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From Genetic to Molecular Basis of Kidney Damage
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From Genetic to Molecular Basis of Kidney Damage

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

Deadline for manuscript submissions: 25 June 2024 | Viewed by 8725

Special Issue Editor

Dr. Mariadelina Simeoni

E-Mail Website
Guest Editor
Department of Translational Medical Sciences, University of Campania ‘Luigi Vanvitelli’, 80138 Napoli, Italy
Interests: chronic renal Failure; molecular biology

Special Issue Information

Dear Colleagues, 

The modern nephrology is characterized by an increasing openness to discovering the genetic and molecular basis of renal damage. This is fundamental for those rare glomerular and tubular diseases, with pathogenetic mechanisms that are not fully clarified, to optimize their diagnostic and therapeutic pathways. Recent advances in molecular biology have also highlighted novel pathogenic aspects of non-hereditary kidney diseases that address further interesting research questions. Moreover, the pathogenetic cross-links between kidney and other organs and apparatus are interesting areas to be explored and often share a common genetic background.  

This Special Issue is therefore open to any high-quality scientific contribution addressed at improving the current knowledge on the genetic basis of primitive and secondary renal diseases.

Dr. Mariadelina Simeoni
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • renal rare diseases
  • inherited glomerulopathies and tubulopathies
  • onconephrology applied to rare cancers and pharmacogenetics in oncology
  • the common genetic basis of cardio-nephrology syndromes
  • the common genetic basis of neuro-nephrology syndromes
  • the common genetic basis of endocrine nephrology syndromes

Published Papers (6 papers)

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Research

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11 pages, 1204 KiB  
Article
DNAJB11 Mutation in ADPKD Patients: Clinical Characteristics in a Monocentric Cohort
by Valeria Aiello, Francesca Ciurli, Amalia Conti, Carlotta Pia Cristalli, Sarah Lerario, Francesca Montanari, Nicola Sciascia, Gisella Vischini, Benedetta Fabbrizio, Roberta Di Costanzo, Giulia Olivucci, Andrea Pietra, Antonia Lopez, Loretta Zambianchi, Gaetano La Manna and Irene Capelli
Genes 2024, 15(1), 3; https://doi.org/10.3390/genes15010003 - 19 Dec 2023
Viewed by 972
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a late-onset cilia-related disorder, characterized by progressive cystic enlargement of the kidneys. It is genetically heterogeneous with PKD1 and PKD2 pathogenic variants identified in approximately 78% and 15% of families, respectively. More recently, additional ADPKD genes, [...] Read more.
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a late-onset cilia-related disorder, characterized by progressive cystic enlargement of the kidneys. It is genetically heterogeneous with PKD1 and PKD2 pathogenic variants identified in approximately 78% and 15% of families, respectively. More recently, additional ADPKD genes, such as DNAJB11, have been identified and included in the diagnostic routine test for renal cystic diseases. However, despite recent progress in ADPKD molecular approach, approximately ~7% of ADPKD-affected families remain genetically unresolved. We collected a cohort of 4 families from our center, harboring heterozygous variants in the DNAJB11 gene along with clinical and imaging findings consistent with previously reported features in DNAJB11 mutated patients. Mutations were identified as likely pathogenetic (LP) in three families and as variants of uncertain significance (VUS) in the remaining one. One patient underwent to kidney biopsy and showed a prevalence of interstitial fibrosis that could be observed in ~60% of the sample. The presence in the four families from our cohort of ADPKD characteristics together with ADTKD features, such as hyperuricemia, diabetes, and chronic interstitial fibrosis, supports the definition of DNAJB11 phenotype as an overlap disease between these two entities, as originally suggested by the literature. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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8 pages, 391 KiB  
Article
Associations of HLA Polymorphisms with Chronic Kidney Disease in Japanese Rheumatoid Arthritis Patients
by Takashi Higuchi, Shomi Oka, Hiroshi Furukawa, Kota Shimada, Atsushi Hashimoto, Akiko Komiya, Toshihiro Matsui, Naoshi Fukui and Shigeto Tohma
Genes 2023, 14(7), 1470; https://doi.org/10.3390/genes14071470 - 19 Jul 2023
Cited by 1 | Viewed by 1052
Abstract
Objectives: The prevalence of chronic kidney disease (CKD) was reported to be higher in rheumatoid arthritis (RA) patients than in normal healthy individuals. Human leukocyte antigen (HLA) was associated with RA or CKD. Few studies on the association of HLA with [...] Read more.
Objectives: The prevalence of chronic kidney disease (CKD) was reported to be higher in rheumatoid arthritis (RA) patients than in normal healthy individuals. Human leukocyte antigen (HLA) was associated with RA or CKD. Few studies on the association of HLA with CKD in RA have been reported. Here, we investigated the association of HLA polymorphisms with CKD in Japanese RA patients. Methods: HLA-DRB1 genotyping was conducted in 351 Japanese RA patients with CKD (estimated glomerular filtration rate [eGFR] lower than 60 [mL/min/1.73 m2]) and 959 without CKD (eGFR equal to or higher than 60 [mL/min/1.73 m2]). Associations of allele carrier frequencies of DRB1 with CKD were examined in the RA patients. Results: There was an association of DRB1*13:02 with CKD in RA, but this did not achieve statistical significance (p = 0.0265, odds ratio [OR] 1.70, pc = 0.7412, 95% confidence interval [CI] 1.09–2.64). The DR6 serological group was associated with CKD in RA (p = 0.0008, OR 1.65, 95% CI 1.24–2.20). A gene-dosage effect of DR6 was not detected. Logistic regression analysis showed that the association of DR6 with CKD in RA was independent of clinical characteristics. Conclusions: The present study first revealed the independent predisposing association of DR6 with CKD in Japanese RA patients, although DR6 is known to be protective against RA. Our data suggest direct or indirect roles of HLA for the development of CKD in RA, but the mechanisms are not clear. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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24 pages, 6471 KiB  
Article
The Genetic Cross-Talk between Periodontitis and Chronic Kidney Failure Revealed by Transcriptomic Analysis
by Dandan Ren, Thomas Ebert, Deborah Kreher, Bero Luke Vincent Ernst, Jonathan de Fallois and Gerhard Schmalz
Genes 2023, 14(7), 1374; https://doi.org/10.3390/genes14071374 - 28 Jun 2023
Viewed by 1215
Abstract
Periodontitis and chronic kidney failure (CKF) are potentially related to each other. This bioinformatics analysis aimed at the identification of potential cross-talk genes and related pathways between periodontitis and CKF. Based on NCBI Gene Expression Omnibus (GEO), datasets GSE10334, GSE16134, and [...] Read more.
Periodontitis and chronic kidney failure (CKF) are potentially related to each other. This bioinformatics analysis aimed at the identification of potential cross-talk genes and related pathways between periodontitis and CKF. Based on NCBI Gene Expression Omnibus (GEO), datasets GSE10334, GSE16134, and GSE23586 were extracted for periodontitis. A differential expression analysis (p < 0.05, |log2(FC)| > 0.5) was performed to assess deregulated genes (DEGs). CKF-related genes were extracted from DisGeNET and examined regarding their overlap with periodontitis-related DEGs. Cytoscape was used to construct and analyze a protein–protein interaction (PPI) network. Based on Cytoscape plugin MCODE and a LASSO regression analysis, the potential hub cross-talk genes were identified. Finally, a complex PPI of the hub genes was constructed. A total of 489 DEGs for periodontitis were revealed. With the 805 CKF-related genes, an overlap of 47 cross-talk genes was found. The PPI network of the potential cross-talk genes was composed of 1081 nodes and 1191 edges. The analysis with MCODE resulted in 10 potential hub genes, while the LASSO regression resulted in 22. Finally, five hub cross-talk genes, CCL5, FCGR3B, MMP-9, SAA1, and SELL, were identified. Those genes were significantly upregulated in diseased samples compared to controls (p ≤ 0.01). Furthermore, ROC analysis showed a high predictive value of those genes (AUC ≥ 73.44%). Potentially relevant processes and pathways were primarily related to inflammation, metabolism, and cardiovascular issues. In conclusion, five hub cross-talk genes, i.e., CCL5, FCGR3B, MMP-9, SAA1, and SELL, could be involved in the interplay between periodontitis and CKF, whereby primarily inflammation, metabolic, and vascular issues appear to be of relevance. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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14 pages, 2798 KiB  
Article
Computational Analysis Reveals Distinctive Interaction of miRNAs with Target Genes in the Pathogenesis of Chronic Kidney Disease
by Hafiz Muhammad Umar Salim, Abdullahi Dandare, Fareeha Khalil, Afrose Liaquat, Muhammad Jawad Khan and Aisha Naeem
Genes 2023, 14(4), 898; https://doi.org/10.3390/genes14040898 - 12 Apr 2023
Viewed by 1722
Abstract
The regulation of genes is crucial for maintaining a healthy intracellular environment, and any dysregulation of gene expression leads to several pathological complications. It is known that many diseases, including kidney diseases, are regulated by miRNAs. However, the data on the use of [...] Read more.
The regulation of genes is crucial for maintaining a healthy intracellular environment, and any dysregulation of gene expression leads to several pathological complications. It is known that many diseases, including kidney diseases, are regulated by miRNAs. However, the data on the use of miRNAs as biomarkers for the diagnosis and treatment of chronic kidney disease (CKD) are not conclusive. The purpose of this study was to elucidate the potential of miRNAs as an efficient biomarker for the detection and treatment of CKD at its early stages. Gene expression profiling data were acquired from the Gene Expression Omnibus (GEO) and differentially expressed genes (DEGs) were identified. miRNAs directly associated with CKD were obtained from an extensive literature search. Network illustration of miRNAs and their projected target differentially expressed genes (tDEGs) was accomplished, followed by functional enrichment analysis. hsa-miR-1-3p, hsa-miR-206, hsa-miR-494 and hsa-miR-577 exhibited a strong association with CKD through the regulation of genes involved in signal transduction, cell proliferation, the regulation of transcription and apoptotic process. All these miRNAs have shown significant contributions to the inflammatory response and the processes which eventually lead to the pathogenesis of CKD. The in silico approach used in this research represents a comprehensive analysis of identified miRNAs and their target genes for the identification of molecular markers of disease processes. The outcomes of the study recommend further efforts for developing miRNA biomarkers set for the early diagnosis of CKD. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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Review

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24 pages, 1542 KiB  
Review
Fabry Disease in Women: Genetic Basis, Available Biomarkers, and Clinical Manifestations
by Raafiah Izhar, Margherita Borriello, Antonella La Russa, Rossella Di Paola, Ananya De, Giovambattista Capasso, Diego Ingrosso, Alessandra F. Perna and Mariadelina Simeoni
Genes 2024, 15(1), 37; https://doi.org/10.3390/genes15010037 - 26 Dec 2023
Viewed by 1460
Abstract
Fabry Disease (FD) is a rare lysosomal storage disorder caused by mutations in the GLA gene on the X chromosome, leading to a deficiency in α-galactosidase A (AGAL) enzyme activity. This leads to the accumulation of glycosphingolipids, primarily globotriaosylceramide (Gb3), in vital organs [...] Read more.
Fabry Disease (FD) is a rare lysosomal storage disorder caused by mutations in the GLA gene on the X chromosome, leading to a deficiency in α-galactosidase A (AGAL) enzyme activity. This leads to the accumulation of glycosphingolipids, primarily globotriaosylceramide (Gb3), in vital organs such as the kidneys, heart, and nervous system. While FD was initially considered predominantly affecting males, recent studies have uncovered that heterozygous Fabry women, carrying a single mutated GLA gene, can manifest a wide array of clinical symptoms, challenging the notion of asymptomatic carriers. The mechanisms underlying the diverse clinical manifestations in females remain not fully understood due to X-chromosome inactivation (XCI). XCI also known as “lyonization”, involves the random inactivation of one of the two X chromosomes. This process is considered a potential factor influencing phenotypic variation. This review delves into the complex landscape of FD in women, discussing its genetic basis, the available biomarkers, clinical manifestations, and the potential impact of XCI on disease severity. Additionally, it highlights the challenges faced by heterozygous Fabry women, both in terms of their disease burden and interactions with healthcare professionals. Current treatment options, including enzyme replacement therapy, are discussed, along with the need for healthcare providers to be well-informed about FD in women, ultimately contributing to improved patient care and quality of life. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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15 pages, 1121 KiB  
Systematic Review
Possible Effects of Uremic Toxins p-Cresol, Indoxyl Sulfate, p-Cresyl Sulfate on the Development and Progression of Colon Cancer in Patients with Chronic Renal Failure
by Rossella Di Paola, Ananya De, Raafiah Izhar, Marianna Abate, Silvia Zappavigna, Anna Capasso, Alessandra F. Perna, Antonella La Russa, Giovambattista Capasso, Michele Caraglia and Mariadelina Simeoni
Genes 2023, 14(6), 1257; https://doi.org/10.3390/genes14061257 - 13 Jun 2023
Cited by 4 | Viewed by 1737
Abstract
Chronic kidney disease (CKD) induces several systemic effects, including the accumulation and production of uremic toxins responsible for the activation of various harmful processes. Gut dysbiosis has been widely described in CKD patients, even in the early stages of the disease. The abundant [...] Read more.
Chronic kidney disease (CKD) induces several systemic effects, including the accumulation and production of uremic toxins responsible for the activation of various harmful processes. Gut dysbiosis has been widely described in CKD patients, even in the early stages of the disease. The abundant discharge of urea and other waste substances into the gut favors the selection of an altered intestinal microbiota in CKD patients. The prevalence of bacteria with fermentative activity leads to the release and accumulation in the gut and in the blood of several substances, such as p-Cresol (p-C), Indoxyl Sulfate (IS) and p-Cresyl Sulfate (p-CS). Since these metabolites are normally eliminated in the urine, they tend to accumulate in the blood of CKD patients proportionally to renal impairment. P-CS, IS and p-C play a fundamental role in the activation of various pro-tumorigenic processes, such as chronic systemic inflammation, the increase in the production of free radicals and immune dysfunction. An up to two-fold increase in the incidence of colon cancer development in CKD has been reported in several studies, although the pathogenic mechanisms explaining this compelling association have not yet been described. Based on our literature review, it appears likely the hypothesis of a role of p-C, IS and p-CS in colon cancer development and progression in CKD patients. Full article
(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Damage)
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