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Comprehensive Genetic Analysis Reveals Complexity of Monogenic Urinary Stone Disease

Cogal, A G; Arroyo, J; Shah, R J; Reese, K J; Walton, B N; Reynolds, L M; Kennedy, G N; Seide, B M; Senum, S R; Baum, M; Erickson, S B; Jagadeesh, S; Soliman, N A; Goldfarb, D S; Beara-Lasic, L; Edvardsson, V O; Palsson, R; Milliner, D S; Sas, D J; Lieske, J C; Harris, P C
Introduction: Because of phenotypic overlap between monogenic urinary stone diseases (USD), gene-specific analyses can result in missed diagnoses. We used targeted next generation sequencing (tNGS), including known and candidate monogenic USD genes, to analyze suspected primary hyperoxaluria (PH) or Dent disease (DD) patients genetically unresolved (negative; N) after Sanger analysis of the known genes. Cohorts consisted of 285 PH (PHN) and 59 DD (DDN) families.
Method(s): Variants were assessed using disease-specific and population databases plus variant assessment tools and categorized using the American College of Medical Genetics (ACMG) guidelines. Prior Sanger analysis identified 47 novel PH or DD gene pathogenic variants.
Result(s): Screening by tNGS revealed pathogenic variants in 14 known monogenic USD genes, accounting for 45 families (13.1%), 27 biallelic and 18 monoallelic, including 1 family with a copy number variant (CNV). Recurrent genes included the following: SLC34A3 (n = 13), CLDN16 (n = 8), CYP24A1 (n = 4), SLC34A1 (n = 3), SLC4A1 (n = 3), APRT (n = 2), CLDN19 (n = 2), HNF4A1 (n = 2), and KCNJ1 (n = 2), whereas ATP6V1B1, CASR, and SLC12A1 and missed CNVs in the PH genes AGXT and GRHPR accounted for 1 pedigree each. Of the 48 defined pathogenic variants, 27.1% were truncating and 39.6% were novel. Most patients were diagnosed before 18 years of age (76.1%), and 70.3% of biallelic patients were homozygous, mainly from consanguineous families.
Conclusion(s): Overall, in patients suspected of DD or PH, 23.9% and 7.3% of cases, respectively, were caused by pathogenic variants in other genes. This study shows the value of a tNGS screening approach to increase the diagnosis of monogenic USD, which can optimize therapies and facilitate enrollment in clinical trials.
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EMBASE:2015372198
ISSN: 2468-0249
CID: 5045042

Prevalence of low molecular weight proteinuria and Dent disease 1 CLCN5 mutations in proteinuric cohorts

Beara-Lasic, Lada; Cogal, Andrea; Mara, Kristin; Enders, Felicity; Mehta, Ramila A; Haskic, Zejfa; Furth, Susan L; Trachtman, Howard; Scheinman, Steven J; Milliner, Dawn S; Goldfarb, David S; Harris, Peter C; Lieske, John C
BACKGROUND:Dent disease type 1 (DD1) is a rare X-linked disorder caused mainly by CLCN5 mutations. Patients may present with nephrotic-range proteinuria leading to erroneous diagnosis of focal segmental glomerulosclerosis (FSGS) and unnecessary immunosuppressive treatments. METHODS:M/TP, and A/TP from the CKiD cohort were compared with DD1 and DC. RESULTS:M/Cr of ≥ 120 mg/g (> 13.6 mg/mmol) creatinine were good screens for Dent disease. CONCLUSIONS:M/Cr ≥ 120 mg/g (> 13.6 mg/mmol) had the highest sensitivity and specificity when differentiating DD1 and studied CKiD populations.
PMID: 30852663
ISSN: 1432-198x
CID: 3732872

Nephrolithiasis in women: how different from men?

Beara-Lasic, Lada; Goldfarb, David S
PURPOSE OF REVIEW/OBJECTIVE:Men have more kidney stones compared with women; however, the difference is progressively decreasing. The reasons for higher prevalence of stones in men, as well as increasing prevalence in women, is a subject of ongoing speculation. In this review, we summarize the evidence of differences between men and women and expand on the speculative causes. RECENT FINDINGS/RESULTS:Stone incidence is rising in women and adolescent girls. Stone disease is more heritable among men than women, and women demonstrate greater influence of the unique environment. Women under the age of 50 years who have been pregnant, have more than double the odds of kidney stones compared with those who have never been pregnant. Women are more burdened with obesity, bariatric surgery and dieting, all associated with increased stones. Women have higher urinary pH because of greater absorption of dietary organic anions leading to increased urinary citrate, compared with men, and they differ in tubular calcium handling. SUMMARY/CONCLUSIONS:It is obvious that the cause of stones in men and women is complex and requires further study. Potential clues offered are in the change of the female environment, influencing increasing incidence in stones, particularly of younger women and female adolescents.
PMID: 31789849
ISSN: 1473-6543
CID: 4217972

Dent disease: A window into calcium and phosphate transport

Anglani, Franca; Gianesello, Lisa; Beara-Lasic, Lada; Lieske, John
This review examines calcium and phosphate transport in the kidney through the lens of the rare X-linked genetic disorder Dent disease. Dent disease type 1 (DD1) is caused by mutations in the CLCN5 gene encoding ClC-5, a Cl- /H+ antiporter localized to early endosomes of the proximal tubule (PT). Phenotypic features commonly include low molecular weight proteinuria (LMWP), hypercalciuria, focal global sclerosis and chronic kidney disease; calcium nephrolithiasis, nephrocalcinosis and hypophosphatemic rickets are less commonly observed. Although it is not surprising that abnormal endosomal function and recycling in the PT could result in LMWP, it is less clear how ClC-5 dysfunction disturbs calcium and phosphate metabolism. It is known that the majority of calcium and phosphate transport occurs in PT cells, and PT endocytosis is essential for calcium and phosphorus reabsorption in this nephron segment. Evidence from ClC-5 KO models suggests that ClC-5 mediates parathormone endocytosis from tubular fluid. In addition, ClC-5 dysfunction alters expression of the sodium/proton exchanger NHE3 on the PT apical surface thus altering transcellular sodium movement and hence paracellular calcium reabsorption. A potential role for NHE3 dysfunction in the DD1 phenotype has never been investigated, either in DD models or in patients with DD1, even though patients with DD1 exhibit renal sodium and potassium wasting, especially when exposed to even a low dose of thiazide diuretic. Thus, insights from the rare disease DD1 may inform possible underlying mechanisms for the phenotype of hypercalciuria and idiopathic calcium stones.
PMID: 31472005
ISSN: 1582-4934
CID: 4054742

Recurrent Calcium Kidney Stones

Beara-Lasic, Lada; Goldfarb, David S
PMID: 31221735
ISSN: 1555-905x
CID: 3939382

Rituximab or Cyclosporine in the Treatment of Membranous Nephropathy

Fervenza, Fernando C; Appel, Gerald B; Barbour, Sean J; Rovin, Brad H; Lafayette, Richard A; Aslam, Nabeel; Jefferson, Jonathan A; Gipson, Patrick E; Rizk, Dana V; Sedor, John R; Simon, James F; McCarthy, Ellen T; Brenchley, Paul; Sethi, Sanjeev; Avila-Casado, Carmen; Beanlands, Heather; Lieske, John C; Philibert, David; Li, Tingting; Thomas, Lesley F; Green, Dolly F; Juncos, Luis A; Beara-Lasic, Lada; Blumenthal, Samuel S; Sussman, Amy N; Erickson, Stephen B; Hladunewich, Michelle; Canetta, Pietro A; Hebert, Lee A; Leung, Nelson; Radhakrishnan, Jay; Reich, Heather N; Parikh, Samir V; Gipson, Debbie S; Lee, Dominic K; da Costa, Bruno R; Jüni, Peter; Cattran, Daniel C
BACKGROUND:B-cell anomalies play a role in the pathogenesis of membranous nephropathy. B-cell depletion with rituximab may therefore be noninferior to treatment with cyclosporine for inducing and maintaining a complete or partial remission of proteinuria in patients with this condition. METHODS:of body-surface area and had been receiving angiotensin-system blockade for at least 3 months to receive intravenous rituximab (two infusions, 1000 mg each, administered 14 days apart; repeated at 6 months in case of partial response) or oral cyclosporine (starting at a dose of 3.5 mg per kilogram of body weight per day for 12 months). Patients were followed for 24 months. The primary outcome was a composite of complete or partial remission of proteinuria at 24 months. Laboratory variables and safety were also assessed. RESULTS:receptor (PLA2R) antibodies, the decline in autoantibodies to anti-PLA2R was faster and of greater magnitude and duration in the rituximab group than in the cyclosporine group. Serious adverse events occurred in 11 patients (17%) in the rituximab group and in 20 (31%) in the cyclosporine group (P = 0.06). CONCLUSIONS:Rituximab was noninferior to cyclosporine in inducing complete or partial remission of proteinuria at 12 months and was superior in maintaining proteinuria remission up to 24 months. (Funded by Genentech and the Fulk Family Foundation; MENTOR ClinicalTrials.gov number, NCT01180036.).
PMID: 31269364
ISSN: 1533-4406
CID: 3968202

A Twin Study of Genetic Influences on Nephrolithiasis in Women and Men

Goldfarb, David S; Avery, Ally R; Beara-Lasic, Lada; Duncan, Glen E; Goldberg, Jack
Background/UNASSIGNED:Nephrolithiasis is a complex phenotype influenced by both genetic and environmental factors. Previously we found a genetic component to stone disease using a sample of male twin pairs. We now report on the genetic contribution to stones in a sample of female and male twin pairs. Methods/UNASSIGNED:We conducted a classic twin study of kidney stones using the Washington State Twin Registry. Data were collected by questionnaire to obtain self-reported history of kidney stones. Univariate structural equation modeling was used to determine the relative contributions of additive genetics, common environment, and unique environment. Results/UNASSIGNED: < 0.05). Conclusions/UNASSIGNED:Nephrolithiasis in women has a heritable component less than that we again demonstrate in men. This finding may in part explain why more stone formers are men than women. Women twins demonstrated a greater effect of the unique environment on stone prevalence. The specific environmental risk factors that account for this effect are not currently known.
PMCID:6451147
PMID: 30993229
ISSN: 2468-0249
CID: 3808072

A custom next generation sequencing (NGS) panel for kidney stone disease resolves diagnosis in mutation negative patients clinically diagnosed with dent disease [Meeting Abstract]

Cogal, A G; Senum, S R; Gall, E C-L; Seide, B M; Banks, C; Olson, J B; Greenwood, T M; Sas, D J; Milliner, D S; Lasic, L B; Lieske, J C; Harris, P C
Background: Dent disease is an X-linked disorder characterized by low molecular weight proteinuria, nephrolithiasis/nephrocalcinosis and CKD. We previously performed molecular screening of suspected Dent patients by Sanger sequencing of the known genes: CLCN5 and OCRL. The majority of cases were genetically resolved, but there remained a cohort with no mutations detected (NMD), which we analyze here employing a NGS panel.
Method(s): A NGS panel consisting of 90 known and candidate genes related to urinary stone risk was developed and 61 NMD suspected Dent families screened. The phenotype of resolved patients was compared to the implicated gene.
Result(s): Likely pathogenic mutations consistent, or in one case divergent, with the presenting phenotype were detected in 5 (8%) of the 61 NMD families (Table). Two cases with SLC34A3 mutations were detected, one with a missense, an inframe deletion and a splicing mutation and a second homozygous for a novel frameshifting duplication. SLC12A1 biallelic missense mutations were found in a patient with a typical Bartter phenotype. A patient with a KCNJ1 frameshifting duplication and missense mutation had nephrocalcinosis, proteinuria, and CKD, but lacked the typical electrolyte abnormalities of Barrter. One subject was homozygous for a previously described CLDN16 missense mutation. An additional patient was found to have two large chromosomal duplications, confirmed by MLPA and microarray analysis, which we have categorized as possibly pathogenic. Three additional patients with weaker biallelic variants in candidate genes are being further assessed.
Conclusion(s): This analysis demonstrates the utility of a panel-based NGS approach in unresolved patients with suspected monogenic causes of nephrocalcinosis or urinary stone disease and is valuable since the phenotypes of these disorders can demonstrate significant divergence and overlap
EMBASE:633736918
ISSN: 1533-3450
CID: 4755732

PREVALENCE AND CHARACTERIZATION OF PROTEINURIA IN A KIDNEY STONE CLINIC COHORT: ARE WE MISSING DENT DISEASE? [Meeting Abstract]

Manohar, Sandhya; Wang, Xiangling; Beara-Lasic, Lada; Lieske, John
ISI:000397702100214
ISSN: 1523-6838
CID: 2541002

Glomerular Pathology in Dent Disease and Its Association with Kidney Function

Wang, Xiangling; Anglani, Franca; Beara-Lasic, Lada; Mehta, Anila J; Vaughan, Lisa E; Herrera Hernandez, Loren; Cogal, Andrea; Scheinman, Steven J; Ariceta, Gema; Isom, Robert; Copelovitch, Lawrence; Enders, Felicity T; Del Prete, Dorella; Vezzoli, Giuseppe; Paglialonga, Fabio; Harris, Peter C; Lieske, John C
BACKGROUND AND OBJECTIVES: Dent disease is a rare X-linked disorder characterized by low molecular weight proteinuria and often considered a renal tubular disease. However, glomerulosclerosis was recently reported in several patients. Thus, Dent disease renal histopathologic features were characterized and assessed, and their association with kidney function was assessed. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Clinical renal pathology reports and slides (where available) were collected from 30 boys and men in eight countries who had undergone clinical renal biopsy between 1995 and 2014. RESULTS: Median (25th, 75th percentiles) age at biopsy was 7.5 (5, 19) years with an eGFR of 69 (44, 94) ml/min per 1.73 m2 and a 24-hour urine protein of 2000 (1325, 2936) mg. A repeat biopsy for steroid-resistant proteinuria was performed in 13% (four of 30) of the patients. Prominent histologic findings included focal global glomerulosclerosis in 83% (25 of 30; affecting 16%+/-19% glomeruli), mild segmental foot process effacement in 57% (13 of 23), focal interstitial fibrosis in 60% (18 of 30), interstitial lymphocytic infiltration in 53% (16 of 30), and tubular damage in 70% (21 of 30). Higher percentages of globally sclerotic glomeruli, foot process effacement, and interstitial inflammation were associated with lower eGFR at biopsy, whereas foot process effacement was associated with steeper annual eGFR decline. CONCLUSIONS: These associations suggest a potential role for glomerular pathology, specifically involving the podocyte, in disease progression, which deserves further study. Furthermore, Dent disease should be suspected in boys and men who have unexplained proteinuria with focal global glomerulosclerosis and segmental foot process effacement on renal biopsy.
PMCID:5142066
PMID: 27697782
ISSN: 1555-905x
CID: 2274482