathology. These noncoding RNAs are specifically comprised of RNA-induced silencing complexes and regulate the expression of specific protein-coding genes through various mechanisms. There is extending evidence that describes the expression profile of a special class of miRNA molecules altered during T2DM development. These modifications can be observed as potential biomarkers for the diagnosis of T2DM and related diseases. In this review study, after reviewing the possible mechanisms involved in T2DM pathophysiology, we update recent information on the miRNA roles in T2DM, inflammation, and insulin resistance.

Modulation of Monocyte Response by Microrna-15b/106a/374a During Antibody-mediated Rejection in Kidney Transplantation

BACKGROUND

Increasing evidence suggest that microRNAs are involved in the physiopathology of acute or chronic renal disease. In kidney transplantation, as key regulators of cellular homeostasis, microRNAs may be involved in the regulation of immune cell function and the allograft response. Here, we investigated the change in circulating microRNA expression profile and their involvement in the profound transcriptional changes associated with antibody-mediated rejection (ABMR).

METHODS

Blood samples were collected at the time of the 710 kidney allograft biopsies at 4 European transplant centers. Messenger RNA and microRNA profiling analyses were performed in a discovery-to-validation study within 3 independent cohorts encompassing N = 126, N = 135, and N = 416 patients, respectively.

RESULTS

Compared with samples with no ABMR, 14 microRNAs were significantly decreased in ABMR samples. Among them, expression levels of microRNA-15b, microRNA-106a, and microRNA-374a gradually decreased with the severity of ABMR lesions. From their in silico-predicted target genes, a high proportion proved to be significantly upregulated in the paired transcriptomic analysis. Gene ontology analyses of microRNA-15b/-106a/-374a suggested enrichment in myeloid-related pathways, which was further refined by in silico and ex vivo transcriptomic analyses, showing a specific origin from classical CD14 + monocytes. Finally, human CD14 + monocytes were subjected to transduction by antago-microRNAs to mimic ABMR pathology. MicroRNA-15b/-106a/-374a impairment resulted in cellular activation with an increased expression of CD69, CRIM1, IPO7, and CAAP1, direct and common targets of the 3 microRNAs.

CONCLUSIONS

Together, our data provide new insights into circulating microRNAs as markers and key players in ABMR, and they suggest monocyte involvement in this process.

Metal-Organic Framework UiO-66-Mediated Dual-Signal Ratiometric Electrochemical Sensor for microRNA Detection with DNA Walker Amplification

Electrochemical nanotags with strong signal input are necessary for a ratiometric electrochemical sensor to overcome the drawbacks of inaccurate detection results. In this paper, the metal-organic framework (MOF) UiO-66 was utilized as an electrochemical signal tag. A stable and strong current response at +0.9 V can be detected in neutral conditions. MicroRNA (miRNA) was employed as the model analyte. Herein, an enzyme-free DNA-walker-based ultrasensitive ratiometric electrochemical biosensor in combination with Zr MOF (UiO-66) signal tags to detect miRNA was demonstrated. In the presence of miRNA, the autonomous walker movement can be initiated by miRNA, leading to the release of biotin-modified fragments. Thus, streptavidin-labeled UiO-66 nanomaterials were not bound to the electrode, generating a low signal response of UiO-66 at +0.9 V. However, the current signal of electrolyte solution as reference at +0.2 V was increased due to the enhancement of electrode conductivity. This ratiometic sensor demonstrated high sensitivity, selectivity, and reproducibility. It can eliminate the disturbance of environmental factors and basic electrode characteristics, providing more accurate signals. A limit of detection (LOD) of 0.17 fM was achieved. Moreover, the method was also used to detect miRNA-21 spiked in real serum samples.

MicroRNAs in kidney injury and disease

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by degrading or repressing the translation of their target messenger RNAs. As miRNAs are critical regulators of cellular homeostasis, their dysregulation is a crucial component of cell and organ injury. A substantial body of evidence indicates that miRNAs are involved in the pathophysiology of acute kidney injury (AKI), chronic kidney disease and allograft damage. Different subsets of miRNAs are dysregulated during AKI, chronic kidney disease and allograft rejection, which could reflect differences in the physiopathology of these conditions. miRNAs that have been investigated in AKI include miR-21, which has an anti-apoptotic role, and miR-214 and miR-668, which regulate mitochondrial dynamics. Various miRNAs are downregulated in diabetic kidney disease, including the miR-30 family and miR-146a, which protect against inflammation and fibrosis. Other miRNAs such as miR-193 and miR-92a induce podocyte dedifferentiation in glomerulonephritis. In transplantation, miRNAs have been implicated in allograft rejection and injury. Further work is needed to identify and validate miRNAs as biomarkers of graft function and of kidney disease development and progression. Use of combinations of miRNAs together with other molecular markers could potentially improve diagnostic or predictive power and facilitate clinical translation. In addition, targeting specific miRNAs at different stages of disease could be a promising therapeutic strategy.

Single-cell mapping of leukocyte immunoglobulin-like receptors in kidney transplant rejection

Leukocyte immunoglobulin-like receptors (LILRs) are a family of inhibitory or stimulatory receptors expressed by immune cell types belonging to both myeloid and lymphoid lineage. Several members of the LILR family recognize major histocompatibility complex class I and thus play important roles in a range of clinical situations including pregnancy. Moreover, paired immunoglobulin-like receptors (PIRs), the murine orthologs of LILRs, are implicated in experimental transplant allorecognition by monocytes and contribute to the induction of donor-specific monocyte-memory. After non-self recognition, activating PIRs are transiently overexpressed at the surface of monocytes and participate in donor-specific monocyte recruitment, leading to graft rejection in vivo. In the present study, we mapped LILR expression and also their respective reported ligands at single cell level in the renal allograft and circulating cells in the context of kidney transplant rejection. Recipient-derived monocytes were shown to infiltrate the donor tissue and to differentiate into macrophages. We thus also investigate LILR expression during in vitro monocyte-to-macrophage differentiation in order to characterize the myeloid population that directly contribute to allorecognition. Altogether our results emphasize non-classical monocytes and CD68+ M1 macrophages as key players in LILRs-ligand interaction in kidney transplantation.

Integrative Omics Analysis Unravels Microvascular Inflammation-Related Pathways in Kidney Allograft Biopsies

In solid-organ transplantation, microRNAs (miRNAs) have emerged as key players in the regulation of allograft cells function in response to injury. To gain insight into the role of miRNAs in antibody-mediated rejection, a rejection phenotype histologically defined by microvascular inflammation, kidney allograft biopsies were subjected to miRNA but also messenger RNA (mRNA) profiling. Using a unique multistep selection process specific to the BIOMARGIN study (discovery cohort, N=86; selection cohort, N=99; validation cohort, N=298), six differentially expressed miRNAs were consistently identified: miR-139-5p (down) and miR-142-3p/150-5p/155-5p/222-3p/223-3p (up). Their expression level gradually correlated with microvascular inflammation intensity. The cell specificity of miRNAs target genes was investigated by integrating their in vivo mRNA targets with single-cell RNA sequencing from an independent allograft biopsy cohort. Endothelial-derived miR-139-5p expression correlated negatively with MHC-related genes expression. Conversely, epithelial-derived miR-222-3p overexpression was strongly associated with degraded renal electrolyte homeostasis and repressed immune-related pathways. In immune cells, miR-150-5p regulated NF-κB activation in T lymphocytes whereas miR-155-5p regulated mRNA splicing in antigen-presenting cells. Altogether, integrated omics enabled us to unravel new pathways involved in microvascular inflammation and suggests that metabolism modifications in tubular epithelial cells occur as a consequence of antibody-mediated rejection, beyond the nearby endothelial compartment.

Getting immunosuppression just right: the role of clinical biomarkers in predicting patient response post solid organ transplantation

INTRODUCTION

Actually, immunosuppression selection isn't based on individual immune alloreactivity, and immunosuppressive drug dosing is mainly based on the development of toxicity and the achievement of specific target concentrations. Since a successful outcome requires optimal patient risk stratification and treatment, several groups have evaluated candidate biomarkers that have shown promise in the assessment of individual immune responses, the prediction of personal pharmacodynamic effects of immunosuppressive drugs and the prognosis and diagnosis of graft outcomes..

AREAS COVERED

This review includes biomarkers that the Scientific Community in Solid Organ Transplantation currently considers to have potential as diagnostic and prognostic biomarkers of graft evolution. We have focused on recent scientific advances and expert recommendations regarding the role of specific and non-specific pharmacodynamic biomarkers that are mainly involved in the T-cell-mediated response.

EXPERT OPINION

Integral pharmacologic monitoring that combines pharmacokinetics, pharmacogenetics and predictive pharmacodynamic biomarkers may provide crucial information and allow personal adjustment of immunosuppressive drugs at an early stage before severe adverse events ensue. Multicentre, randomized, prospective and interventional trials are needed to fine tune the established cut-off values for each biomarker and the optimal monitoring frequency for each biomarker and to accurately evaluate possible clinical confounding factors to enable correct clinical qualification.