Nanyawan Rungroj

Molecular mechanisms of autosomal dominant and recessive distal renal tubular acidosis caused by SLC4A1 (AE1) mutations

Mutations of SLC4A1 (AE1) encoding the kidney anion (Cl−/HCO3−) exchanger 1 (kAE1 or band 3) can result in either autosomal dominant (AD) or autosomal recessive (AR) distal renal tubular acidosis (dRTA). The molecular mechanisms associated with SLC4A1 mutations resulting in these different modes of inheritance are now being unveiled using transfected cell systems. The dominant mutants kAE1 R589H, R901X and S613F, which have normal or insignificant changes in anion transport function, exhibit intracellular retention with endoplasmic reticulum (ER) localization in cultured non-polarized and polarized cells, while the dominant mutants kAE1 R901X and G609R are mis-targeted to apical membrane in addition to the basolateral membrane in cultured polarized cells. A dominant-negative effect is likely responsible for the dominant disease because heterodimers of kAE1 mutants and the wild-type protein are intracellularly retained. The recessive mutants kAE1 G701D and S773P however exhibit distinct trafficking defects. The kAE1 G701D mutant is retained in the Golgi apparatus, while the misfolded kAE1 S773P, which is impaired in ER exit and is degraded by proteosome, can only partially be delivered to the basolateral membrane of the polarized cells. In contrast to the dominant mutant kAE1, heterodimers of the recessive mutant kAE1 and wild-type kAE1 are able to traffic to the plasma membrane. The wild-type kAE1 thus exhibits a ‘dominant-positive effect’ relative to the recessive mutant kAE1 because it can rescue the mutant proteins from intracellular retention to be expressed at the cell surface. Consequently, homozygous or compound heterozygous recessive mutations are required for presentation of the disease phenotype. Future work using animal models of dRTA will provide additional insight into the pathophysiology of this disease.

Evidence suggesting a genetic contribution to kidney stone in northeastern Thai population

Genetic factor may play a role in the pathogenesis of kidney stone that is found in the northeastern (NE) Thai population. Herein, we report initial evidence suggesting genetic contribution to the disease in this population. We examined 1,034 subjects including 135 patients with kidney stone, 551 family members, and 348 villagers by radiography of kidney–ureter–bladder (KUB) and other methods, and also analyzed stones removed by surgical operations. One hundred and sixteen of 551 family members (21.05%) and 23 of the 348 villagers (6.61%) were affected with kidney stone. The relative risk (λR) of the disease among family members was 3.18. Calcium stones (whewellite, dahllite, and weddellite) were observed in about 88% of stones analyzed. Our data indicate familial aggregation of kidney stone in this population supporting that genetic factor should play some role in its pathogenesis. Genetic and genomic studies will be conducted to identify the genes associated with the disease.

Prothrombin Haplotype Associated With Kidney Stone Disease in Northeastern Thai Patients

OBJECTIVE To evaluate genetic variations associated with kidney stone disease in Northeastern Thai patients. METHODS Altogether, 67 single nucleotide polymorphisms (SNP) distributed within 8 candidate genes, namely TFF1, S100A8, S100A9, S100A12, AMBP, SPP1, UMOD, and F2, which encode stone inhibitor proteins, including trefoil factor 1, calgranulin (A, B, and C), bikunin, osteopontin, tamm-Horsfall protein, and prothrombin, respectively, were initially genotyped in 112 individuals each and in additional subjects to consist of 164 patients and 216 control subjects in total. RESULTS We found that minor allele and homozygous genotype frequencies of 8 of 10 SNPs distributed within the F2 gene were significantly higher in the control group than in the patient group. Two F2 haplotypes were found to be dually associated with kidney stone risk, one (TGCCGCCGCG) with increased disease risk and the other (CGTTCCGCTA) with decreased disease risk. However, these 2 haplotypes were associated with the disease risks in only the female, not the male, group. CONCLUSIONS The results of our study indicate that genetic variation of F2 is associated with kidney stone risk in Northeastern Thai female patients.

Simple, Efficient, and Cost-Effective Multiplex Genotyping with Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Hemoglobin Beta Gene Mutations

A number of common mutations in the hemoglobin beta (HBB) gene cause beta-thalassemia, a monogenic disease with high prevalence in certain ethnic groups. As there are 30 HBB variants that cover more than 99.5% of HBB mutant alleles in the Thai population, an efficient and cost-effective screening method is required. Three panels of multiplex primer extensions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were developed. The first panel simultaneously detected 21 of the most common HBB mutations, while the second panel screened nine additional mutations, plus seven of the first panel for confirmation; the third panel was used to confirm three HBB mutations, yielding a 9-Da mass difference that could not be clearly distinguished by the previous two panels. The protocol was both standardized using 40 samples of known genotypes and subsequently validated in 162 blind samples with 27 different genotypes (including a normal control), comprising heterozygous, compound heterozygous, and homozygous beta-thalassemia. Results were in complete agreement with those from the genotyping results, conducted using three different methods overall. The method developed here permitted the detection of mutations missed using a single genotyping procedure. The procedure should serve as the method of choice for HBB genotyping due to its accuracy, sensitivity, and cost-effectiveness, and can be applied to studies of other gene variants that are potential disease biomarkers.

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP)

BackgroundWe have previously developed a long RT-PCR method for selective amplification of full-length PKD1 transcripts (13.6 kb) and a long-range PCR for amplification in the reiterated region (18 kb) covering exons 14 and 34 of the PKD1 gene. These have provided us with an opportunity to study PKD1 mutations especially in its reiterated region which is difficult to examine. In this report, we have further developed the method of multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP) for analysis of PKD1 mutations in the patients with autosomal dominant polycystic kidney disease (ADPKD). Novel and de novo PKD1 mutations are identified and reported.MethodsFull-length PKD1 cDNA isolated from the patients with ADPKD was fractionated into nine overlapping segments by nested-PCR. Each segment was digested with sets of combined restriction endonucleases before the SSCP analysis. The fragments with aberrant migration were mapped, isolated, and sequenced. The presence of mutation was confirmed by the long-range genomic DNA amplification in the PKD1 region, sequencing, direct mutation detection, and segregation analysis in the affected family.ResultsFive PKD1 mutations identified are two frameshift mutations caused by two di-nucleotide (c. 5225_5226delAG and c.9451_9452delAT) deletions, a nonsense (Q1828X, c.5693C>T) mutation, a splicing defect attributable to 31 nucleotide deletion (g.33184_33214del31), and an in-frame deletion (L3287del, c.10070_10072delCTC). All mutations occurred within the reiterated region of the gene involving exons 15, 26, 15, 19 and 29, respectively. Three mutations (one frameshift, splicing defect, and in-frame deletion) are novel and two (one frameshift and nonsense) known. In addition, two mutations (nonsense and splicing defect) are possibly de novo.ConclusionThe MRF-SSCP method has been developed to analyze PCR products generated by the long RT-PCR and nested-PCR technique for screening PKD1 mutations in the full-length cDNA. Five mutations identified were all in the reiterated region of this gene, three of which were novel. The presence of de novo PKD1 mutations indicates that this gene is prone to mutations.

Association between Human Prothrombin Variant (T165M) and Kidney Stone Disease

We previously reported the association between prothrombin (F2), encoding a stone inhibitor protein - urinary prothrombin fragment 1 (UPTF1), and the risk of kidney stone disease in Northeastern Thai patients. To identify specific F2 variation responsible for the kidney stone risk, we conducted sequencing analysis of this gene in a group of the patients with kidney stone disease. Five intronic SNPs (rs2070850, rs2070852, rs1799867, rs2282687, and rs3136516) and one exonic non-synonymous single nucleotide polymorphism (nsSNP; rs5896) were found. The five intronic SNPs have no functional change as predicted by computer programs while the nsSNP rs5896 (c.494 C>T) located in exon 6 results in a substitution of threonine (T) by methionine (M) at the position 165 (T165M). The nsSNP rs5896 was subsequently genotyped in 209 patients and 216 control subjects. Genotypic and allelic frequencies of this nsSNP were analyzed for their association with kidney stone disease. The frequency of CC genotype of rs5896 was significantly lower in the patient group (13.4%) than that in the control group (22.2%) (P = 0.017, OR 0.54, 95% CI 0.32–0.90), and the frequency of C allele was significantly lower in the patient group (36.1%) than that in the control group (45.6%) (P = 0.005, OR 0.68, 95% CI 0.51–0.89). The significant differences of genotype and allele frequencies were maintained only in the female group (P = 0.033 and 0.003, respectively). The effect of amino-acid change on UPTF1 structure was also examined by homologous modeling and in silico mutagenesis. T165 is conserved and T165M substitution will affect hydrogen bond formation with E180. In conclusion, our results indicate that prothrombin variant (T165M) is associated with kidney stone risk in the Northeastern Thai female patients.

Correlation between genotypes of F2 rs5896 (p.Thr165Met) polymorphism and urinary prothrombin fragment 1

resolution melting (PCR-HRM) analysis and confirmed by DNA sequencing. Subjects that were taking medications that could cause the development of stones or that could affect mineral metabolism were excluded. To avoid potential effects of renal disease, subjects with dipstick proteinuria or glucosuria above trace levels were also excluded. Urine specimens were collected in the presence of 1 M sodium azide and were determined to be free of blood, haemoglobin, and nitrites using Combur Test M (Roche Diagnostics, Mannheim, Germany). One hundred millilitre aliquots of urine specimens were centrifuged at 3500 g (Beckman JA-14; Beckman Coulter, Inc. Brea, CA, USA) for 10 min, concentrated through a 3000 NMWL Amicon Ultra-15 Centrifugal Filter Device (Millipore Corporation, Billerica, MA, USA), and dialyzed using a 10,000 MWCO dialysis tube (SnakeSkin; Thermo Fisher Scientific, Inc., Waltham, MA, USA), with stirring at 4 °C for 20 h against water and with three changes of the bath. Urine samples were then lyophilized and reconstituted in rehydration buffer (8 M urea and 2% CHAPS). Protein concentration was determined by Bradford protein assay and proteins were then separated by electrophoresis on polyacrylamide gel. The electrophoretic mobility pattern and relative quantities of UPTF1 in the concentrated urine samples from each group were loaded with equal amounts of urine creatinine (50 μg) and examined by Western blot analysis using sheep anti-human prothrombin fragment 1 (CL20111AP; Cedarlane Laboratories Ltd, Burlington, NC, USA) and donkey anti-sheep IgG-HRP (sc-2473; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) [6]. Chemiluminescent signals generated by SuperSignal West Pico Chemiluminescent Substrate (Thermo Fisher Scientific, Inc., Waltham, MA, USA) were detected using a G:BOX chemiluminescence imaging system (Syngene, Cambridge, UK). Specific band intensities of UPTF1 from Urinary prothrombin fragment 1 (UPTF1) is an F1 activation peptide of human prothrombin [1]. This 31-kDa glycoprotein, which was originally referred to as crystal matrix protein, was found to be the major protein incorporated within calcium oxalate (CaOx) crystals generated from human urine in vitro [2]. This protein is a potent inhibitor of CaOx crystal growth and aggregation in undiluted human urine and in inorganic conditions [3, 4]. A single nucleotide polymorphism (SNP) (rs5896: NM_000506.4:c.494C>T; NP_000497.1:p.Thr165Met) that is a genetic variation of F2 gene encoding human prothrombin was reported to be associated with kidney stone disease (KSD) risk in a group of female patients from Northeastern Thailand [5]. We hypothesised that this F2 variation correlates with human urinary prothrombin level. The aim of this study was to investigate the association between this genetic variation and UPTF1 protein in normal female subjects. Twenty-four hour urine samples were collected from five female subjects in each of the SNP rs5896 TT, TC, and CC genotype groups. The subjects’ DNA samples were genotyped by polymerase chain reaction-high

Loss-of-function mutations of SCN10A encoding Na V 1.8 α subunit of voltage-gated sodium channel in patients with human kidney stone disease

Human kidney stone disease (KSD) causes significant morbidity and public health burden worldwide. The etiology of KSD is heterogeneous, ranging from monogenic defects to complex interaction between genetic and environmental factors. However, the genetic defects causing KSD in the majority of affected families are still unknown. Here, we report the discovery of mutations of SCN10A, encoding NaV1.8 α subunit of voltage-gated sodium channel, in families with KSD. The region on chromosome 3 where SCN10A locates was initially identified in a large family with KSD by genome-wide linkage analysis and exome sequencing. Two mutations (p.N909K and p.K1809R) in the same allele of SCN10A co-segregated with KSD in the affected family. Additional mutation (p.V1149M) of SCN10A was identified in another affected family, strongly supporting the causal role of SCN10A for KSD. The amino acids at these three positions, N909, K1809, and V1149, are highly conserved in vertebrate evolution, indicating their structural and functional significances. NaV1.8 α subunit mRNA and protein were found to express in human kidney tissues. The mutant proteins expressed in cultured cells were unstable and causing reduced current density as analyzed by whole-cell patch-clamp technique. Thus, loss-of-function mutations of SCN10A were associated with KSD in the families studied.

Molecular Diagnosis of Solute Carrier Family 4 Member 1 (SLC4A1) Mutation–Related Autosomal Recessive Distal Renal Tubular Acidosis

Background Two common mutations of the solute carrier family 4 member 1 (SLC4A1) gene, namely, Southeast Asian ovalocytosis (SAO) and band 3 Bangkok 1 (G701D), cause autosomal recessive distal renal tubular acidosis (AR dRTA) in ethnic Southeast Asian populations. In this study, we applied the high-resolution melting (HRM) method for screening of AR dRTA associated with SLC4A1 mutations in 10 new patients with unknown cause(s) of AR dRTA. Methods We analyzed SAO and G701D mutations in the patients and their family members using HRM. The results were confirmed by polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) and DNA sequencing techniques. Results All patients carried homozygous G701D mutation, whereas their family members had heterozygous G701D or homozygous wild-type. Conclusions Homozygous G701D is a common cause of AR dRTA in ethnic Thai pediatric populations. HRM can be used as a rapid screening method for common SLC4A1 mutations that cause AR dRTA in Southeast Asian and other populations.