Next-Generation Sequencing for New Gene Identification and for Diagnosis in Steroid-Resistant Nephrotic Syndrome

Nephrotic syndrome is clinically characterized by massive proteinuria, and hypoalbuminemia. It represents a heterogeneous group of glomerular disorders characterized by distinct causes and histopathologic lesions. The present thesis evaluates the contribution of genetics in conditions commonly associated with NS: the immune complex-mediated membranoproliferative glomerulonephritis (IC-MPGN), the C3 glomerulopathy (C3G) and the podocytopathies, usually characterized by steroid-resistant nephrotic syndrome (SRNS). The first part of the thesis focused on IC-MPGN and C3G. We found likely pathogenic (LP) variants in complement alternative pathway genes in 18% of patients and describe, for the first time, thrombomodulin rare pathogenic variants in C3G patients. Interestingly, mutations alone did not increase the risk of developing IC-MPGN or C3G, but they did so when combined with common susceptibility variants. The prevalence of alternative pathway abnormalities (mutations and/or C3 Nephritic Factors, C3NeFs) was similar in IC-MPGN (53-56%) and C3G (64-65%). To investigate for more homogeneous subgroups within IC-MPGN/C3G, an operator-independent approach was applied using genetic, biochemical, histological and clinical data. Four different groups emerged showing distinct pathogenesis, and histological and clinical features. In the second part, the genetic causes of podocytopathies were investigated. LP variants in podocytopathy-associated genes are found in 23% of SRNS patients, prevalently in COL4A3-5 genes. Moreover, 8% of patients carried LP variants in Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT)-associated genes, which were not previously associated with podocytopathies. LP variants in CAKUT-associated and podocytopathy-associated genes frequently combined together. Finally, possibly pathogenic variants in EPB41L45, a candidate gene for podocytopathies, were identified in 3 unrelated patients. In conclusion, this thesis contributes to understand the complex genetic basis of both IC-MPGN/C3G and podocytopathies. It introduces new players in the pathogenesis of these diseases. Finally, it provides evidence of the presence of subgroups within IC-MPGN/C3G with distinct underlying mechanisms, and clinical and histopathologic features

International therapeutic guidelines for patients with HCV-related extrahepatic disorders. A multidisciplinary expert statement

Hepatitis C virus (HCV) is both hepatotrophic and lymphotropic virus that causes liver as well extrahepatic manifestations including cryoglobulinemic vasculitis, the most frequent and studied condition, lymphoma, and neurologic, cardiovascular, endocrine-metabolic or renal diseases. HCV-extrahepatic manifestations (HCV-EHMs) may severely affect the overall prognosis, while viral eradication significantly reduces non-liver related deaths. Different clinical manifestations may coexist in the same patient. Due to the variety of HCV clinical manifestations, a multidisciplinary approach along with appropriate therapeutic strategies are required. In the era of interferon-free anti-HCV treatments, international recommendations for the therapeutic management of HCV-EHMs are needed. This implies the need to define the best criteria to use antivirals and/or other therapeutic approaches. The present recommendations, based on qualified expert experience and specific literature, will focus on etiological (antiviral) therapies and/or traditional pathogenetic treatments that still maintain their therapeutic utility

Rare Kidney Diseases

Rare kidney diseases comprise a large group of different life-threatening or chronically debilitating disorders that affect very small numbers of people (<1 in 2000 individuals in Europe and <200,000 in USA) with local or systemic manifestations. For several years, the research and development of treatments in this field have been neglected in favor of more common diseases. The main reasons for the lack of interest in rare kidney diseases seem to be the small numbers of patients and limited epidemiological data on the natural history of many of these diseases. Rare diseases can affect people differently. Even patients with the same condition can exhibit very different signs and symptoms, or there may be many subtypes of the same condition. This diversity constitutes a significant challenge to healthcare practitioners and scientists alike, in terms of being able to acquire sufficient experience for the most appropriate and timely definition, diagnosis, and management. Fortunately, in the last ten years, concerted efforts have led to a marked improvement in the understanding of these disorders. In particular, an important step forward has been taken with the employment of innovative technologies (including next-generation sequencing), in order to replace obsolete phenotypic classifications and to discover new useful diagnostic biomarkers. These new tools are, in fact, becoming part of routine clinical practice, increasing diagnostic accuracy and facilitating genetic counseling. Moreover, biomedical research, providing insights into the pathologies of these rare diseases and elucidating their underlying mechanisms, is revealing new therapeutic avenues and driving the industry to develop safer and more effective orphan drugs. Finally, in this field, it is desirable that, in the future, the crosstalk between basic scientists and clinicians could achieve a great clinical benefit by improving the quality of life of these patients as well. This Special Issue welcomes scientific contributions and critical reviews describing new pathogenetic insights, reporting novel and specific disease biomarkers, and underlying new pharmacological targets or therapies for rare diseases of the kidney and urinary tract

Urinary Tract Infection and Nephropathy

In this book, experts from different countries demonstrate clinical and research advances in nephropathy and urinary tract infection (UTI). Chapters cover such topics as membranous nephropathy, diabetic nephropathy, multidrug resistance in UTI, pathogens and bacteria associated with UTI, and more

The banff 2019 kidney meeting report (I): updates on and clarification of criteria for T cell- and antibody-mediated rejection.

The XV. Banff conference for allograft pathology was held in conjunction with the annual meeting of the American Society for Histocompatibility and Immunogenetics in Pittsburgh, PA (USA) and focused on refining recent updates to the classification, advances from the Banff working groups, and standardization of molecular diagnostics. This report on kidney transplant pathology details clarifications and refinements to the criteria for chronic active (CA) T cell-mediated rejection (TCMR), borderline, and antibody-mediated rejection (ABMR). The main focus of kidney sessions was on how to address biopsies meeting criteria for CA TCMR plus borderline or acute TCMR. Recent studies on the clinical impact of borderline infiltrates were also presented to clarify whether the threshold for interstitial inflammation in diagnosis of borderline should be i0 or i1. Sessions on ABMR focused on biopsies showing microvascular inflammation in the absence of C4d staining or detectable donor-specific antibodies; the potential value of molecular diagnostics in such cases and recommendations for use of the latter in the setting of solid organ transplantation are presented in the accompanying meeting report. Finally, several speakers discussed the capabilities of artificial intelligence and the potential for use of machine learning algorithms in diagnosis and personalized therapeutics in solid organ transplantation

The Banff 2019 Kidney Meeting Report (I): Updates on and clarification of criteria for T cell– and antibody-mediated rejection

The XV. Banff conference for allograft pathology was held in conjunction with the annual meeting of the American Society for Histocompatibility and Immunogenetics in Pittsburgh, PA (USA) and focused on refining recent updates to the classification, advances from the Banff working groups, and standardization of molecular diagnostics. This report on kidney transplant pathology details clarifications and refinements to the criteria for chronic active (CA) T cell–mediated rejection (TCMR), borderline, and antibody-mediated rejection (ABMR). The main focus of kidney sessions was on how to address biopsies meeting criteria for CA TCMR plus borderline or acute TCMR. Recent studies on the clinical impact of borderline infiltrates were also presented to clarify whether the threshold for interstitial inflammation in diagnosis of borderline should be i0 or i1. Sessions on ABMR focused on biopsies showing microvascular inflammation in the absence of C4d staining or detectable donor-specific antibodies; the potential value of molecular diagnostics in such cases and recommendations for use of the latter in the setting of solid organ transplantation are presented in the accompanying meeting report. Finally, several speakers discussed the capabilities of artificial intelligence and the potential for use of machine learning algorithms in diagnosis and personalized therapeutics in solid organ transplantation

Identification of nephropathy candidate genes by comparing sclerosis-prone and sclerosis-resistant mouse strain kidney transcriptomes

Abstract Background The genetic architecture responsible for chronic kidney disease (CKD) remains incompletely described. The Oligosyndactyly (Os) mouse models focal and segmental glomerulosclerosis (FSGS), which is associated with reduced nephron number caused by the Os mutation. The Os mutation leads to FSGS in multiple strains including the ROP-Os/+. However, on the C57Bl/6J background the mutation does not cause FSGS, although nephron number in these mice are equivalent to those in ROP-Os/+ mice. We exploited this phenotypic variation to identify genes that potentially contribute to glomerulosclerosis. Methods To identify such novel genes, which regulate susceptibility or resistance to renal disease progression, we generated and compared the renal transcriptomes using serial analysis of gene expression (SAGE) from the sclerosis-prone ROP-Os/+ and sclerosis resistant C57-Os/+ mouse kidneys. We confirmed the validity of the differential gene expression using multiple approaches. We also used an Ingenuity Pathway Analysis engine to assemble differentially regulated molecular networks. Cell culture techniques were employed to confirm functional relevance of selected genes. Results A comparative analysis of the kidney transcriptomes revealed multiple genes, with expression levels that were statistically different. These novel, candidate, renal disease susceptibility/resistance genes included neuropilin2 (Nrp2), glutathione-S-transferase theta (Gstt1) and itchy (Itch). Of 34 genes with the most robust statistical difference in expression levels between ROP-Os/+ and C57-Os/+ mice, 13 and 3 transcripts localized to glomerular and tubulointerstitial compartments, respectively, from micro-dissected human FSGS biopsies. Network analysis of all significantly differentially expressed genes identified 13 connectivity networks. The most highly scored network highlighted the roles for oxidative stress and mitochondrial dysfunction pathways. Functional analyses of these networks provided evidence for activation of transforming growth factor beta (TGFβ) signaling in ROP-Os/+ kidneys despite similar expression of the TGFβ ligand between the tested strains. Conclusions These data demonstrate the complex dysregulation of normal cellular functions in this animal model of FSGS and suggest that therapies directed at multiple levels will be needed to effectively treat human kidney diseases.http://deepblue.lib.umich.edu/bitstream/2027.42/112491/1/12882_2011_Article_362.pd

Locus specific databases: integrating sequence, structural and clinical analysis in relation to disorders of the coagulation and complement systems.

Following the success of the Human Genome Mutation Database, increasing numbers of locus-specific mutation databases are being compiled in order to present more detailed descriptions of the mutations in specific proteins and diseases. However, until now, many coagulation or complement disorders have no up-to-date, accurate repository of information. Structural analyses of disease-associated mutations can provide important new tools for identifying the underlying biochemical defect of disease. Type I mutations may affect the correct folding, secretion, expression or degradation of the protein. Alternatively, Type II mutations can disrupt the catalytic or substrate-binding functional site of the protein. Alternatively, mutations may not be the causative factor for disease. Including sequence and structural information to propose consensus domain structures can unravel these effects of mutations. Central repositories of data that combine structural, sequence and phenotypic information on mutations and proteins can facilitate the diagnosis and understanding of the associated diseases, and define the molecular consequences of disease. This thesis describes interactive web databases of genotypic, phenotypic, clinical and structural information on mutations associated with complement Factor H (FH) and coagulation Factor XI (FXI). Mutations within FH are associated with aHUS (atypical Haemolytic Uraemic Syndrome), MPGN (Membranoproliferative Glomerulonephritis) and AMD (Age-related Macular Degeneration), whereas mutations within FXI are associated with a FXI deficiency bleeding disorder. The methods used within the FH and FXI databases were extended and combined with a database management system to design a mutation database for the five Vitamin K dependent serine proteases of coagulation in order to study the effects of mutations within conserved domains. The database management system incorporates new tools that have been designed to automatically scan full length references to find text describing mutations. This significantly reduces the time and expertise required to maintain the databases

Epidemic of chronic kidney disease of unknown causes in Nicaragua: epidemiology, causal hypotheses, and public health interventions

Tesis doctoral inédta leída en la Universidad Autónoma de Madrid, Facultad de Medicina, Departamento de Medicina Preventiva, Salud Pública y Microbiología. Fecha de lectura:14 de Octubre de 201