Urinary miRNAs as Biomarkers for Noninvasive Evaluation of Radiation-Induced Renal Tubular Injury

Renal Tubular Epithelial Cell-Derived hsa_circ_0008925 From Urine Is Related to Chronic Renal Fibrosis

Renal fibrosis (RF) is a crucial pathological factor in the progression of chronic kidney disease (CKD) to end-stage renal failure, and accurate and noninvasive assays to monitor the progression of renal fibrosis are needed. Circular RNAs (circRNAs) are noncoding RNAs that can be used as diagnostic biomarkers and therapeutic targets for human diseases. In this study, we analysed the expression of hsa_circ_0008925 in human urinary renal tubular cells and investigated its role in renal fibrosis. Urinary samples were collected from CKD patients with varying degrees of renal fibrosis; renal tubular epithelial cells were isolated from the urinary samples using magnetic bead sorting. In patients with moderate-severe renal fibrosis, the expression of hsa_circ_0008925 in urinary renal tubular epithelial cells was elevated compared to that in patients with no renal fibrosis to mild renal fibrosis. Spearman correlation analysis indicated that the hsa_circ_0008925 expression was positively correlated with serum creatinine (Scr, rs = 0.424, p = 0.031). The expression of hsa_circ_0008925 was elevated in TGF-β1-treated HK-2 cells in vitro. Silencing of hsa_circ_0008925 using siRNA inhibited TGF-β1-induced fibrosis in HK2 cells. RNA pull-down and mass spectrometric analyses indicated that serine/arginine-rich splicing factor 6 (SRSF6) is the downstream of hsa_circ_0008925. Silencing mmu_circ_0002215 and inhibiting SRSF6 alleviated renal fibrosis in a UUO model in vivo. Inhibiting hsa_circ_0008925/SRSF6 alleviated renal fibrosis in vitro and in vivo. These findings suggest that targeting the hsa_circ_0008925/SRSF6 pathway could hold promise as a potential therapeutic strategy for treating renal fibrosis.

Radio-miRs: a comprehensive view of radioresistance-related microRNAs

Radiotherapy is a key treatment option for a wide variety of human tumors, employed either alone or alongside with other therapeutic interventions. Radiotherapy uses high-energy particles to destroy tumor cells, blocking their ability to divide and proliferate. The effectiveness of radiotherapy is due to genetic and epigenetic factors that determine how tumor cells respond to ionizing radiation. These factors contribute to the establishment of resistance to radiotherapy, which increases the risk of poor clinical prognosis of patients. Although the mechanisms by which tumor cells induce radioresistance are unclear, evidence points out several contributing factors including the overexpression of DNA repair systems, increased levels of reactive oxygen species, alterations in the tumor microenvironment, and enrichment of cancer stem cell populations. In this context, dysregulation of microRNAs or miRNAs, critical regulators of gene expression, may influence how tumors respond to radiation. There is increasing evidence that miRNAs may act as sensitizers or enhancers of radioresistance, regulating key processes such as the DNA damage response and the cell death signaling pathway. Furthermore, expression and activity of miRNAs have shown informative value in overcoming radiotherapy and long-term radiotoxicity, revealing their potential as biomarkers. In this review, we will discuss the molecular mechanisms associated with the response to radiotherapy and highlight the central role of miRNAs in regulating the molecular mechanisms responsible for cellular radioresistance. We will also review radio-miRs, radiotherapy-related miRNAs, either as sensitizers or enhancers of radioresistance that hold promise as biomarkers or pharmacological targets to sensitize radioresistant cells.

Biology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel

This historical review of extracellular vesicles in the setting of exposure to ionizing radiation (IR) traces our understanding of how vesicles were initially examined and reported in the literature in the late 1970s (for secreted exosomes) and early 1980s (for plasma membrane-derived, exfoliated vesicles) to where we are now and where we may be headed in the next decade. An emphasis is placed on biophysical properties of extracellular vesicles, energy consumption and the role of vesiculation as an essential component of membrane turnover. The impact of intercellular signal trafficking by vesicle surface and intra-vesicular lipids, proteins, nucleic acids and metabolites is reviewed in the context of biomarkers for estimating individual radiation dose after exposure to radiation, pathogenesis of disease and development of cell-free therapeutics. Since vesicles express both growth stimulatory and inhibitory molecules, a hypothesis is proposed to consider superposition in a shared space and entanglement of molecules by energy sources that are external to human cells. Implications of this approach for travel in deep space are briefly discussed in the context of clinical disorders that have been observed after space travel.

Effects of Recombinant α1-Microglobulin on Early Proteomic Response in Risk Organs after Exposure to 177Lu-Octreotate

Recombinant α1-microglobulin (A1M) is proposed as a protector during 177Lu-octreotate treatment of neuroendocrine tumors, which is currently limited by bone marrow and renal toxicity. Co-administration of 177Lu-octreotate and A1M could result in a more effective treatment by protecting healthy tissue, but the radioprotective action of A1M is not fully understood. The aim of this study was to examine the proteomic response of kidneys and bone marrow early after 177Lu-octreotate and/or A1M administration. Mice were injected with 177Lu-octreotate and/or A1M, while control mice received saline or A1M vehicle solution. Bone marrow, kidney medulla, and kidney cortex were sampled after 24 h or 7 d. The differential protein expression was analyzed with tandem mass spectrometry. The dosimetric estimation was based on 177Lu activity in the kidney. PHLDA3 was the most prominent radiation-responsive protein in kidney tissue. In general, no statistically significant difference in the expression of radiation-related proteins was observed between the irradiated groups. Most canonical pathways were identified in bone marrow from the 177Lu-octreotate+A1M group. Altogether, a tissue-dependent proteomic response followed exposure to 177Lu-octreotate alone or together with A1M. Combining 177Lu-octreotate with A1M did not inhibit the radiation-induced protein expression early after exposure, and late effects should be further studied.

Biomarkers to Predict Lethal Radiation Injury to the Rat Lung

Currently, there are no biomarkers to predict lethal lung injury by radiation. Since it is not ethical to irradiate humans, animal models must be used to identify biomarkers. Injury to the female WAG/RijCmcr rat has been well-characterized after exposure to eight doses of whole thorax irradiation: 0-, 5-, 10-, 11-, 12-, 13-, 14- and 15-Gy. End points such as SPECT imaging of the lung using molecular probes, measurement of circulating blood cells and specific miRNA have been shown to change after radiation. Our goal was to use these changes to predict lethal lung injury in the rat model, 2 weeks post-irradiation, before any symptoms manifest and after which a countermeasure can be given to enhance survival. SPECT imaging with 99mTc-MAA identified a decrease in perfusion in the lung after irradiation. A decrease in circulating white blood cells and an increase in five specific miRNAs in whole blood were also tested. Univariate analyses were then conducted on the combined dataset. The results indicated that a combination of percent change in lymphocytes and monocytes, as well as pulmonary perfusion volume could predict survival from radiation to the lungs with 88.5% accuracy (95% confidence intervals of 77.8, 95.3) with a p-value of < 0.0001 versus no information rate. This study is one of the first to report a set of minimally invasive endpoints to predict lethal radiation injury in female rats. Lung-specific injury can be visualized by 99mTc-MAA as early as 2 weeks after radiation.

MicroRNAs as Biomarkers for Ionizing Radiation Injury

Accidental radiation exposures such as industrial accidents and nuclear catastrophes pose a threat to human health, and the potential or substantial injury caused by ionizing radiation (IR) from medical treatment that cannot be ignored. Although the mechanisms of IR-induced damage to various organs have been gradually investigated, medical treatment of irradiated individuals is still based on clinical symptoms. Hence, minimally invasive biomarkers that can predict radiation damage are urgently needed for appropriate medical management after radiation exposure. In the field of radiation biomarker, finding molecular biomarkers to assess different levels of radiation damage is an important direction. In recent years, microRNAs have been widely reported as several diseases’ biomarkers, such as cancer and cardiovascular diseases, and microRNAs are also of interest to the ionizing radiation field as radiation response molecules, thus researchers are turning attention to the potential of microRNAs as biomarkers in tumor radiation response and the radiation toxicity prediction of normal tissues. In this review, we summarize the distribution of microRNAs, the progress on research of microRNAs as markers of IR, and make a hypothesis about the origin and destination of microRNAs in vivo after IR.

A Next-Generation Sequencing of Plasma Exosome-Derived microRNAs and Target Gene Analysis with a Microarray Database of Thermally Injured Skins: Identification of Blood-to-Tissue Interactions at Early Burn Stage

BACKGROUND

Plasma exosome-derived microRNA (miRNA) profiles following thermal injury and their relationship with gene expression derangements in burned skin remain unexplored. This study focused on the identification of key miRNA-mRNA axes in potential blood-to-tissue interactions at early burn stage.

METHODS

Plasma exosomes were obtained from 6 severe burn patients 4-7 days post injury and 6 healthy volunteers. Next-generation sequencing (NGS) of exosomal small RNAs presented the differentially expressed miRNAs (DEMs). Target genes of the DEMs were predicted in the mirDIP database. Dataset GSE8056 was enrolled to acquire differentially expressed genes (DEGs) in burned skin compared to normal skin. Overlap between the DEGs and target genes of the DEMs were focus genes. The protein-protein interaction (PPI) network and enrichment analyses of the focus genes demonstrated hub genes and suggested underlying mechanisms and pathways. The hub genes and upstream DEMs were selected to construct key miRNA-mRNA axes.

RESULTS

The NGS of plasma exosome-derived small RNAs identified 85 DEMs (14 downregulated miRNAs and 71 upregulated miRNAs) with 12,901 predicted target genes. Dataset GSE8056 exhibited 1861 DEGs in partial-thickness burned skins 4-7 days postburn. The overlap between DEGs and target genes of DEMs displayed 1058 focus genes. The top 9 hub genes (CDK1, CCNB1, CCNA2, BUB1B, PLK1, KIF11, AURKA, NUSAP1 and CDCA8) in the PPI network of the focus genes pointed to 16 upstream miRNAs in DEMs, including 4 downregulated miRNAs (hsa-miR-6848-3p, has-miR-4684-3p, has-miR-4786-5p and has-miR-365a-5p) and 12 upregulated miRNAs (hsa-miR-6751-3p, hsa-miR-718, hsa-miR-4754, hsa-miR-6754-3p, hsa-miR-4739, hsa-miR-6739-5p, hsa-miR-6884-3p, hsa-miR-1224-3p, hsa-miR-6878-3p, hsa-miR-6795-3p, hsa-miR-550a-3p, and hsa-miR-550b-3p). A key miRNA-mRNA network in potential blood-to-tissue interactions at early burn stage was therefore constructed.

CONCLUSION

An NGS and bioinformatic analysis in the study identified key miRNA-mRNA axes in potential blood-to-tissue interactions at early burn stage, suggesting plasma exosome-derived miRNAs may impact on the alteration patterns of gene expressions in a burn wound.

Molecular Changes in miRNA in Irradiated Rat Kidneys: Role of miR-34a and its Vascular Targets in the Notch Pathway

The mechanism(s) of vascular regression in adult organs remains an unexplored gap. Irradiation to the kidney results in vascular regression and renal failure. The goal of this work was to determine molecular mechanism(s) of radiation-induced vascular regression and its mitigation by the drug lisinopril. Female WAG/RijCmcr rats received either 13 Gy X-ray irradiation, sparing one leg, or no irradiation, the latter serving as age-matched controls. Some irradiated animals received lisinopril. Kidney miRNA-seq was performed 35 days postirradiation, before symptoms of nephropathy. MicroRNA expression profiles were compared with data from humans. MicroRNA targets were predicted using TargetScan and confirmed by qRT-PCR and Western blot. Renal vascular endothelial cell density was evaluated at 100 days to confirm vascular regression. The normal rat kidney microRNA profile resembled that of humans. MiR-34a was increased >7-fold and emerged as the predominant rat microRNA altered by radiation. Expression of Jagged1, a ligand in the Notch pathway of vascular development and a target of miR-34a-5p was decreased by radiation but not in irradiated rats receiving lisinopril. Radiation decreased endothelial cells in the kidneys at 100 days, confirming vascular regression. In conclusion, the results of this study showed that radiation greatly increased miRNA34-a in rat kidneys, while lisinopril mitigated radiation-induced decrease of the Notch ligand, Jagged1, a molecular target of miRNA34-a.

Exosomes: Emerging Therapy Delivery Tools and Biomarkers for Kidney Diseases

Exosomes are nanometer-sized small EVs coated with bilayer structure, which are released by prokaryotic and eukaryotic cells. Exosomes are rich in a variety of biologically active substances, such as proteins, nucleotides, and lipids. Exosomes are widely present in various body fluids and cell culture supernatants, and it mediates the physiological and pathological processes of the body through the shuttle of these active ingredients to target cells. In recent years, studies have shown that exosomes from a variety of cell sources can play a beneficial role in acute and chronic kidney disease. In particular, exosomes derived from mesenchymal stem cells have significant curative effects on the prevention and treatment of kidney disease in preclinical trials. Besides, some encapsulated substances are demonstrated to exert beneficial effects on various diseases, so they have attracted much attention. In addition, exosomes have extensive sources, stable biological activity, and good biocompatibility and are easy to store and transport; these advantages endow exosomes with superior diagnostic value. With the rapid development of liquid biopsy technology related to exosomes, the application of exosomes in the rapid diagnosis of kidney disease has become more prominent. In this review, the latest development of exosomes, including the biosynthesis process, the isolation and identification methods of exosomes are systematically summarized. The utilization of exosomes in diagnosis and their positive effects in the repair of kidney dysfunction are discussed, along with the specific mechanisms. This review is expected to be helpful for relevant studies and to provide insight into future applications in clinical practice.

Transcriptomics for radiation biodosimetry: progress and challenges

PURPOSE

Transcriptomic-based approaches are being developed to meet the needs for large-scale radiation dose and injury assessment and provide population triage following a radiological or nuclear event. This review provides background and definition of the need for new biodosimetry approaches, and summarizes the major advances in this field. It discusses some of the major model systems used in gene signature development, and highlights some of the remaining challenges, including individual variation in gene expression, potential confounding factors, and accounting for the complexity of realistic exposure scenarios.

CONCLUSIONS

Transcriptomic approaches show great promise for both dose reconstruction and for prediction of individual radiological injury. However, further work will be needed to ensure that gene expression signatures will be robust and appropriate for their intended use in radiological or nuclear emergencies.

MicroRNA: a novel implication for damage and protection against ionizing radiation

Ionizing radiation (IR) is a form of high energy. It poses a serious threat to organisms, but radiotherapy is a key therapeutic strategy for various cancers. It is significant to reduce radiation injury but maximize the effect of radiotherapy. MicroRNAs (miRNAs) are posttranscriptionally regulatory factors involved in cellular radioresponse. In this review, we show how miRNAs regulate important genes on cellular response to IR-induced damage and how miRNAs participate in IR-induced carcinogenesis. Additionally, we summarize the experimental and clinical evidence for miRNA involvement in radiotherapy and discuss their potential for improvement of radiotherapy. Finally, we highlight the role that miRNAs play in accident exposure to IR or radiotherapy as predictive biomarker. miRNA therapeutics have shown great perspective in radiobiology; miRNA may become a novel strategy for damage and protection against IR.

An indispensable tool: Exosomes play a role in therapy for radiation damage

Radiotherapy is one of the three main treatments for tumors. Almost 70% of tumor patients undergo radiotherapy at different periods. Although radiotherapy can enhance the local control rate of tumors and patients' quality of life, normal tissues often show radiation damage following radiotherapy. In recent years, several studies have shown that exosomes could be biomarkers for diseases and be involved in the treatment of radiation damage. Exosomes are nanoscale vesicles containing complex miRNAs and proteins. They can regulate the inflammatory response, enhance the regeneration effect of damaged tissue, and promote the repair of damaged tissues and cells, extending their survival time. In addition, their functions are achieved by paracrine signaling. In this review, we discuss the potential of exosomes as biomarkers and introduce the impact of exosomes on radiation damage in different organs and the hematopoietic system in detail.

Urinary MicroRNAs in Environmental Health: Biomarkers of Emergent Kidney Injury and Disease

PURPOSE OF REVIEW

There is a critical need for sensitive biomarkers of renal disease and progression. Micro(mi)RNAs are attractive as next-generation biomarkers in kidney disease, particularly as urine miRNAs can inform kidney function and cellular integrity. This review summarizes recent epidemiologic and toxicologic advances using urinary miRNAs and exosomal miRNAs as novel biomarkers of chemical exposure and of kidney damage and disease.

RECENT FINDINGS

Urine miRNA biomarkers offer improved stability over protein in stored samples, relative ease of collection and quantitation, and conserved sequence homology across species. Particularly in the case of emergent environmental health threats such as chronic kidney disease of unknown origin, urinary miRNAs hold promise as biomarkers of disease and/or exposure. We present evidence to address scientific knowledge gaps, comment on the relevance of urine-derived miRNAs in environmental health research, and discuss limitations and recommendations for future directions needed to advance miRNA biomarker strategies.

Exosomal Small RNA Sequencing Uncovers Dose-Specific MiRNA Markers for Ionizing Radiation Exposure

Introduction:

Acute exposure to ionizing radiation (IR) is hazardous or even lethal. Accurate estimation of the doses of IR exposure is critical to wisely determining the following treatments. Exosomes are nanoscale vesicles harboring biomolecules and mediate the communications among cells and tissues to influence biological processes. Screening out the microRNAs (miRNAs) contained in exosomes as biomarkers can be useful for estimating the IR exposure doses and exploring the correlation between these miRNAs and the occurrence of disease.

Methods:

We treated mice with 2.0, 6.5, and 8.0 Gy doses of IR and collected the mice sera at 0, 24, 48, and 72 hours after exposure. Then, the serum exosomes were isolated by ultracentrifuge and the small RNA portion was extracted for sequencing and the following bioinformatics analysis. Qualitative polymerase chain reaction was performed to validate the potential dose-specific markers.

Results:

Fifty-six miRNAs (31 upregulated, 25 downregulated) were differentially expressed after exposure of the above 3 IR doses and may act as common IR exposure miRNA markers. Bioinformatic analysis also identified several dosage-specific responsive miRNAs. Importantly, IR-induced miR-151-3p and miR-128-3p were significantly and stably increased at 24 hours in different mouse strains with distinct genetic background after exposed to 8.0 Gy of IR.

Conclusion:

Our study shows that miR-151-3p and miR-128-3p can be used as dose-specific biomarkers of 8.0 Gy IR exposure, which can be used to determine the exposure dose by detecting the amount of the 2 miRNAs in serum exosomes.

Hydrophobic sand is a viable method of urine collection from the rat for extracellular vesicle biomarker analysis

Previously we have shown in rats a new method of urine collection, hydrophobic sand, to be an acceptable alternate in place of the traditional method using metabolic cages. Hydrophobic sand is non-toxic, induces similar or lower levels of stress in the rat, and does not contaminate clinical urine markers nor metal concentrations in collected samples (Hoffman et al., 2017 and 2018). Urine is often used in humans and many animal models as a readily-attainable biosample which contains proteins and microRNAs (miRNAs) within extracellular vesicles (EVs) that can be isolated to indicate changes in health. In order to ensure hydrophobic sand did not in any way contaminate or disrupt the extraction and analysis of these EVs and miRNAs, we used urine samples from the same 8 rats in the within-subjects crossover experiment comparing hydrophobic sand and metabolic cage collection methods. We isolated EVs and miRNAs from the urine set and examined their quantity and quality between the urine collection methods. We found no significant differences in particle size, particle concentration, total RNA, or the type and abundance of miRNAs contained within the urine EVs due to urine collection method, suggesting hydrophobic sand represents an easy-to-use, non-invasive method to collect rodent urine for EVs and biomarker studies.

Measurement of γ-H2AX foci, miRNA-101, and gene expression as a means to quantify radiation-absorbed dose in cancer patients who had undergone radiotherapy

Radiological accidents and nuclear terrorism pose an increased threat to members of the public who, following such an event, would need to be assessed for medical care by fast triage. Assay methods such as chromosome aberrations (CA), cytokinesis-block micronucleus (CBMN) and fluorescence in situ hybridization (FISH) techniques have been well established for dose estimation and their potential for handling more samples has also been proved with automation. However, culturing of lymphocytes is an inevitable step, which limits the potential of these markers for triage. In vitro analysis of gamma-H2AX (γ-H2AX), gene and microRNA (miRNA) markers do not require culturing of lymphocytes, and as such have been suggested as attractive tools for triage. Despite studies reporting in vitro dose-response curves, limited evidence is available evaluating the suitability of these assays in real situations. In this study, we have measured the absorbed dose using γ-H2AX, gene (GADD45A, FDXR, and CDKN1A) and miRNA-101 expression in blood samples of cancer patients (n = 20) who had undergone partial-body radiotherapy and compared with the derived equivalent whole-body doses (EWBD). The obtained results from all patients showed a significant (p < 0.05) increase of γ-H2AX foci in post-irradiated as compared to pre-irradiated samples. Moreover, estimated doses using γ-H2AX foci showed a correlation with the derived EWBD (r² = 0.60, p = 0.0003) and was also shown to be dependent on the irradiated body volume. Consistent with γ-H2AX foci frequency, an increase in fold change expression of genes and miRNA-101 was observed. However, the estimated dose significantly varied among the subjects and showed poor correlation (r² = 0.09, 0.04, 0.01 and 0.03 for GADD45A, FDXR, CDKN1A and miRNA-101, respectively) with EWBD. The overall results suggest that the established in vitro γ-H2AX assay is suitable for the detection of radiation exposure and can also provide an estimate of the dose in in vivo irradiated samples. The genes and miRNA-101 markers showed increased expression; nevertheless, there is a need for further improvements to measure doses accurately using these markers.

[Value of podocalyxin levels in urinary extracellular vesicles for diagnosis of diabetic nephropathy]

OBJECTIVE

To explore the value of detecting podocalyxin (PCX) level in urinary extracellular vesicles for the diagnosis of diabetic nephropathy.

METHODS

This study was conducted among 57 diabetic patients admitted during the period from March to September, 2017, including 34 with uncomplicated diabetics and 23 with diabetic nephropathy; 21 patients with other types of nephropathy and 11 healthy individuals were also included to serve as the controls. Transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) were used to verify the separation of urinary extracellular vesicles. The molecular markers of extracellular vesicles (TSG101 and podocalyxin [PCX]) were detected using Western blotting. PCX levels in extracellular vesicles were also detected using ELISA.

RESULTS

TEM reveal the presence of numerous extracellular vesicles in the urine with intact morphology and different sizes, and most of them were below 300 nm in diameter as shown by NTA. TSG101 expression was detected in the samples from all the 4 groups. Positive expression of PCX was detected in the samples from patients with diabetic nephropathy but not in the other groups. In patients with diabetic nephropathy, the mean PCX levels (3.27±2.30 ng/μmol)was significantly higher than those in the healthy control group (1.22±0.36 ng/μmol), uncomplicated diabetes group (2.22±1.29 ng/μmol) and nephropathy group (1.24±0.45 ng/μmol).

CONCLUSIONS

PCX level in urinary extracellular vesicles is significantly increased in patients with diabetic nephropathy, suggesting the value of PCX as a potential marker for clinical diagnosis of diabetic nephropathy.