Long Noncoding RNAs in Urine Are Detectable and May Enable Early Detection of Acute T Cell-Mediated Rejection of Renal Allografts

A meta-analysis of UCA1 accuracy in the detection of bladder cancer

INTRODUCTION

Bladder cancer (BCa) exhibits a relatively high prevalence, yet convenient tools for its early detection are lacking. Our study aims to assess the diagnostic value of Urothelial Carcinoma-Associated 1 (UCA1) in the early detection of BCa.

METHODS

Systematic searches were performed in electronic databases (PubMed, Web of Science, Science Direct, CNKI, Wanfang, and VIP) until 20 July 2023. QUADAS-2 was used for quality assessment, while Meta-DiSc 1.4 and STATA 14.0 were employed for statistical analysis.

RESULTS

A total of 1252 BCa patients and 779 controls, from 12 identified articles, were included. UCA1 showed strong discriminatory ability in BCa detection, with an overall sensitivity of 0.84 specificity of 0.91, and a 0.91 area under the curve (AUC). Strikingly, UCA1 expressed in urine and tissue exhibited higher diagnostic value (0.92 AUC) compared to that in blood (0.86 AUC). Furthermore, urine UCA1 demonstrated remarkable diagnostic performance with 91% sensitivity and 98% specificity. Deeks' funnel plot detected no substantial publication bias.

CONCLUSION

UCA1 could serve as a potential biomarker for BCa detection with good diagnostic performance. Besides, compared to UCA1 in blood, urine and tissue UCA1 exhibited higher diagnostic value. Further prospective clinical research is needed to corroborate the conclusion.

PROSPERO REGISTRATION

CRD42023463210.

Prospects and challenges of noncoding-RNA-mediated inhibition of heat shock protein 90 for cancer therapy

Heat Shock Protein 90 (HSP90) is a potential drug target for cancer therapy as it is often dysregulated in several cancers, including lung, breast, pancreatic, and prostate cancers. In cancer, HSP90 fails to maintain the structural and functional integrity of its several client proteins which are involved in the hallmarks of cancer such as cell proliferation, invasion, migration, angiogenesis, and apoptosis. Several small molecule inhibitors of HSP90 have been shown to exhibit anticancer effects in vitro and in vivo animal models. However, a few of them are currently under clinical studies. The status and potential limitations of these inhibitors are discussed here. Studies demonstrate that several noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) regulate HSP90 and its client proteins to modulate cellular processes to exhibit oncogenic or tumor suppressing properties. Over the last decade, miRNAs and lncRNAs have drawn significant interest from the scientific community as therapeutic agents or targets for clinical applications. Here, we discuss the detailed mechanistic regulation of HSP90 and its client proteins by ncRNAs. Moreover, we highlight the significance of these ncRNAs as potential therapeutic agents/targets, and the challenges associated with ncRNA-based therapies. This article aims to provide a holistic view on HSP90-regulating ncRNAs for the development of novel therapeutic strategies to combat cancer.

Noncoding RNAs in diagnosis and prognosis of graft-versus-host disease (GVHD)

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a functional therapy for a plethora of hematologic malignancies and immune disorders. Graft-versus-host disease (GVHD), on the other hand, is one of the major complications ahead of a successful HSCT, contributing to transplant-associated morbidity and mortality. Notably, little is known about the underlying mechanism of this event; therefore, exploring precise biomarkers and uncovering the molecular pathogenesis of GVHD is valuable for early diagnosis and treatment optimization. Thanks to the advances in sequencing techniques, the noncoding sequences of the human genome-formerly considered "junk"-are now identified as functional molecules. Noncoding RNAs (ncRNA) control cellular responses by regulating gene expression, and previous studies have shown that these tiny molecules, especially microRNAs (miRNAs), can affect allogeneic T cell responses in both animal models and clinical experiments. The present study gives an overview of the functions of various miRNAs in regulating T cell responses in GVHD. We also provide an outlook on miRNAs and long noncoding RNAs (lncRNAs) potential role in GVHD with the hope of providing a future research direction for expanding their application as the sensitive and noninvasive diagnostic or prognostic biomarkers and also the promising therapeutic targets for improving outcomes after allogeneic HSCT.

The Novel Regulatory Role of the lncRNA–miRNA–mRNA Axis in Chronic Inflammatory Airway Diseases

Chronic inflammatory airway diseases, characterized by airway inflammation and airway remodelling, are increasing as a cause of morbidity and mortality for all age groups and races across the world. The underlying molecular mechanisms involved in chronic inflammatory airway diseases have not been fully explored. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have recently attracted much attention for their roles in the regulation of a variety of biological processes. A number of studies have confirmed that both lncRNAs and miRNAs can regulate the initiation and progression of chronic airway diseases by targeting mRNAs and regulating different cellular processes, such as proliferation, apoptosis, inflammation, migration, and epithelial–mesenchymal transition (EMT). Recently, accumulative evidence has shown that the novel regulatory mechanism underlying the interaction among lncRNAs, miRNAs and messenger RNAs (mRNAs) plays a critical role in the pathophysiological processes of chronic inflammatory airway diseases. In this review, we comprehensively summarized the regulatory roles of the lncRNA–miRNA–mRNA network in different cell types and their potential roles as biomarkers, indicators of comorbidities or therapeutic targets for chronic inflammatory airway diseases, particularly chronic obstructive pulmonary disease (COPD) and asthma.

Epigenetic Regulation in Kidney Transplantation

Kidney transplantation is a standard care for end stage renal disease, but it is also associated with a complex pathogenesis including ischemia-reperfusion injury, inflammation, and development of fibrosis. Over the past decade, accumulating evidence has suggested a role of epigenetic regulation in kidney transplantation, involving DNA methylation, histone modification, and various kinds of non-coding RNAs. Here, we analyze these recent studies supporting the role of epigenetic regulation in different pathological processes of kidney transplantation, i.e., ischemia-reperfusion injury, acute rejection, and chronic graft pathologies including renal interstitial fibrosis. Further investigation of epigenetic alterations, their pathological roles and underlying mechanisms in kidney transplantation may lead to new strategies for the discovery of novel diagnostic biomarkers and therapeutic interventions.

An Update of Long-Noncoding RNAs in Acute Kidney Injury

Acute kidney injury (AKI) is a global public health concern with high morbidity, mortality, and medical costs. Despite advances in medicine, effective therapeutic regimens for AKI remain limited. Long non-coding RNAs (lncRNAs) are a subtype of non-coding RNAs, which longer than 200 nucleotides and perform extremely diverse functions in biological processes. Recently, lncRNAs have emerged as promising biomarkers and key mediators to AKI. Meanwhile, existing research reveals that the aberrant expression of lncRNAs has been linked to major pathological processes in AKI, including the inflammatory response, cell proliferation, and apoptosis, via forming the lncRNA/microRNA/target gene regulatory axis. Following a comprehensive and systematic search of the available literature, 87 relevant papers spanning the years 2005 to 2021 were identified. This review aims to provide and update an overview of lncRNAs in AKI, and further shed light on their potential utility as AKI biomarkers and therapeutic targets.

Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Organ Transplantation

Organ transplantation is the most preferred treatment option for end-stage organ diseases; however, allograft rejection is the major hurdle in successful long-term transplant survival. In spite of developing better HLA matching and more effective immunosuppressive regimen, one-year graft survival has been increased by nearly 90% and the incidence of acute rejection by one-year post-transplantation has been decreased by 12.2% in the last decades, chronic allograft rejection has remained as one of the major obstacles to the long-lasting survival of the transplanted allograft. Therefore, seemingly preventing the allograft rejection and inducing immunological tolerance against transplanted allografts is one of the primary goals in transplantation research to enable long-lasting graft survival. Various mechanisms such as long noncoding RNAs (lncRNAs) have been proposed that induce immune tolerance by modulating the gene expression and regulating innate and adaptive immune responses during transplantation. Besides, because of involvement in regulating epigenetic, transcriptional, and post-translational mechanisms, lncRNAs could affect allograft status. Therefore, these molecules could be considered as the potential targets for prediction, prognosis, diagnosis, and treatment of graft rejection. It is suggested that the noninvasive predictive biomarkers hold promise to overcome the current limitations of conventional tissue biopsy in the diagnosis of rejection. Hence, this review aims to provide a comprehensive overview of lncRNAs and their function to facilitate diagnosis, prognosis, and prediction of the risk of graft rejection, and the suggestive therapeutic choices after transplantation.

High PIRCHE Scores May Allow Risk Stratification of Borderline Rejection in Kidney Transplant Recipients

Background

The diagnosis of borderline rejection (BLR) ranges from mild inflammation to clinically significant TCMR and is associated with an increased risk of allograft dysfunction. Currently, there is no consensus regarding its treatment due in part to a lack of biomarkers to identify cases with increased risk for immune-mediated injury.

Methods

We identified 60 of 924 kidney transplant recipients (KTRs) with isolated and untreated BLR. We analyzed the impact of predicted indirectly recognizable HLA epitopes (PIRCHE) score on future rejection, de novo DSA development, and recovery to baseline allograft function. Additionally, we compared the outcomes of different Banff rejection phenotypes.

Results

Total PIRCHE scores were significantly higher in KTRs with BLR compared to the entire study population (p=0.016). Among KTRs with BLR total PIRCHE scores were significantly higher in KTRs who developed TCMR/ABMR in follow-up biopsies (p=0.029). Notably, the most significant difference was found in PIRCHE scores for the HLA-A locus (p=0.010). PIRCHE scores were not associated with the development of de novo DSA or recovery to baseline allograft function among KTRs with BLR (p>0.05). However, KTRs under cyclosporine-based immunosuppression were more likely to develop de novo DSA (p=0.033) than those with tacrolimus, whereas KTRs undergoing retransplantation were less likely to recover to baseline allograft function (p=0.003).

Conclusions

High PIRCHE scores put KTRs with BLR at an increased risk for future TCMR/ABMR and contribute to improved immunological risk stratification. The benefit of anti-rejection treatment, however, needs to be evaluated in future studies.

Urinary Biomarkers for Kidney Allograft Injury

The current standard of serum creatinine and biopsy to monitor allograft health has many limitations. The most significant drawback of the current standard is the lack of sensitivity and specificity to allograft injuries, which are diagnosed only after significant damage to the allograft. Thus, it is of critical need to identify a biomarker that is sensitive and specific to the early detection of allograft injuries. Urine, as the direct renal ultrafiltrate that can be obtained noninvasively, directly reflects intrarenal processes in the allograft at greater accuracy than analysis of peripheral blood. We review transcriptomic, metabolomic, genomic, and proteomic discovery-based approaches to identifying urinary biomarkers for the noninvasive detection of allograft injuries, as well as the use of urine cell-free DNA in the QSant urine assay as a sensitive surrogate for the renal allograft biopsy for rejection diagnosis.

Long non-coding RNA OIP5-AS1 (Cyrano): A context-specific regulator of normal and disease processes

Long non-coding (lnc) RNAs have been implicated in a plethora of normal biological functions, and have also emerged as key molecules in various disease processes. OIP5-AS1, also commonly known by the alias Cyrano, is a lncRNA that displays broad expression across multiple tissues, with significant enrichment in particular contexts including within the nervous system and skeletal muscle. Thus far, this multifaceted lncRNA has been found to have regulatory functions in normal cellular processes including cell proliferation and survival, as well as in the development and progression of a myriad disease states. These widespread effects on normal and disease states have been found to be mediated through context-specific intermolecular interactions with dozens of miRNAs and proteins identified to date. This review explores recent studies to highlight OIP5-AS1's contextual yet pleiotropic roles in normal homeostatic functions as well as disease oetiology and progression, which may influence its utility in the generation of future theranostics.

Expanding the Non-Invasive Diagnosis of Acute Rejection in Kidney Transplants Through Detection of Donor-Derived DNA in Urine: Proof-of-Concept Study

Background

Approximately 10%-20% of kidney transplant (KT) recipients suffer from acute rejection (AR); thus, sensitive and accurate monitoring of allograft status is recommended. We evaluated the clinical utility of donor-derived DNA (dd-DNA) detection in the urine of KT recipients as a non-invasive means for diagnosing AR.

Methods

Urine samples serially collected from 39 KT recipients were tested for 39 single-nucleotide variant loci selected according to technical criteria (i.e., high minor allele frequency and low analytical error) using next-generation sequencing. The fraction of dd-DNA was calculated and normalized by the urine creatinine (UCr) level (%dd-DNA/UCr). The diagnostic performance of %dd-DNA/UCr for AR was assessed by ROC curve analysis.

Results

There was an increasing trend of %dd-DNA/UCr in the AR group before subsequent graft injury, which occurred before (median of 52 days) histological rejection. The serum creatinine (SCr) level differed significantly between the AR and non-AR groups at two and four months of follow-up, whereas %dd-DNA/UCr differed between the groups at six months of follow-up. The combination of %dd-DNA/UCr, SCr, and spot urine protein (UPtn)/UCr showed high discriminating power, with an area under the ROC curve of 0.93 (95% confidence interval: 0.81-1.00) and a high negative predictive value of 100.0%.

Conclusions

Although the dd-DNA-based test cannot eliminate the need for biopsy, the high negative predictive value of this marker could increase the prebiopsy probability of detecting treatable injury to make biopsy an even more effective diagnostic tool.

Emerging roles of long non-coding RNAs in allotransplant rejection

Allotransplantation has extensively been employed for managing end-stage organ failure and malignant tumors. Acute and chronic post-transplant rejections are major causes of late morbidity and mortality after allotransplantation. However, there are no objective diagnostic criteria and specific therapy for post-transplant rejections. Owing to key advances in high-throughput RNA sequencing techniques, a wealth of studies have disclosed that long noncoding RNA (lncRNA) expression increased or decreased evidently in biopsies, blood, plasma, urine and specific cells of rejecting patients, and the dysregulated lncRNAs affected the cellular functions and differentiation of the immune system. Hence, we present an overview of the functions of lncRNAs expressed in various immune cells related to allotransplant rejection. Moreover, our review explores the regulatory interplay of relevant lncRNAs and recipients with or without allograft rejection after solid organ transplantations or hematopoietic stem cell transplantation, then discuss whether these relevant lncRNAs can be molecular biomarkers for diagnosis and new therapeutic targets in the management of post-transplanted patients.

Transforming Growth Factor-β and Long Non-coding RNA in Renal Inflammation and Fibrosis

Renal fibrosis is one of the most characterized pathological features in chronic kidney disease (CKD). Progressive fibrosis eventually leads to renal failure, leaving dialysis or allograft transplantation the only clinical option for CKD patients. Transforming growth factor-β (TGF-β) is the key mediator in renal fibrosis and is an essential regulator for renal inflammation. Therefore, the general blockade of the pro-fibrotic TGF-β may reduce fibrosis but may risk promoting renal inflammation and other side effects due to the diverse role of TGF-β in kidney diseases. Long non-coding RNAs (lncRNAs) are RNA transcripts with more than 200 nucleotides and have been regarded as promising therapeutic targets for many diseases. This review focuses on the importance of TGF-β and lncRNAs in renal inflammation, fibrogenesis, and the potential applications of TGF-β and lncRNAs as the therapeutic targets and biomarkers in renal fibrosis and CKD are highlighted.

LncRNA EGOT/miR-211-5p Affected Radiosensitivity of Rectal Cancer by Competitively Regulating ErbB4

BACKGROUND/AIMS

Long non-coding ribonucleic acids (lncRNAs) are involved in the progression of cancers and affect the response to radiation therapy. This study was to investigate the mechanism of lncRNA EGOT in the radiosensitivity of rectal cancer.

METHODS

The mRNA expression of EGOT, miR-211-5p and ErbB4 in rectal cancer tissues and cells was detected by qRT-PCR. The protein expression of ErbB4 was detected by Western blot. Dual-luciferase reporter assay and ribonucleic acid immunoprecipitation (RIP) were used to confirm the interaction between EGOT and miR-211-5p or miR-211-5p and ErbB4. Transfection technology was used to down-regulate and up-regulate the expression of EGOT and miR-211-5p in rectal cancer cells, respectively. MTT, colony formation and flow cytometry were used to detect the effect of EGOT and miR-211-5p on proliferation, invasion, migration and apoptosis of rectal cancer cells.

RESULTS

The expression of EGOT was up-regulated in rectal cancer tissues and cells, and the expression of EGOT was related to the late stage of pathology. EGOT knockdown inhibited the proliferation and colony formation of rectal cancer cells and induced the apoptosis of rectal cancer cells. Moreover, EGOT knockdown was significantly enhanced the effects of radiotherapy on rectal cancer in vivo and in vitro. Furthermore, EGOT was found to serve as a sponge of miR-211-5p, and ErbB4 was a downstream target of miR-211-5p. EGOT enhanced the expression of ErbB4 by regulating miR-211-5p. MiR-211-5p inhibitor restored the effect of EGOT knockdown on the radiosensitivity of rectal cancer.

CONCLUSION

Down-regulation of EGOT could inhibit the growth of rectal cancer cells by regulating the miR-211-5p/ErbB4 axis and improve the radiosensitivity of rectal cancer cells. EGOT may be a new therapeutic target for rectal cancer.

The Functional Role of Long Non-coding RNA UCA1 in Human Multiple Cancers: a Review Study

In various cancers, high-grade tumor and poor survival rate in patients with upregulated lncRNAs UCA1 have been confirmed. Urothelial carcinoma associated 1 (UCA1) is an oncogenic non-coding RNA with a length of more than 200 nucleotides. The UCA1 regulate critical biological processes that are involved in cancer progression, including cancer cell growth, invasion, migration, metastasis, and angiogenesis. So It should not surprise that UCA1 overexpresses in variety of cancers type, including pancreatic cancer, ovarian cancer, gastric cancer, colorectal cancer, breast cancer, prostate cancer, endometrial cancer, cervical cancer, bladder cancer, adrenal cancer, hypopharyngeal cancer, oral cancer, gallbladder cancer, nasopharyngeal cancer, laryngeal cancer, osteosarcoma, esophageal squamous cell carcinoma, renal cell carcinoma, cholangiocarcinoma, leukemia, glioma, thyroid cancer, medulloblastoma, hepatocellular carcinoma and multiple myeloma. In this article, we review the biological function and regulatory mechanism of UCA1 in several cancers and also, we will discuss the potential of its as cancer biomarker and cancer treatment.

RNA-seq of human T cells after hematopoietic stem cell transplantation identifies Linc00402 as a regulator of T cell alloimmunity

Mechanisms governing allogeneic T cell responses after solid organ and allogeneic hematopoietic stem cell transplantation (HSCT) are incompletely understood. To identify lncRNAs that regulate human donor T cells after clinical HSCT, we performed RNA sequencing on T cells from healthy individuals and donor T cells from three different groups of HSCT recipients that differed in their degree of major histocompatibility complex (MHC) mismatch. We found that lncRNA differential expression was greatest in T cells after MHC-mismatched HSCT relative to T cells after either MHC-matched or autologous HSCT. Differential expression was validated in an independent patient cohort and in mixed lymphocyte reactions using ex vivo healthy human T cells. We identified Linc00402, an uncharacterized lncRNA, among the lncRNAs differentially expressed between the mismatched unrelated and matched unrelated donor T cells. We found that Linc00402 was conserved and exhibited an 88-fold increase in human T cells relative to all other samples in the FANTOM5 database. Linc00402 was also increased in donor T cells from patients who underwent allogeneic cardiac transplantation and in murine T cells. Linc00402 was reduced in patients who subsequently developed acute graft-versus-host disease. Linc00402 enhanced the activity of ERK1 and ERK2, increased FOS nuclear accumulation, and augmented expression of interleukin-2 and Egr-1 after T cell receptor engagement. Functionally, Linc00402 augmented the T cell proliferative response to an allogeneic stimulus but not to a nominal ovalbumin peptide antigen or polyclonal anti-CD3/CD28 stimulus. Thus, our studies identified Linc00402 as a regulator of allogeneic T cell function.

Identification of the candidate lncRNA biomarkers for acute kidney injury: a systematic review and meta-analysis

Background: This meta-analysis aims to summarize the studies of lncRNAs dysregulation in individual acute kidney injury (AKI) and identify the potential lncRNA biomarkers of AKI.Research design and methods: We systematically searched four databases to identify the lncRNA expression studies of AKI in animal models and patients. The lncRNAs expression data were extracted from 38 included studies, and lncRNA vote-counting strategy was applied to identify significant lncRNA biomarkers. The predicted targets of lncRNA biomarkers were obtained by searching Co-LncRNA, RBPmap, and LncBase v.2. Further, GO enrichment analysis and KEGG pathway analysis were performed.Results: We recognized a significant lncRNA signature of 21 up-regulated and 11 down-regulated lncRNAs, among which TapSAKI, XIST, MALAT1, CASC2, and HOXA-AS2 were dysregulated both in AKI rodent models and patients. About 28.0% of these lncRNAs mainly exist in the nucleus, which was also the most enriched GO cellular components term. The most relevant GO terms in biological process and molecular function associated with these lncRNAs were splicing, processing, and binding of mRNA.Conclusions: The present meta-analysis identified 31 significant dysregulated lncRNAs from 38 studies. TapSAKI, XIST, MALAT1, CASC2, and HOXA-AS2 were considered as the potential predictive biomarkers and therapeutic targets of AKI.

Long non-coding RNAs: A double-edged sword in aging kidney and renal disease

Aging as one of intrinsic biological processes is a risk factor for many chronic diseases. Kidney disease is a global problem and health care burden worldwide. The diagnosis of kidney disease is currently based on serum creatinine and urea levels. Novel biomarkers may improve diagnostic accuracy, thereby allowing early prevention and treatment. Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and could bind DNA, RNA and protein. Emerging evidence has demonstrated that lncRNAs played an important role in all stages of kidney disease. To date, only some lncRNAs were well identified and characterized, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains undefined. In this review, we summarized the lncRNA expression profiling of large-scale identified lncRNAs on kidney diseases including acute kidney injury, chronic kidney disease, diabetic nephropathy and kidney transplantation. We further discussed a number of annotated lncRNAs linking with complex etiology of kidney diseases. Finally, several lncRNAs were highlighted as diagnostic biomarkers and therapeutic targets. Targeting lncRNAs may represent a precise therapeutic strategy for progressive renal fibrosis.

Urinary Biomarkers for Diagnosis and Prediction of Acute Kidney Allograft Rejection: A Systematic Review

Noninvasive tools for diagnosis or prediction of acute kidney allograft rejection have been extensively investigated in recent years. Biochemical and molecular analyses of blood and urine provide a liquid biopsy that could offer new possibilities for rejection prevention, monitoring, and therefore, treatment. Nevertheless, these tools are not yet available for routine use in clinical practice. In this systematic review, MEDLINE was searched for articles assessing urinary biomarkers for diagnosis or prediction of kidney allograft acute rejection published in the last five years (from 1 January 2015 to 31 May 2020). This review follows the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines. Articles providing targeted or unbiased urine sample analysis for the diagnosis or prediction of both acute cellular and antibody-mediated kidney allograft rejection were included, analyzed, and graded for methodological quality with a particular focus on study design and diagnostic test accuracy measures. Urinary C-X-C motif chemokine ligands were the most promising and frequently studied biomarkers. The combination of precise diagnostic reference in training sets with accurate validation in real-life cohorts provided the most relevant results and exciting groundwork for future studies.

Role of novel biomarkers in kidney transplantation

Clinical application of biomarkers is an integral component of transplant care. Clinicians and scientists alike are in search of better biomarkers than the current serologic (serum creatinine, donor-specific antibodies), urine-derived (urinalysis, urine protein), and histologic ones we now use. The science behind recent biomarker discovery spans across multiple molecular biologic disciplines, including transcriptomics, proteomics, and metabolomics. Innovative methodology and integration of basic and clinical approaches have allowed researchers to unearth molecular phenomena preceding clinical disease. Biomarkers can be classified in several ways. In this review, we have classified them via their origin and outcome: Primarily immunologic, i.e., representative of immune regulation and dysfunction and non-immunologic, pertaining to delayed graft function, cardiovascular events/mortality, infection, malignancy, post-transplant diabetes, graft, and patient survival. Novel biomarker uses to guide the diagnosis and management of transplant-related outcomes is a promising area of research. However, the use of biomarkers to predict outcomes after kidney transplantation is not well studied. In this review, we summarize the recent studies illustrating biomarker use and transplant outcomes.

Long noncoding RNA-GAS5 retards renal fibrosis through repressing miR-21 activity

BACKGROUND/AIMS

Long noncoding RNA (lncRNA) is a large and diverse class of RNA molecules, and has received widespread attention for its role in the regulation of various biological processes, including stem cell transformation, neurological disease, and tumorigenesis. However, the role of lncRNA in renal fibrosis remains unclear.

METHODS

We investigated the expression of lncRNA-GAS5 by quantitative real-time polymerase chain reaction (PCR) or fluorescence in situ hybridization in chronic kidney disease (CKD) by designing both in vivo and in vitro experiments. With over-expression of GAS5 or knockdown GAS5, miR-21 and its downstream target genes were tested using quantitative real-time PCR or western blots. Mutants of miR-21 were designed and transfected in cells. GAS5 in the plasma and urine of patients with CKD was measured by quantitative real-time PCR.

RESULTS

In normal rats, GAS5 was predominantly expressed in renal tubular epithelial cells. GAS5 induction was significantly reduced in obstructive kidneys at 7 days after unilateral ureteral obstruction. In vitro, GAS5 was inhibited in cultured normal rat renal proximal tubular cells (NRK-52E) after incubation with transforming growth factor β at 24 h. Ectopic over-expression of GAS5 repressed extracellular matrix (ECM) levels such as collagen type III and fibronectin 1. Conversely, knockdown GAS5 augmented ECM accumulation in NRK-52E cells. GAS5 suppressed miR-21 activity in a direct and mechanistic manner. It subsequently turned off the expression of miR-21 downstream target genes, matrix metallopeptidase 2 and 9, which resulted in excessive ECM synthesis and deposition. Of note, plasma GAS5 was positively correlated with estimated glomerular filtration rate levels in CKD patients with different etiologies while urine GAS5 was negatively correlated.

CONCLUSION

Activation of lncRNA-GAS5 attenuates kidney fibrosis by modulating miR-21 activity and may serve as a surrogate biomarker in monitoring CKD progression.

Emerging role of lncRNAs in renal fibrosis

Fibrosis is the final common pathological feature of a wide variety of chronic kidney disease (CKD). However, an understanding of the mechanisms underlying the development of renal fibrosis remains challenging and controversial. As the current focus of molecular research, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular noncoding RNAs (circRNAs), have powerful and abundant biological functions, which essentially makes them mediators of the physiological and pathological processes of various system diseases. The role of ncRNAs in renal fibrosis has also received great attention in recent years, but most research has mainly focused on miRNAs. In fact, although a large number of studies of lncRNAs have emerged recently, the role these molecules play in renal fibrosis haven't been fully understood till now. Thus, this review discusses the discovery of lncRNAs and their biological functions in different types of renal fibrosis, as well as the imminent applications of these findings in clinical use. Undoubtedly, in the future, further understanding of the function of all types of lncRNAs will reveal large breakthroughs in the treatment of renal fibrosis.

Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection

Introduction

Peripheral blood (PB) molecular patterns characterizing the different effector immune pathways driving distinct kidney rejection types remain to be fully elucidated. We hypothesized that transcriptome analysis using RNA sequencing (RNAseq) in samples of kidney transplant patients would enable the identification of unique protein-coding and noncoding genes that may be able to segregate different rejection phenotypes.

Methods

We evaluated 37 biopsy-paired PB samples from the discovery cohort, with stable (STA), antibody-mediated rejection (AMR), and T cell-mediated rejection (TCMR) by RNAseq. Advanced machine learning tools were used to perform 3-way differential gene expression analysis to identify gene signatures associated with rejection. We then performed functional in silico analysis and validation by Fluidigm (San Francisco, CA) in 62 samples from 2 independent kidney transplant cohorts.

Results

We found 102 genes (63 coding genes and 39 noncoding genes) associated with AMR (54 upregulated), TCMR (23 upregulated), and STA (25 upregulated) perfectly clustered with each rejection phenotype and highly correlated with main histologic lesions (ρ = 0.91). For the genes associated with AMR, we found enrichment in regulation of endoplasmic reticulum stress, adaptive immunity, and Ig class-switching. In the validation, we found that the SIGLEC17P pseudogene and 9 SIGLEC17P-related coding genes were highly expressed among AMR but not in TCMR and STA samples.

Conclusions

This analysis identifies a critical gene signature in PB in kidney transplant patients undergoing AMR, sufficient to differentiate them from patients with TCMR and immunologically quiescent kidney allografts. Our findings provide the basis for new studies dissecting the role of noncoding genes in the pathophysiology of kidney allograft rejection and their potential value as noninvasive biomarkers of the rejection process.

Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Renal Fibrosis

Many studies have made clear that most of the genome is transcribed into noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), both of which can affect different cell features. LncRNAs are long heterogeneous RNAs that regulate gene expression and a variety of signaling pathways involved in cellular homeostasis and development. Several studies have demonstrated that lncRNA is an important class of regulatory molecule that can be targeted to change cellular physiology and function. The expression or dysfunction of lncRNAs is closely related to various hereditary, autoimmune, and metabolic diseases, and tumors. Specifically, recent work has shown that lncRNAs have an important role in kidney pathogenesis. The effective roles of lncRNAs have been recognized in renal ischemia, injury, inflammation, fibrosis, glomerular diseases, renal transplantation, and renal-cell carcinoma. The present review focuses on the emerging role and function of lncRNAs in the pathogenesis of kidney inflammation and fibrosis as novel essential regulators. Although lncRNAs are important players in the initiation and progression of many pathological processes, their role in renal fibrosis remains unclear. This review summarizes the current understanding of lncRNAs in the pathogenesis of kidney fibrosis and elucidates the potential role of these novel regulatory molecules as therapeutic targets for the clinical treatment of kidney inflammation and fibrosis.

LncRNAs adjacent to pepsinogen C in gastric diseases and diagnostic efficiencies of joint detection in gastric diseases

Aims: We aimed to explore diagnostic efficiencies of long noncoding RNAs (lncRNAs) adjacent to PGC combining with sPGC and anti-Helicobacter pylori IgG in identifying GC (gastric cancer) and precancerous disease. Patients & methods: A total of 265 patients with different gastric diseases were collected. ELISA was to detect sPGC and anti-H. pylori IgG. LncRNAs was determined by qRT-PCR. Results: The area under receiver operating characteristic curve of lncRNAs in discriminating GC+AG (atrophic gastritis) and superficial gastritis (SG) were 79.0, 68.1 and 75.9%. The diagnostic performance of lncRNAs with sPGC had increasing trends in distinguishing GC from non-GC, SG from GC+AG comparing with lncRNAs, with no statistic difference. Diagnosis efficacies of lncRNAs with anti-H. pylori IgG improved dramatically. Conclusions: Serum lncRNAs could distinguish GC, AG and SG. Diagnosis efficiencies of lncRNAs with sPGC and anti-H. pylori-IgG could be improved.

Diagnostic, Prognostic, and Therapeutic Value of Non-Coding RNA Expression Profiles in Renal Transplantation

End-stage renal disease is a public health problem responsible for millions of deaths worldwide each year. Although transplantation is the preferred treatment for patients in need of renal replacement therapy, long-term allograft survival remains challenging. Advances in high-throughput methods for large-scale molecular data generation and computational analysis are promising to overcome the current limitations posed by conventional diagnostic and disease classifications post-transplantation. Non-coding RNAs (ncRNAs) are RNA molecules that, despite lacking protein-coding potential, are essential in the regulation of epigenetic, transcriptional, and post-translational mechanisms involved in both health and disease. A large body of evidence suggests that ncRNAs can act as biomarkers of renal injury and graft loss after transplantation. Hence, the focus of this review is to discuss the existing molecular signatures of non-coding transcripts and their value to improve diagnosis, predict the risk of rejection, and guide therapeutic choices post-transplantation.

Comprehensive Analysis of Aberrantly Expressed Profiles of lncRNAs and miRNAs with Associated ceRNA Network in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma

Lung cancer (LC) continues to be the leading cause of cancer-related deaths worldwide and the prognosis remains poor worldwide. At present, the long non-coding RNAs (lncRNAs) was considered as a part of competing endogenous RNA (ceRNA) network act as natural microRNA (miRNA) sponges to regulate protein-coding gene expression. However, functional roles of lncRNA-mediated ceRNAs in LC are insufficiently understood. To classify the specific mechanism of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), we comprehensively compared the expression profiles of mRNAs, lncRNAs and miRNAs obtained from 509 LUAD, 473 LUSC tissues and 49 adjacent non-cancerous lung tissues, based on The Cancer Genome Atlas (TCGA). After screening for differently expressed (DE) mRNAs, DEmiRNAs, DElncRNAs and weighted gene co-expression network analysis (WGCNA) (|log2FC| > 2.0 and an adjusted p value <0.05), a total of 4478 DEmRNAs, 526 DElncRNAs and 75 DEmiRNAs in LUAD, while 6237 DEmRNAs, 843 DElncRNAs and 117 DEmiRNAs in LUSC were discovered. Interaction (PPI) network analysis was performed to identify 656 nodes and 2987 edges (minimum required interaction score > 0.9), as well as 8 different protein-protein interactions. Gene ontology (GO) analysis mainly associated with cell proliferation. KEGG pathway enrichment analyses most partly associated with metabolism pathway and cytokine-cytokine receptor interaction. Finally, the dysregulated lncRNA-miRNA-ceRNA network was constructed based on correlation analyses and a total of 62 dysregulated lncRNAs, 28 DEmRNAs and 18 DEmiRNAs were involved. The most significant lncRNAs included DElncRNAs, LINC00641 and AC004947.2, miRNAs included miR-6860, miR-1285-3p, miR-767-3p and miR-7974, mRNAs included MAP3K3, FGD3 and ATP1B2. Then we analyzed and described the potential characteristics of biological function and pathological roles of the LUAD and LUSC ceRNA co-regulatory network. Our findings revealed ceRNA network will be beneficial for promoting the understanding of lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of LUAD and LUSC.

Identifying 4 Novel lncRNAs as Potential Biomarkers for Acute Rejection and Graft Loss of Renal Allograft

Acute rejection (AR) after kidney transplant is one of the major obstacles to obtain ideal graft survival. Reliable molecular biomarkers for AR and renal allograft loss are lacking. This study was performed to identify novel long noncoding RNAs (lncRNAs) for diagnosing AR and predicting the risk of graft loss. The several microarray datasets with AR and nonrejection specimens of renal allograft downloaded from Gene Expression Omnibus database were analyzed to screen differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). Univariate and multivariate Cox regression analyses were used to identify optimal prognosis-related DElncRNAs for constructing a risk score model. 39 common DElncRNAs and 185 common DEmRNAs were identified to construct a lncRNA-mRNA regulatory relationship network. DElncRNAs were revealed to regulate immune cell activation and proliferation. Then, 4 optimal DElncRNAs, ATP1A1-AS1, CTD-3080P12.3, EMX2OS, and LINC00645, were selected from 17 prognostic DElncRNAs to establish the 4-lncRNA risk score model. In the training set, the high-risk patients were more inclined to graft loss than the low-risk patients. Time-dependent receiver operating characteristics analysis revealed the model had good sensitivity and specificity in prediction of 1-, 2-, and 3-year graft survival after biopsy (AUC = 0.891, 0.836, and 0.733, respectively). The internal testing set verified the result well. Gene set enrichment analysis which expounded NOD-like receptor, the Toll-like receptor signaling pathways, and other else playing important role in immune response was enriched by the 4 lncRNAs. Allograft-infiltrating immune cells analysis elucidated the expression of 4 lncRNAs correlated with gamma delta T cells and eosinophils, etc. Our study identified 4 novel lncRNAs as potential biomarkers for AR of renal allograft and constructed a lncRNA-based model for predicting the risk of graft loss, which would provide new insights into mechanisms of AR.

Long noncoding RNA MIAT: A potential role in the diagnosis and mediation of acute myocardial infarction

The long noncoding RNA myocardial infarction associated transcript (MIAT) has been shown to be a risk allele for myocardial infarction in a previous study. However, there is still controversy about whether MIAT can be used as a biomarker for acute myocardial infarction (AMI). Peripheral blood from patients with AMI and non‑AMI patients was collected to detect the expression levels of MIAT by reverse transcription‑quantitative PCR. Correlation analysis and receiver operating characteristic (ROC) curve analysis were performed to calculate the diagnostic value of MIAT. A rat AMI model was established to detect the expression of MIAT in plasma and cardiac samples. Neonatal rat cardiomyocytes were isolated and exposed to hypoxia, and MIAT small interfering RNAs were transfected into cells to test the expression levels of MIAT and to perform apoptosis‑related assays. The results showed that the plasma levels of MIAT were significantly increased in patients with AMI compared with non‑AMI patients. Correlation analysis showed that MIAT was positively associated with creatine kinase‑MB and cardiac troponin T (cTnT). ROC analysis indicated that MIAT had the same diagnostic value as cTnT. In addition, MIAT was expressed at low levels in the normal rat heart and was highly expressed in AMI hearts. Knockdown of MIAT significantly inhibited cardiomyocyte apoptosis. The present study demonstrated that MIAT may act as a novel potential biomarker for the diagnosis of AMI.

Endogenous intronic antisense long non-coding RNA, MGAT3-AS1, and kidney transplantation

β-1,4-mannosylglycoprotein 4-β-N-acetylglucosaminyltransferase (MGAT3) is a key molecule for the innate immune system. We tested the hypothesis that intronic antisense long non-coding RNA, MGAT3-AS1, can predict delayed allograft function after kidney transplantation. We prospectively assessed kidney function and MGAT3-AS1 in 129 incident deceased donor kidney transplant recipients before and after transplantation. MGAT3-AS1 levels were measured in mononuclear cells using qRT-PCR. Delayed graft function was defined by at least one dialysis session within 7 days of transplantation. Delayed graft function occurred in 22 out of 129 transplant recipients (17%). Median MGAT3-AS1 after transplantation was significantly lower in patients with delayed graft function compared to patients with immediate graft function (6.5 × 10⁻⁶, IQR 3.0 × 10⁻⁶ to 8.4 × 10⁻⁶; vs. 8.3 × 10⁻⁶, IQR 5.0 × 10⁻⁶ to 12.8 × 10⁻⁶; p < 0.05). The median preoperative MGAT3-AS1 was significantly lower in kidney recipients with delayed graft function (5.1 × 10⁻⁶, IQR, 2.4 × 10⁻⁶ to 6.8 × 10⁻⁶) compared to recipients with immediate graft function (8.9 × 10⁻⁶, IQR, 6.8 × 10⁻⁶ to 13.4 × 10⁻⁶; p < 0.05). Receiver-operator characteristics showed that preoperative MGAT3-AS1 predicted delayed graft function (area under curve, 0.83; 95% CI, 0.65 to 1.00; p < 0.01). We observed a positive predictive value of 0.57, and a negative predictive value of 0.95. Long non-coding RNA, MGAT3-AS1, indicates short-term outcome in patients with deceased donor kidney transplantation.

LncRNAs as Regulators of Autophagy and Drug Resistance in Colorectal Cancer

Colorectal cancer (CRC) is a common malignancy with 1. 8 million cases in 2018. Autophagy helps to maintain an adequate cancer microenvironment in order to provide nutritional supplement under adverse conditions such as starvation and hypoxia. Additionally, most of the cases of CRC are unresponsive to chemotherapy, representing a significant challenge for cancer therapy. Recently, autophagy induced by therapy has been shown as a unique mechanism of resistance to anticancer drugs. In this regard, long non-coding RNAs (lncRNAs) analysis are important for cancer detection, progression, diagnosis, therapy response, and prognostic values. With increasing development of quantitative detection techniques, lncRNAs derived from patients' non-invasive samples (i.e., blood, stools, and urine) has become into a novel approach in precision oncology. Tumorspecific GAS5, HOTAIR, H19, and MALAT are novels CRC related lncRNAs detected in patients. Nonetheless, the effect and mechanism of lncRNAs in cancer autophagy and chemoresistance have not been extensively characterized. Chemoresistance and autophagy are relevant for cancer treatment and lncRNAs play a pivotal role in resistance acquisition for several drugs. LncRNAs such as HAGLROS, KCNQ1OT1, and H19 are examples of lncRNAs related to chemoresistance leaded by autophagy. Finally, clinical implications of lncRNAs in CRC are relevant, since they have been associated with tumor differentiation, tumor size, histological grade, histological types, Dukes staging, degree of differentiation, lymph node metastasis, distant metastasis, recurrent free survival, and overall survival (OS).

Long Non-coding RNA Expression Profiling in Biopsy to Identify Renal Allograft at Risk of Chronic Damage and Future Graft Loss

The loss of allograft from chronic damage is still the major risk that renal transplant recipients face today. Biomarkers for early detection of chronic damage are needed to improve the long-term graft survival. This study aimed to identify long non-coding RNA (lncRNA) biomarkers associated with chronic damage and graft loss after renal transplantation. Gene Expression Omnibus (GEO) datasets including GSE57387 (n = 101), GSE21374 (n = 282), and GSE25902 (n = 24) from three high-quality studies were analyzed. By repurposing the publicly available array-based data coupled with Affymetrix Human Exon 1.0 ST and Human U133 Plus 2.0 arrays, we obtained expression profiles of 11323 and 3383 lncRNAs in biopsies after renal transplantation, respectively. The logistic regression model and Cox regression model were applied to identify lncRNAs associated with chronic damage and graft survival. High AC093673.5 expression was identified as significantly associated with the three endpoints including chronic damage, progressive chronic histological damage, and graft failure across these three datasets. A six-lncRNA signature was created to predict renal allograft at risk of chronic damage with a high predictive ability (AUC = 0.94). Gene set enrichment analysis (GSEA) indicated that our lncRNA signature was related with allograft rejection and immunity. Our study highlights the importance of lncRNAs in chronic graft damage and allograft loss, supporting their potential role as prognosis biomarkers.

Circular RNAs in Urine of Kidney Transplant Patients with Acute T Cell-Mediated Allograft Rejection

BACKGROUND

Circular RNAs (circRNAs) have recently been described as novel noncoding regulators of gene expression. They are detectable in the blood of patients with acute kidney injury. We tested whether circRNAs were present in urine and could serve as new predictors of outcome in renal transplant patients with acute rejection.

METHODS

A global circRNA expression analysis using RNA from urine of patients with acute T cell-mediated renal allograft rejection and control transplant patients was performed. Dysregulated circRNAs were confirmed in a cohort of 62 patients with acute rejection, 10 patients after successful antirejection therapy, 18 control transplant patients without rejection, and 13 stable transplant patients with urinary tract infection.

RESULTS

A global screen revealed several circRNAs to be altered in urine of patients with acute rejection. Concentrations of 2 circRNAs including hsa_circ_0001334 and hsa_circ_0071475 were significantly increased. These were validated in the whole cohort of patients. hsa_circ_0001334 was upregulated in patients with acute rejection compared with controls. Concentrations of hsa_circ_0001334 normalized in patients with acute rejection following successful antirejection therapy. hsa_circ_0001334 was associated with higher decline in glomerular filtration rate 1 year after transplantation.

CONCLUSIONS

CircRNA concentrations are significantly dysregulated in patients with acute rejection at subclinical time points. Urinary hsa_circ_0001334 is a novel biomarker of acute kidney rejection, identifying patients with acute rejection and predicting loss of kidney function.

Noncoding RNAs in acute kidney injury

Acute kidney injury (AKI) is an important health issue concerning ∼50% of patients treated in intensive care units. AKI mainly occurs after sepsis, acute ischemia, nephrotoxicity, or hypoxia and leads to severe damage of the kidney and to an increased risk of mortality. The diagnosis of AKI is currently based on creatinine urea levels and diuresis. Yet, novel markers may improve the accuracy of this diagnosis at an early stage of the disease, thereby allowing early prevention and therapy, ultimately leading to a reduction in the need for renal replacement therapy and decreased mortality. Non-protein-coding RNAs or noncoding RNAs are central players in development and disease. They are important regulatory molecules that allow a fine-tuning of gene expression and protein synthesis. This regulation is necessary to maintain homeostasis, and its dysregulation is often associated with disease development. Noncoding RNAs are present in the kidney and in body fluids and their expression is modulated during AKI. This review article assembles the current knowledge of the role of noncoding RNAs, including microRNAs, long noncoding RNAs and circular RNAs, in the pathogenesis of AKI. Their potential as biomarkers and therapeutic targets as well as the challenges to translate research findings to clinical application are discussed. Although microRNAs have entered clinical testing, preclinical and clinical trials are needed before long noncoding RNAs and circular RNAs may be considered as useful biomarkers or therapeutic targets of AKI.

Expression analysis of long non-coding RNAs in a renal ischemia-reperfusion injury model

PURPOSE

To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model.

METHODS

Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases.

RESULTS

Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R.

CONCLUSION

Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.

Non-coding RNAs in kidney injury and repair

Acute kidney injury (AKI) is a major kidney disease featured by a rapid decline of renal function. Pathologically, AKI is characterized by tubular epithelial cell injury and death. Besides its acute consequence, AKI contributes critically to the development and progression of chronic kidney disease (CKD). After AKI, surviving tubular cells regenerate to repair. Normal repair restores tubular integrity, while maladaptive or incomplete repair results in renal fibrosis and eventually CKD. Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins, which mainly include microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and tRNAs. Accumulating evidence suggests that ncRNAs play important roles in kidney injury and repair. In this review, we summarize the recent advances in the understanding of the roles of ncRNAs, especially miRNAs and lncRNAs in kidney injury and repair, discuss the potential application of ncRNAs as biomarkers of AKI as well as therapeutic targets for treating AKI and impeding AKI-CKD transition, and highlight the future research directions of ncRNAs in kidney injury and repair.

Analysis of long noncoding RNAs for acute rejection and graft outcome in kidney transplant biopsies

AIM

To analyse long noncoding RNAs (lncRNA) in kidney transplant biopsies.

METHODS

Using a data mining approach, we constructed expression profiles in kidney transplant cohorts (n = 1105) from Gene Expression Omnibus. Integrative analysis of the lncRNAs with acute rejection (AR), T-cell-mediated acute rejection (TCMR) and graft loss were performed.

RESULTS

Six lncRNAs were identified as are associated with AR in the training and validating datasets, and with a risk score was generated with 3-lncRNAs that were predictive of graft loss (AUC = 0.73). MIR155HG is associated with AR, TCMR and graft loss. Plus it might be involved in several graft rejection and immune associated pathways.

CONCLUSION

Understanding the role of lncRNAs in AR and graft outcome in kidney transplant biopsies needs to be further investigated.

The Long Noncoding RNA MALAT1 Induces Tolerogenic Dendritic Cells and Regulatory T Cells via miR155/Dendritic Cell-Specific Intercellular Adhesion Molecule-3 Grabbing Nonintegrin/IL10 Axis

By shaping T cell immunity, tolerogenic dendritic cells (tDCs) play critical roles in the induction of immune tolerance after transplantation. However, the role of long noncoding RNAs (lncRNAs) in the function and immune tolerance of dendritic cells (DCs) is largely unknown. Here, we found that the lncRNA MALAT1 is upregulated in the infiltrating cells of tolerized mice with cardiac allografts and activated DCs. Functionally, MALAT1 overexpression favored a switch in DCs toward a tolerant phenotype. Mechanistically, ectopic MALAT1 promoted dendritic cell-specific intercellular adhesion molecule-3 grabbing nonintegrin (DC-SIGN) expression by functioning as an miR155 sponge, which is essential for the tolerogenic maintenance of DCs and the DC-SIGN-positive subset with more potent tolerogenic ability. The adoptive transfer of MALAT1-overexpressing DCs promoted cardiac allograft survival and protected from the development of experimental autoimmune myocarditis, accompanied with increasing antigen-specific regulatory T cells. Therefore, overexpressed MALAT1 induces tDCs and immune tolerance in heart transplantation and autoimmune disease by the miRNA-155/DC-SIGH/IL10 axis. This study highlights that the lncRNA MALAT1 is a novel tolerance regulator in immunity that has important implications in settings in which tDCs are preferred.

Novel non-invasive biomarkers diagnostic of acute rejection in renal transplant recipients: A systematic review

BACKGROUND AND OBJECTIVES

Acute rejection is a significant complication detrimental to kidney transplant function. Current accepted means of diagnosis is percutaneous renal biopsy, a costly and invasive procedure. There is an urgent need to detect and validate non-invasive biomarkers capable of replacing the biopsy.

DESIGN, SETTING, PARTICIPANTS AND MEASUREMENTS

Comprehensive literature searches of Medline, EMBASE and Cochrane Central Register of Controlled Trials databases were performed. Eligible studies were included as per inclusion criteria and assessed for quality using the GRADE quality of evidence tool. Outcomes evaluated included biomarker diagnostic performance, number of patients/samples, mean age and gender ratio, immunosuppression regime, in addition to clinical applications of the biomarker(s) tested. PRISMA guidelines were followed. Where possible, statistical analysis of comparative performance data was performed.

RESULTS

23 studies were included in this review, including 19 adult, 3 paediatric and 1 mixed studies. A total of 2858 participants and 50 candidate non-invasive tests were identified. Sensitivity, specificity and area under the curve performance values ranged 36%-100%, 30%-100% and 0.55-0.98, respectively.

CONCLUSIONS

Although larger, more robust multi-centre validation studies are needed before non-invasive biomarkers can replace the biopsy, numerous candidate tests have demonstrated significant promise for various facets of postoperative management. Suggested uses include: ruling out patients with a low risk of acute rejection to avoid the need for biopsy, non-invasive testing where the biopsy is contraindicated and a prompt diagnosis is needed, and integration into a serial blood monitoring protocol in conjunction with serum creatinine.

The Circular RNA ciRs-126 Predicts Survival in Critically Ill Patients With Acute Kidney Injury

Introduction

Circular RNAs (circRNAs) have recently been described as novel noncoding regulators of gene expression. They might have an impact on microRNA expression by their sponging activity. The detectability in blood of these RNA transcripts has been demonstrated in patients with cancer and cardiovascular disease. We tested the hypothesis that circulating circRNAs in blood of critically ill patients with acute kidney injury (AKI) at inception of renal replacement therapy may also be dysregulated and associated with patient survival.

Methods

We performed a global circRNA expression analysis using RNA isolated from blood of patients with AKI as well as controls. This global screen revealed several dysregulated circRNAs in patients with AKI. Most highly increased circRNA-array−based transcripts as well as expression of the circRNA target miR-126-5p were confirmed in blood of 109 patients with AKI, 30 age-matched healthy controls, 25 critically ill non-AKI patients, and 20 patients on maintenance hemodialysis by quantitative real-time polymerase chain reaction.

Results

Circulating concentrations of 3 novel circRNAs were amplified in blood of patients with AKI and in controls. Circular RNA sponge of miR-126 (or ciRs-126) was most highly altered compared to healthy controls and disease controls (fold change of 52.1). ciRs-126 was shown to bioinformatically sponge miR-126-5p, which was found to be highly suppressed in AKI patients and hypoxic endothelial cells. Cox regression and Kaplan−Meier curve analysis revealed ciRs-126 as an independent predictor of 28-day survival (P < 0.01).

Conclusion

Circulating concentrations of circRNAs in patients with AKI are detectable. ciRs-126 may potentially sponge miR-126-5p and acts as a predictor of mortality in this patient cohort.

Urinary Biomarkers for Chronic Kidney Disease with a Focus on Gene Transcript

Objective:

In the upcoming era of precision medicine, searching for the early, noninvasive biomarkers has been the cornerstone and major challenge in the management of chronic kidney disease (CKD). Urine contains rich biological information which could be the ideal source for noninvasive biomarkers of CKD. This review will discuss the recent advance in urinary biomarker.

Data Sources:

This review was based on data in articles published in the PubMed databases up to June 20, 2017, with the following keywords: “Chronic kidney disease”, “Biomarker”, and “Urine”.

Study Selection:

Original articles and important reviews on urinary biomarker were selected for this review.

Results:

Urinary biomarker studies of CKD mainly focused on urine sediment, supernatant, and urinary extracellular vesicles. The gene transcript (microRNA [miRNA], messenger RNA [mRNA]) biomarkers have been recently shown with diagnostic potential for CKD reflecting kidney function and histological change. However, challenges regarding technique and data analysis need to be resolved before translation to clinic.

Conclusions:

Different fractions of urine contain rich information for biomarker discovery, among which urine (extracellular vesicles) mRNA, miRNA, might represent promising biomarker for CKD.

The use of long non-coding RNAs as prognostic biomarkers and therapeutic targets in prostate cancer

Prostate cancer is the most common cancer in men and the second leading cause of cancer-related deaths. The most used biomarker to detect prostate cancer is Prostate Specific Antigen (PSA), whose levels are measured in serum. However, it has been recently established that molecular markers of cancer should not be based solely on genes and proteins but should also reflect other genomic traits; long non-coding RNAs (lncRNAs) serve this purpose. lncRNAs are transcripts of >200 bases that do not encode proteins and that have been shown to display abnormal expression profiles in different types of cancer. Experimental studies have highlighted lncRNAs as potential biomarkers for prognoses and treatments in patients with different types of cancer, including prostate cancer, where the PCA3 lncRNA is currently used as a diagnostic tool and management strategy. With the development of genomic technologies, particularly next-generation sequencing (NGS), several other lncRNAs have been linked to prostate cancer and are currently under validation for their medical use. In this review, we will discuss different strategies for the discovery of novel lncRNAs that can be evaluated as prognostic biomarkers, the clinical impact of these lncRNAs and how lncRNAs can be used as potential therapeutic targets.

Cell-free lncRNA expression signatures in urine serve as novel non-invasive biomarkers for diagnosis and recurrence prediction of bladder cancer

Cell-free long non-coding RNAs (lncRNAs) are stably present in urine and can serve as non-invasive biomarkers for cancer. We aimed to identify signatures of lncRNAs in urine for diagnosis and prognosis of bladder cancer (BC). Screening of lncRNAs by microarray analysis was performed using urine samples of 10 BC patients and 10 controls. Expressions of candidate lncRNAs were evaluated in the training and validation set including 230 BC patients and 230 controls by quantitative reverse transcription polymerase chain reaction (qRT-PCR). A two-lncRNA panel (uc004cox.4 and GAS5) was constructed and provided high diagnostic accuracy of BC with an area under the curve (AUC) of 0.885 (95% CI, 0.836-0.924). The AUCs of the lncRNA panel for Ta, T1 and T2-T4 were 0.843, 0.867 and 0.923, respectively, significantly higher than those of urine cytology (all P < .05). Kaplan-Meier analysis revealed that higher level of uc004cox.4 was associated with poor recurrence-free survival (RFS) of non-muscle invasive BC (NMIBC) (P = .008). Additionally, Cox regression analysis indicated that uc004cox.4 was an independent prognostic factor for RFS of NMIBC (P = .018). Taken together, our findings indicated that urinary lncRNA signatures possessed potential clinical value for BC diagnosis. Moreover, uc004cox.4 could provide prognostic information for NMIBC.

Long non-coding RNAs: An essential emerging field in kidney pathogenesis

Human Genome Project has made it clear that a majority of the genome is transcribed into the non-coding RNAs including microRNAs as well as long non-coding RNAs (lncRNAs) which both can affect different features of cells. LncRNAs are long heterogenous RNAs that regulate gene expression and a variety of signaling pathways involved in cellular homeostasis and development. Studies over the past decade have shown that lncRNAs have a major role in the kidney pathogenesis. The effective roles of lncRNAs have been recognized in renal ischemia, injury, inflammation, fibrosis, glomerular diseases, renal transplantation, and renal cell carcinoma. The present review outlines the role and function of lncRNAs in kidney pathogenesis as novel essential regulators. Molecular mechanism insights into the functions of lncRNAs in kidney pathophysiological processes may contribute to effective future therapeutics.

New insights into molecular mechanisms of epigenetic regulation in kidney disease

The number of patients with kidney failure has increased in recent years. Different factors contribute to the progression of chronic kidney disease, including glomerular sclerosis, atherosclerosis of the renal arteries and tubulointerstitial fibrosis. Tubulointerstitial injury is induced by hypoxia and other inflammatory signals, leading to fibroblast activation. Technological advances using high-throughput sequencing has enabled the determination of the expression profile of almost all genes, revealing that gene expression is intricately regulated by DNA methylation, histone modification, changes in chromosome conformation, long non-coding RNAs and microRNAs. These epigenetic modifications are stored as cellular epigenetic memory. Epigenetic memory leads to adult-onset disease or ageing in the long term and may possibly play an important role in the kidney disease process. Herein we emphasize the importance of clarifying the molecular mechanisms underlying epigenetic modifications because this may lead to the development of new therapeutic targets in kidney disease.

Extracellular vesicles in renal disease

Extracellular vesicles, such as exosomes and microvesicles, are host cell-derived packages of information that allow cell-cell communication and enable cells to rid themselves of unwanted substances. The release and uptake of extracellular vesicles has important physiological functions and may also contribute to the development and propagation of inflammatory, vascular, malignant, infectious and neurodegenerative diseases. This Review describes the different types of extracellular vesicles, how they are detected and the mechanisms by which they communicate with cells and transfer information. We also describe their physiological functions in cellular interactions, such as in thrombosis, immune modulation, cell proliferation, tissue regeneration and matrix modulation, with an emphasis on renal processes. We discuss how the detection of extracellular vesicles could be utilized as biomarkers of renal disease and how they might contribute to disease processes in the kidney, such as in acute kidney injury, chronic kidney disease, renal transplantation, thrombotic microangiopathies, vasculitides, IgA nephropathy, nephrotic syndrome, urinary tract infection, cystic kidney disease and tubulopathies. Finally, we consider how the release or uptake of extracellular vesicles can be blocked, as well as the associated benefits and risks, and how extracellular vesicles might be used to treat renal diseases by delivering therapeutics to specific cells.

Urinary long noncoding RNAs in nonmuscle-invasive bladder cancer: new architects in cancer prognostic biomarkers

Several reports over the last 10 years provided evidence that long noncoding RNAs (lncRNAs) are often altered in bladder cancers. lncRNAs are longer than 200 nucleotides and function as important regulators of gene expression, interacting with the major pathways of cell growth, proliferation, differentiation, and survival. A large number of lncRNAs has oncogenic function and is more expressed in tumor compared with normal tissues. Their overexpression may be associated with tumor formation, progression, and metastasis in a variety of tumors including bladder cancer. Although lncRNAs have been shown to have critical regulatory roles in cancer biology, the biological functions and prognostic values in nonmuscle-invasive bladder cancer remain largely unknown. Nevertheless, a growing body of evidence suggests that several lncRNAs expression profiles in bladder malignancies are associated with poor prognosis, and they can be detected in biological fluids, such as urines. Here, we review current progress in the biology and the implication of lncRNAs associated with bladder cancer, and we discuss their potential use as diagnosis and prognosis biomarkers in bladder malignancies with a focus on their role in high-risk nonmuscle-invasive tumors.

Noncoding RNA and epigenetic gene regulation in renal diseases

Kidneys have a major role in normal physiology and metabolic homeostasis. Loss or impairment of kidney function is a common occurrence in several metabolic disorders, including hypertension and diabetes. Chronic kidney disease (CKD) affect nearly 10% of the population worldwide; ranks 18th in the list of causes of death; and contributes to a significant proportion of healthcare costs. The tissue repair and regenerative potential of kidneys are limited and they decline during aging. Recent studies have demonstrated a key role for epigenetic processes and players, such as DNA methylation, histone modifications, noncoding (nc)RNA, and so on, in both kidney development and disease. In this review, we highlight these recent findings with an emphasis on aberrant epigenetic changes that accompany renal diseases, key targets, and their therapeutic value.

Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches

Advances in RNA-sequencing techniques have led to the discovery of thousands of non-coding transcripts with unknown function. There are several types of non-coding linear RNAs such as microRNAs (miRNA) and long non-coding RNAs (lncRNA), as well as circular RNAs (circRNA) consisting of a closed continuous loop. This review guides the reader through important aspects of non-coding RNA biology. This includes their biogenesis, mode of actions, physiological function, as well as their role in the disease context (such as in cancer or the cardiovascular system). We specifically focus on non-coding RNAs as potential therapeutic targets and diagnostic biomarkers.