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16 pages, 4489 KiB

Open AccessArticle

Mutation Analysis of Autosomal-Dominant Polycystic Kidney Disease Patients

by Yasuo Suzuki, Kan Katayama, Ryosuke Saiki, Yosuke Hirabayashi, Tomohiro Murata, Eiji Ishikawa, Masaaki Ito and Kaoru Dohi

Genes 2023, 14(2), 443; https://doi.org/10.3390/genes14020443 - 9 Feb 2023

Cited by 5 | Viewed by 2875

Abstract

Autosomal-dominant polycystic kidney disease (ADPKD) is characterized by bilateral kidney cysts that ultimately lead to end-stage kidney disease. While the major causative genes of ADPKD are PKD1 and PKD2, other genes are also thought to be involved. Fifty ADPKD patients were analyzed [...] Read more.

Autosomal-dominant polycystic kidney disease (ADPKD) is characterized by bilateral kidney cysts that ultimately lead to end-stage kidney disease. While the major causative genes of ADPKD are PKD1 and PKD2, other genes are also thought to be involved. Fifty ADPKD patients were analyzed by exome sequencing or multiplex ligation-dependent probe amplification (MLPA), followed by long polymerase chain reaction and Sanger sequencing. Variants in PKD1 or PKD2 or GANAB were detected in 35 patients (70%). Exome sequencing identified 24, 7, and 1 variants in PKD1, PKD2, and GANAB, respectively, in 30 patients. MLPA analyses identified large deletions in PKD1 in three patients and PKD2 in two patients. We searched 90 cyst-associated genes in 15 patients who were negative by exome sequencing and MLPA analyses, and identified 17 rare variants. Four of them were considered “likely pathogenic” or “pathogenic” variants according to the American College of Medical Genetics and Genomics guidelines. Of the 11 patients without a family history, four, two, and four variants were found in PKD1, PKD2, and other genes, respectively, while no causative gene was identified in one patient. While the pathogenicity of each variant in these genes should be carefully assessed, a comprehensive genetic analysis may be useful in cases of atypical ADPKD. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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22 pages, 1027 KiB

Open AccessArticle

Novel and Founder Pathogenic Variants in X-Linked Alport Syndrome Families in Greece

by Despina Hadjipanagi, Gregory Papagregoriou, Constantina Koutsofti, Christiana Polydorou, Polichronis Alivanis, Aimilios Andrikos, Stalo Christodoulidou, Manthos Dardamanis, Athanasios A. Diamantopoulos, Anastasios Fountoglou, Eleni Frangou, Eleni Georgaki, Ioannis Giannikouris, Velissarios Gkinis, Pavlos C. Goudas, Rigas G. Kalaitzidis, Nikolaos Kaperonis, Georgios Koutroumpas, George Makrydimas, Grigorios Myserlis, Andromachi Mitsioni, Christos Paliouras, Fotios Papachristou, Dorothea Papadopoulou, Nikolaos Papagalanis, Aikaterini Papagianni, Garyfalia Perysinaki, Ekaterini Siomou, Konstantinos Sombolos, Ioannis Tzanakis, Georgios V. Vergoulas, Nicoletta Printza and Constantinos Deltas Show full author list Hide full author list

Genes 2022, 13(12), 2203; https://doi.org/10.3390/genes13122203 - 24 Nov 2022

Cited by 4 | Viewed by 2936

Abstract

Alport syndrome (AS) is the most frequent monogenic inherited glomerulopathy and is also genetically and clinically heterogeneous. It is caused by semi-dominant pathogenic variants in the X-linked COL4A5 (NM_000495.5) gene or recessive variants in the COL4A3/COL4A4 (NM_000091.4/NM_000092.4) genes. The disease manifests [...] Read more.

Alport syndrome (AS) is the most frequent monogenic inherited glomerulopathy and is also genetically and clinically heterogeneous. It is caused by semi-dominant pathogenic variants in the X-linked COL4A5 (NM_000495.5) gene or recessive variants in the COL4A3/COL4A4 (NM_000091.4/NM_000092.4) genes. The disease manifests in early childhood with persistent microhematuria and can progress to proteinuria and kidney failure in adolescence or early adulthood if left untreated. On biopsy, pathognomonic features include alternate thinning, thickening and lamellation of the glomerular basement membrane (GBM), in the presence of podocyte foot process effacement. Although previous studies indicate a prevalence of AS of about 1/50,000, a recent publication reported a predicted rate of pathogenic COL4A5 variants of 1/2320. We herewith present 98 patients (40 M/58 F) from 26 Greek families. We are selectively presenting the families segregating the X-linked form of AS with pathogenic variants in the COL4A5 gene. We found 21 different pathogenic variants, 12 novel: eight glycine and one proline substitutions in the collagenous domain, one cysteine substitution in the NC1 domain, two premature termination of translation codons, three splicing variants, one 5-bp insertion/frameshift variant, one indel-frameshift variant and four gross deletions. Notably, patients in six families we describe here and three families we reported previously, carried the COL4A5-p.G624D substitution, a founder defect encountered all over Europe which is hypomorphic with mostly milder symptomatology. Importantly, on several occasions, the correct genetic diagnosis reclassified patients as patients with AS, leading to termination of previous immunosuppressive/cyclosporine A therapy and a switch to angiotensin converting enzyme inhibitors (ACEi). With the understanding that all 98 patients span a wide range of ages from infancy to late adulthood, 15 patients (11 M/4 F) reached kidney failure and 11 (10 M/1 F) received a transplant. The prospects of avoiding lengthy diagnostic investigations and erroneous medications, and the advantage of delaying kidney failure with very early administration of renin-angiotensin-aldosterone system (RAAS) blockade, highlights the importance of timely documentation of AS by genetic diagnosis. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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14 pages, 262 KiB

Open AccessArticle

Theory Designed Strategies to Support Implementation of Genomics in Nephrology

by Arushi Kansal, Catherine Quinlan, Zornitza Stark, Peter G. Kerr, Andrew J. Mallett, Chandni Lakshmanan, Stephanie Best and Kushani Jayasinghe

Genes 2022, 13(10), 1919; https://doi.org/10.3390/genes13101919 - 21 Oct 2022

Cited by 8 | Viewed by 2096

Abstract

(1) Background: Genomic testing is increasingly utilized as a clinical tool; however, its integration into nephrology remains limited. The purpose of this study was to identify barriers and prioritize interventions for the widespread implementation of genomics in nephrology. (2) Methods: Qualitative, semi-structured interviews [...] Read more.

(1) Background: Genomic testing is increasingly utilized as a clinical tool; however, its integration into nephrology remains limited. The purpose of this study was to identify barriers and prioritize interventions for the widespread implementation of genomics in nephrology. (2) Methods: Qualitative, semi-structured interviews were conducted with 25 Australian adult nephrologists to determine their perspectives on interventions and models of care to support implementation of genomics in nephrology. Interviews were guided by a validated theoretical framework for the implementation of genomic medicine—the Consolidated Framework of Implementation Research (CFIR). (3) Results: Nephrologists were from 18 hospitals, with 7 having a dedicated multidisciplinary kidney genetics service. Most practiced in the public healthcare system (n = 24), a large number were early-career (n = 13), and few had genomics experience (n = 4). The top three preferred interventions were increased funding, access to genomics champions, and education and training. Where interventions to barriers were not reported, we used the CFIR/Expert Recommendations for Implementing Change matching tool to generate theory-informed approaches. The preferred model of service delivery was a multidisciplinary kidney genetics clinic. (4) Conclusions: This study identified surmountable barriers and practical interventions for the implementation of genomics in nephrology, with multidisciplinary kidney genetics clinics identified as the preferred model of care. The integration of genomics education into nephrology training, secure funding for testing, and counselling along with the identification of genomics champions should be pursued by health services more broadly. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

7 pages, 223 KiB

Open AccessArticle

Participant Choice towards Receiving Potential Additional Findings in an Australian Nephrology Research Genomics Study

by Rosie O’Shea, Alasdair Wood, Chirag Patel, Hugh J. McCarthy, Amali Mallawaarachchi, Catherine Quinlan, Cas Simons, Zornitza Stark and Andrew J. Mallett

Genes 2022, 13(10), 1804; https://doi.org/10.3390/genes13101804 - 6 Oct 2022

Cited by 1 | Viewed by 1460

Abstract

The choices of participants in nephrology research genomics studies about receiving additional findings (AFs) are unclear as are participant factors that might influence those choices. Methods: Participant choices and factors potentially impacting decisions about AFs were examined in an Australian study applying [...] Read more.

The choices of participants in nephrology research genomics studies about receiving additional findings (AFs) are unclear as are participant factors that might influence those choices. Methods: Participant choices and factors potentially impacting decisions about AFs were examined in an Australian study applying research genomic testing following uninformative diagnostic genetic testing for suspected monogenic kidney disease. Results: 93% of participants (195/210) chose to receive potential AFs. There were no statistically significant differences between those consenting to receive AFs or not in terms of gender (p = 0.97), median age (p = 0.56), being personally affected by the inherited kidney disease of interest (p = 0.38), or by the inheritance pattern (p = 0.12–0.19). Participants were more likely to choose not to receive AFs if the family proband presented in adulthood (p = 0.01), if there was family history of another genetic disorder (p = 0.01), and where the consent process was undertaken by an adult nephrologist (p = 0.01). Conclusion: The majority of participants in this nephrology research genomics study chose to receive potential AFs. Younger age of the family proband, family history of an alternate genetic disorder, and consenting by some multidisciplinary team members might impact upon participant choices. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

10 pages, 2312 KiB

Open AccessArticle

Mutation Analysis of Thin Basement Membrane Nephropathy

by Yosuke Hirabayashi, Kan Katayama, Mutsuki Mori, Hiroshi Matsuo, Mika Fujimoto, Kensuke Joh, Tomohiro Murata, Masaaki Ito and Kaoru Dohi

Genes 2022, 13(10), 1779; https://doi.org/10.3390/genes13101779 - 2 Oct 2022

Cited by 7 | Viewed by 2721

Abstract

Thin basement membrane nephropathy (TBMN) is characterized by the observation of microhematuria and a thin glomerular basement membrane on kidney biopsy specimens. Its main cause is heterozygous mutations of COL4A3 or COL4A4, which also cause late-onset focal segmental glomerulosclerosis (FSGS) or autosomal [...] Read more.

Thin basement membrane nephropathy (TBMN) is characterized by the observation of microhematuria and a thin glomerular basement membrane on kidney biopsy specimens. Its main cause is heterozygous mutations of COL4A3 or COL4A4, which also cause late-onset focal segmental glomerulosclerosis (FSGS) or autosomal dominant Alport syndrome (ADAS). Thirteen TBMN cases were analyzed using Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and exome sequencing. Ten heterozygous variants were detected in COL4A3 or COL4A4 in nine patients via Sanger sequencing, three of which were novel variants. The diagnostic rate of “likely pathogenic” or “pathogenic” under the American College of Medical Genetics and Genomics guidelines was 53.8% (7 out of 13 patients). There were eight single nucleotide variants, seven of which were glycine substitutions in the collagenous domain, one of which was a splice-site single nucleotide variant, and two of which were deletion variants. One patient had digenic variants in COL4A3 and COL4A4. While MLPA analyses showed negative results, exome sequencing identified three heterozygous variants in causative genes of FSGS in four patients with no apparent variants on Sanger sequencing. Since patients with heterozygous mutations of COL4A3 or COL4A4 showed a wide spectrum of disease from TBMN to ADAS, careful follow-up will be necessary for these patients. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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9 pages, 1035 KiB

Open AccessArticle

Vignette-Based Reflections to Inform Genetic Testing Policies in Living Kidney Donors

by Gurmukteshwar Singh, Reginald Gohh, Dinah Clark, Kartik Kalra, Manoj Das, Gitana Bradauskaite, Anthony J. Bleyer, Bekir Tanriover, Alex R. Chang and Prince M. Anand

Genes 2022, 13(4), 592; https://doi.org/10.3390/genes13040592 - 26 Mar 2022

Cited by 3 | Viewed by 2787

Abstract

Family history of kidney disease increases risk of end-stage kidney disease (ESKD) in donors. Pre-donation genetic testing is recommended in evaluation guidelines and regulatory policy. Collaborating across several institutions, we describe cases to illustrate the utility as well as practical issues in incorporating [...] Read more.

Family history of kidney disease increases risk of end-stage kidney disease (ESKD) in donors. Pre-donation genetic testing is recommended in evaluation guidelines and regulatory policy. Collaborating across several institutions, we describe cases to illustrate the utility as well as practical issues in incorporating genetic testing in transplant protocols. Case 1 is from 2009, before pervasive genetic testing. A healthy 27-year-old Caucasian male had an uneventful donor evaluation for his mother, who had early onset ESKD of unclear cause. He participated in paired-exchange kidney donation, but developed progressive kidney disease and gout over the next 10 years. A uromodulin gene mutation (NM_003361.3(UMOD):c.377 G>A p.C126Y) was detected and kidney biopsy showed tubulointerstitial kidney disease. The patient subsequently required kidney transplantation himself. Case 2 was a 36-year-old African American female who had an uneventful kidney donor evaluation. She underwent gene panel-based testing to rule out ApolipoproteinL1 risk variants, for which was negative. Incidentally, a sickle-cell trait (NM_000518.5(HBB):c.20A>T p.Glu7Val) was noted, and she was declined for kidney donation. This led to significant patient anguish. Case 3 was a 26-year-old Caucasian female who underwent panel-based testing because the potential recipient, her cousin, carried a variant of uncertain significance in the hepatocyte nuclear factor-1-β (HNF1B) gene. While the potential donor did not harbor this variant, she was found to have a likely pathogenic variant in complement factor I (NM_000204.4(CFI):c.1311dup:p.Asp438Argfs*8), precluding kidney donation. Our cases emphasize that while genetic testing can be invaluable in donor evaluation, transplant centers should utilize detailed informed consent, develop care pathways for secondary genetic findings, and share experience to develop best practices around genetic testing in donors. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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13 pages, 1495 KiB

Open AccessArticle

A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

by Sonia Mota-Zamorano, Luz María González, Nicolás Roberto Robles, José Manuel Valdivielso, Bárbara Cancho, Juan López-Gómez and Guillermo Gervasini

Genes 2021, 12(12), 1992; https://doi.org/10.3390/genes12121992 - 15 Dec 2021

Cited by 4 | Viewed by 2845

Abstract

Diabetic kidney disease (DKD) has been pointed out as a prominent cause of chronic and end-stage renal disease (ESRD). There is a genetic predisposition to DKD, although clinically relevant loci are yet to be identified. We utilized a custom target next-generation sequencing 70-gene [...] Read more.

Diabetic kidney disease (DKD) has been pointed out as a prominent cause of chronic and end-stage renal disease (ESRD). There is a genetic predisposition to DKD, although clinically relevant loci are yet to be identified. We utilized a custom target next-generation sequencing 70-gene panel to screen a discovery cohort of 150 controls, DKD and DKD-ESRD patients. Relevant SNPs for the susceptibility and clinical evolution of DKD were replicated in an independent validation cohort of 824 controls and patients. A network analysis aiming to assess the impact of variability along specific pathways was also conducted. Forty-eight SNPs displayed significantly different frequencies in the study groups. Of these, 28 with p-values lower than 0.01 were selected for replication. MYH9 rs710181 was inversely associated with the risk of DKD (OR = 0.52 (0.28–0.97), p = 0.033), whilst SOWAHB rs13140552 and CNDP1 rs4891564 were not carried by cases or controls, respectively (p = 0.044 and 0.023). In addition, the RGMA rs1969589 CC genotype was significantly correlated with lower albumin-to-creatinine ratios in the DKD patients (711.8 ± 113.0 vs. 1375.9 ± 474.1 mg/g for TC/TT; mean difference = 823.5 (84.46–1563.0); p = 0.030). No biological pathway stood out as more significantly affected by genetic variability. Our findings reveal new variants that could be useful as biomarkers of DKD onset and/or evolution. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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Review

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18 pages, 848 KiB

Open AccessReview

Genetic Modifiers of Mendelian Monogenic Collagen IV Nephropathies in Humans and Mice

by Constantinos Deltas, Gregory Papagregoriou, Stavroula F. Louka, Apostolos Malatras, Frances Flinter, Daniel P. Gale, Susie Gear, Oliver Gross, Julia Hoefele, Rachel Lennon, Jeffrey H. Miner, Alessandra Renieri, Judy Savige and A. Neil Turner

Genes 2023, 14(9), 1686; https://doi.org/10.3390/genes14091686 - 25 Aug 2023

Cited by 9 | Viewed by 2769

Abstract

Familial hematuria is a clinical sign of a genetically heterogeneous group of conditions, accompanied by broad inter- and intrafamilial variable expressivity. The most frequent condition is caused by pathogenic (or likely pathogenic) variants in the collagen-IV genes, COL4A3/A4/A5. Pathogenic variants in COL4A5 [...] Read more.

Familial hematuria is a clinical sign of a genetically heterogeneous group of conditions, accompanied by broad inter- and intrafamilial variable expressivity. The most frequent condition is caused by pathogenic (or likely pathogenic) variants in the collagen-IV genes, COL4A3/A4/A5. Pathogenic variants in COL4A5 are responsible for the severe X-linked glomerulopathy, Alport syndrome (AS), while homozygous or compound heterozygous variants in the COL4A3 or the COL4A4 gene cause autosomal recessive AS. AS usually leads to progressive kidney failure before the age of 40-years when left untreated. People who inherit heterozygous COL4A3/A4 variants are at-risk of a slowly progressive form of the disease, starting with microscopic hematuria in early childhood, developing Alport spectrum nephropathy. Sometimes, they are diagnosed with benign familial hematuria, and sometimes with autosomal dominant AS. At diagnosis, they often show thin basement membrane nephropathy, reflecting the uniform thin glomerular basement membrane lesion, inherited as an autosomal dominant condition. On a long follow-up, most patients will retain normal or mildly affected kidney function, while a substantial proportion will develop chronic kidney disease (CKD), even kidney failure at an average age of 55-years. A question that remains unanswered is how to distinguish those patients with AS or with heterozygous COL4A3/A4 variants who will manifest a more aggressive kidney function decline, requiring prompt medical intervention. The hypothesis that a subgroup of patients coinherit additional genetic modifiers that exacerbate their clinical course has been investigated by several researchers. Here, we review all publications that describe the potential role of candidate genetic modifiers in patients and include a summary of studies in AS mouse models. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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20 pages, 316 KiB

Open AccessReview

A Comparative Presentation of Mouse Models That Recapitulate Most Features of Alport Syndrome

by Stavros Nikolaou and Constantinos Deltas

Genes 2022, 13(10), 1893; https://doi.org/10.3390/genes13101893 - 18 Oct 2022

Cited by 6 | Viewed by 3738

Abstract

Alport syndrome is a hereditary kidney disease caused by mutations in the three genes encoding for collagen IV: COL4A3, COL4A4, and COL4A5. Several mouse models have been created for the study of this disease with variable phenotypic outcomes. This review is [...] Read more.

Alport syndrome is a hereditary kidney disease caused by mutations in the three genes encoding for collagen IV: COL4A3, COL4A4, and COL4A5. Several mouse models have been created for the study of this disease with variable phenotypic outcomes. This review is an up-to-date presentation of the current mouse models existing in the literature with a detailed comparison of the phenotypic features characterizing each model. Although in humans it is primarily a glomerulopathy, data suggest that in some mouse models, the initial symptoms appear in the tubule-interstitial region rather than the glomerulus. Additionally, in some other models, the severity of disease in the tubule-interstitial region is affected by the genetic background. In conclusion, the phenotypic spectrum of each model appears to be affected by the model’s genetic background, the position of the genetic alteration within the gene, and the type of the genetic alteration. Despite these disparities, mouse models recapitulate with relatively high fidelity several features of the human disease, which makes them useful for studies aimed at better understanding cellular pathomechanisms and for finding new treatments. Full article

(This article belongs to the Special Issue Nephrogenetics and Kidney Genomics—the Future Is Now?)

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