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Genetic Markers and Liquid Biopsy for Kidney Diseases
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Genetic Markers and Liquid Biopsy for Kidney Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2024) | Viewed by 19694

Special Issue Editors

Prof. Dr. Guorong Li

E-Mail Website
Guest Editor
Department of Urology, North Hospital, CHU Saint-Etienne, 42100 Saint-Etienne, France
Interests: molecular markers; liquid biopsy; renal cell carcinomas; liquid biopy technology; urological cancer
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Christophe Mariat

E-Mail Website
Guest Editor
Department of Nephrology and Kidney Transplantation, North Hospital, CHU Saint Etienne, 42100 Saint Etienne, France
Interests: chronic kidney diseases; molecular markers; kidney biopsy; liquid biopsy; kidney transplatation; nephropathy

Special Issue Information

Dear Colleagues,

In the modern era, technical advances in molecular biology have proven successful in the understanding of the pathogenesis of kidney diseases. The recent advents of next-generation sequencing and high-throughput functional genomics techniques have allowed us to produce molecular fingerprints that characterize the expressions of genes within different kidney cells. As a result, significant molecular markers have been found among kidney diseases.

However, many kidney diseases such as rejection of kidney transplantation, kidney cancer, IgA nephropathy and other chronic kidney diseases are still diagnosed by kidney tissue biopsy. This tissue biopsy is invasive and can introduce some serious complications. Liquid biopsy analyzes biomarkers in bodily fluids. Liquid biopsies are preferable to tissue biopsies because they are less invasive. Liquid biopsy technologies based on circulating DNA/RNA, extracellular vesicles and exosomes have been explosive. The analysis of gene expressions by liquid biopsy technology represents a promising new avenue for the diagnosis and prognosis of kidney diseases.

This Special Issue in Genes titled “Genetic Markers and Liquid Biopsy for Kidney Diseases” will provide a monographic portrait of the current advances in molecular biomarkers and liquid biopsy technology for the clinical management of kidney diseases including kidney cancer, kidney transplantation, nephropathy and chronic kidney disease. We especially welcome review articles (either systematic or discursive), mini-reviews, new methods, original research studies and short communications of preliminary, but significant, experimental results.

Prof. Dr. Guorong Li
Prof. Dr. Christophe Mariat
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular markers
  • renal cell carcinoma
  • kidney transplantation
  • nephropathy
  • chronic kidney disease
  • acute kidney injury
  • kidney biopsy
  • liquid biopsy
  • liquid biopsy technology
  • circulating DNA or RNA
  • extracellular vesicles
  • exosomes

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Published Papers (6 papers)

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Research

Jump to: Review, Other

13 pages, 2719 KiB  
Article
Evaluating the Urinary Exosome microRNA Profile of von Hippel Lindau Syndrome Patients with Clear Cell Renal Cell Carcinoma
by Beatriz Walter-Rodriguez, Christopher J. Ricketts, W. Marston Linehan and Maria J. Merino
Genes 2024, 15(7), 905; https://doi.org/10.3390/genes15070905 - 11 Jul 2024
Cited by 1 | Viewed by 1137
Abstract
Introduction: Renal cell carcinoma is one of the ten more common malignant tumors worldwide, with a high incidence and mortality rate. Kidney cancer frequently presents at an advanced stage, and it is almost invariably fatal. Much progress has been made in identifying molecular [...] Read more.
Introduction: Renal cell carcinoma is one of the ten more common malignant tumors worldwide, with a high incidence and mortality rate. Kidney cancer frequently presents at an advanced stage, and it is almost invariably fatal. Much progress has been made in identifying molecular targets for therapy in the hope of improving survival rates, but still, we have no good markers for early detection or progression of the disease. Von Hippel Lindau syndrome (VHL) is an autosomal dominant cancer hereditary syndrome in which affected individuals are at risk of developing bilateral and multifocal renal cell carcinomas (RCC) as well as other tumors. These patients provide an ideal platform to investigate the potential of urinary exosomal miRNA biomarkers in the early development of ccRCC, as these patients are regularly imaged and tumors are actively monitored until the tumor reaches 3 cm before surgical excision. This allows for pre- and post-surgical urine collection and comparison to excised tumor tissues. Studying different biomarkers in urine can provide comprehensive molecular profiling available to patients and physicians and can be a great source of additional tumor genetic information. Methods: Pre- and postoperative urine samples were obtained from a cohort of VHL patients undergoing surveillance and surgical excision of ccRCCs, and exosomes were extracted. MicroRNA-Seq analysis was performed on miRNA extracted from both urine-derived exosomes and FFPE material from excised ccRCCs. Results: MicroRNA-Seq analysis highlighted a significant difference in the urinary exosome-derived miRNA expression profiles between VHL patients and normal control individuals. This included decreased expression of the miR-320 family, such as miR-320a, known to be decreased in sporadic ccRCC and suppressed by the HIF1α transcription factor activated by the loss of the VHL gene. MiR-542-5p represented a potential marker of VHL-associated ccRCC that was lowly expressed in normal control urinary exosomes, significantly increased in the preoperative urinary exosomes of tumor-bearing VHL patients, and subsequently reduced to normal levels of expression after tumor excision. In concordance with this, the expression of miR-542-5p was increased in the VHL-associated ccRCC in comparison to the normal kidney. Conclusions: This study shows the potential for miRNA profiling of exosomes from readily available biofluids to both distinguish VHL patient urine from normal control urine microRNAs and to provide biomarkers for the presence of VHL syndrome-associated ccRCC. Further validation studies are necessary to demonstrate the utility of urinary exosome-derived miRNAs as biomarkers in kidney cancer. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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Review

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12 pages, 584 KiB  
Review
Liquid Biopsy: A New Avenue for the Diagnosis of Kidney Disease: Diabetic Kidney Disease, Renal Cancer, and IgA Nephropathy
by Jill Dybiec, Weronika Frąk, Joanna Kućmierz, Julita Tokarek, Armanda Wojtasińska, Ewelina Młynarska, Jacek Rysz and Beata Franczyk
Genes 2024, 15(1), 78; https://doi.org/10.3390/genes15010078 - 7 Jan 2024
Cited by 1 | Viewed by 3041
Abstract
Kidney diseases are some of the most common healthcare problems. As the population of elderly individuals with concurrent health conditions continues to rise, there will be a heightened occurrence of these diseases. Due to the renal condition being one of the longevity predictors, [...] Read more.
Kidney diseases are some of the most common healthcare problems. As the population of elderly individuals with concurrent health conditions continues to rise, there will be a heightened occurrence of these diseases. Due to the renal condition being one of the longevity predictors, early diagnosis of kidney dysfunction plays a crucial role. Currently, prevalent diagnostic tools include laboratory tests and kidney tissue biopsies. New technologies, particularly liquid biopsy and new detection biomarkers, hold promise for diagnosing kidney disorders. The aim of this review is to present modern diagnostic methods for kidney diseases. The paper focuses on the advances in diagnosing three common renal disorders: diabetic kidney disease, renal cancer, and immunoglobulin A nephropathy. We highlight the significance of liquid biopsy and epigenetic changes, such as DNA methylation, microRNA, piRNAs, and lncRNAs expression, or single-cell transcriptome sequencing in the assessment of kidney diseases. This review underscores the importance of early diagnosis for the effective management of kidney diseases and investigates liquid biopsy as a promising approach. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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32 pages, 3774 KiB  
Review
Liquid Biopsy at the Frontier of Kidney Diseases: Application of Exosomes in Diagnostics and Therapeutics
by Ewud Agborbesong, John Bissler and Xiaogang Li
Genes 2023, 14(7), 1367; https://doi.org/10.3390/genes14071367 - 28 Jun 2023
Cited by 4 | Viewed by 1856
Abstract
In the era of precision medicine, liquid biopsy techniques, especially the use of urine analysis, represent a paradigm shift in the identification of biomarkers, with considerable implications for clinical practice in the field of nephrology. In kidney diseases, the use of this non-invasive [...] Read more.
In the era of precision medicine, liquid biopsy techniques, especially the use of urine analysis, represent a paradigm shift in the identification of biomarkers, with considerable implications for clinical practice in the field of nephrology. In kidney diseases, the use of this non-invasive tool to identify specific and sensitive biomarkers other than plasma creatinine and the glomerular filtration rate is becoming crucial for the diagnosis and assessment of a patient’s condition. In recent years, studies have drawn attention to the importance of exosomes for diagnostic and therapeutic purposes in kidney diseases. Exosomes are nano-sized extracellular vesicles with a lipid bilayer structure, composed of a variety of biologically active substances. In the context of kidney diseases, studies have demonstrated that exosomes are valuable carriers of information and are delivery vectors, rendering them appealing candidates as biomarkers and drug delivery vehicles with beneficial therapeutic outcomes for kidney diseases. This review summarizes the applications of exosomes in kidney diseases, emphasizing the current biomarkers of renal diseases identified from urinary exosomes and the therapeutic applications of exosomes with reference to drug delivery and immunomodulation. Finally, we discuss the challenges encountered when using exosomes for therapeutic purposes and how these may affect its clinical applications. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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12 pages, 617 KiB  
Review
The Role of PLA2R in Primary Membranous Nephropathy: Do We Still Need a Kidney Biopsy?
by Thomas McDonnell, Henry H. L. Wu, Smeeta Sinha and Rajkumar Chinnadurai
Genes 2023, 14(7), 1343; https://doi.org/10.3390/genes14071343 - 26 Jun 2023
Cited by 6 | Viewed by 3615
Abstract
Membranous nephropathy (MN) is the most prevalent cause of nephrotic syndrome amongst the non-diabetic adult population. A fifth of idiopathic nephrotic syndrome cases can be attributed to MN, rising to more than 40% in older patients over 60 years. Most MN cases are [...] Read more.
Membranous nephropathy (MN) is the most prevalent cause of nephrotic syndrome amongst the non-diabetic adult population. A fifth of idiopathic nephrotic syndrome cases can be attributed to MN, rising to more than 40% in older patients over 60 years. Most MN cases are classified as being of a primary cause, where there is absence of a secondary disease process explaining its manifestation. Traditionally, the standard approach of diagnosing MN involves performing a kidney biopsy as histological evaluation offers not only conclusive evidence of the diagnosis but also provides valuable information regarding disease chronicity and the presence of any other kidney histopathological features. Nevertheless, kidney biopsy is an invasive procedure which poses risks for the patient including bleeding and pain and bears greater costs for the health system. The identification of the phospholipase A2 receptor (PLA2R) antigen in 2009 was a landmark discovery, one which has evolved our understanding of the disease processes in MN and subsequently our management approach of this condition. Antibodies against PLA2R (PLA2RAb) have since emerged as an attractive non-invasive test option to be applied for the diagnosis and prognostication of primary MN. However, much debate and unknowns remain about the accuracy and reliability of testing for PLA2RAb across various primary MN scenarios. We provide a review summarizing the historical journey of PLA2R in relation to its significance in primary MN and, more importantly, evidence emerging over the years which contemplated the role of PLA2RAb as a diagnostic and prognostic tool in primary MN. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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9 pages, 380 KiB  
Review
BK Virus Infection and BK-Virus-Associated Nephropathy in Renal Transplant Recipients
by Margherita Borriello, Diego Ingrosso, Alessandra Fortunata Perna, Angela Lombardi, Paolo Maggi, Lucia Altucci and Michele Caraglia
Genes 2022, 13(7), 1290; https://doi.org/10.3390/genes13071290 - 21 Jul 2022
Cited by 21 | Viewed by 7198
Abstract
Poliomavirus BK virus (BKV) is highly infective, causing asymptomatic infections during childhood. After the initial infection, a stable state of latent infection is recognized in kidney tubular cells and the uroepithelium with negligible clinical consequences. BKV is an important risk factor for BKV-associated [...] Read more.
Poliomavirus BK virus (BKV) is highly infective, causing asymptomatic infections during childhood. After the initial infection, a stable state of latent infection is recognized in kidney tubular cells and the uroepithelium with negligible clinical consequences. BKV is an important risk factor for BKV-associated diseases, and, in particular, for BKV-associated nephropathy (BKVN) in renal transplanted recipients (RTRs). BKVN affects up to 10% of renal transplanted recipients, and results in graft loss in up to 50% of those affected. Unfortunately, treatments for BK virus infection are restricted, and there is no efficient prophylaxis. In addition, consequent immunosuppressive therapy reduction contributes to immune rejection. Increasing surveillance and early diagnosis based upon easy and rapid analyses are resulting in more beneficial outcomes. In this report, the current status and perspectives in the diagnosis and treatment of BKV in RTRs are reviewed. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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Other

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7 pages, 1040 KiB  
Brief Report
CD44 Expression in Clear Cell Renal Cell Carcinoma (ccRCC) Correlates with Tumor Grade and Patient Survival and Is Affected by Gene Methylation
by Anastasios D. Papanastasiou, Stavros Peroukidis, Chaido Sirinian, Elisavet Arkoumani, Dimitrios Chaniotis and Adamantia Zizi-Sermpetzoglou
Genes 2024, 15(5), 537; https://doi.org/10.3390/genes15050537 - 24 Apr 2024
Cited by 1 | Viewed by 1261
Abstract
Clear cell RCC (ccRCC) represents the most common type of kidney cancer, with surgery being the only potential curative treatment. Almost one-third of ccRCC patients relapse either locally or as cases of distant metastases. Several biomarkers have been employed in order to separate [...] Read more.
Clear cell RCC (ccRCC) represents the most common type of kidney cancer, with surgery being the only potential curative treatment. Almost one-third of ccRCC patients relapse either locally or as cases of distant metastases. Several biomarkers have been employed in order to separate ccRCC patients with better prognosis or to predict treatment outcomes, with limited results. CD44 is a membrane glycoprotein with multiple roles in normal development but also cancer. Recently, the CD44 standard isoform has been implicated in tumor progression and the metastasis cascade through microenvironment interactions. Here, through CD44 immunohistochemical staining of ccRCC patient samples and TCGA data analysis, we sought to elucidate the expression patterns (mRNA and protein) of CD44 in clear cell RCC and correlate its expression with clinicopathological parameters. We were able to show that CD44 expression presents a positive association with tumor grade and overall survival, predicting a worse patient outcome in ccRCC. In addition, our data indicate that the CD44 mRNA upregulation can be attributed to reduced gene methylation, implicating epigenetic gene regulation in ccRCC development and progression. Full article
(This article belongs to the Special Issue Genetic Markers and Liquid Biopsy for Kidney Diseases)
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