Distal renal tubular acidosis in a Libyan patient: Evidence for digenic inheritance

https://doi.org/10.1016/j.ejmg.2017.10.002Get rights and content

Abstract

Aim of the study

Recent advances in understanding the underlying molecular mechanism for distal renal tubular acidosis (dRTA), led to an increased attention towards the primary and the familial forms of the disease. Mutations in ATP6V1B1 and ATP6V0A4 are usually responsible for the recessive form of the disease. Mutations in gene AE1 encoding the Cl-/HCO3- exchanger, usually present as dominant dRTA, but a recessive pattern has been recently described. Our objective is to identify the mutational spectrum responsible of dRTA in a consanguineous Libyan family.

Materials and methods

Both ATP6V0A4 and ATP6V1B1 genes were preferentially screened in our patient. Additional whole exome sequencing (WES) in the same patient, offered a wider view on potential chromosomal rearrangements as well as the mutational spectrum of other genes involved in this disease.

Results

The patient is a heterozygote for two different mutations, one in each of the genes ATP6V0A4 and ATP6V1B1, while no deleterious variation was detected in the remaining genes responsible for the recessive form of dRTA. Homozygosity mapping and WES confirmed our findings and supported the hypothesis of a digenic inheritance model existing as an explanation for dRTA.

Conclusions

To our knowledge, this is the first report describing a Libyan patient with dRTA who suffered from early-onset sensorineural hearing loss, with a digenic mode of inheritance, supported by the identification of two novel mutations. This study increases the understanding of how dRTA is genetically transmitted, while offers a good outline towards the molecular diagnostics and genetic counseling for dRTA in Lybians.

Introduction

Distal renal tubular acidosis (dRTA, MIM 602722) is characterized by impaired urine acidification due to the inability of the distal renal tubule to appropriately excrete H+ into the urine (Karet, 2009, Rodriguez Soriano, 2002), causing metabolic acidosis, often accompanied by hypokalemia, nephrocalcinosis, and/or nephrolithiasis (Elhayek et al., 2013, Karet et al., 1999, Shao et al., 2010).

The disease can be caused either by a defect in the H + -ATPase, which is responsible for acid (H+) secretion at the apical membrane of the epithelial α-intercalated cells or by an abnormality of the kidney anion exchanger 1 (kAE1) that functions in chloride (Cl−) and bicarbonate (HCO3−) anion exchange at the basolateral membrane. Both autosomal dominant (AD) and autosomal recessive (AR) inheritance patterns have been reported in primary dRTA.

Mutations in at least two genes ATP6V1B1 and ATP6V0A4, which encode the transmembrane a4 and catalytic b1 subunits of the apical H + -ATPase respectively, have been reported to cause autosomal recessive dRTA with sensorineural hearing loss (SNHL) or normal hearing (Karet et al., 1999, Ruf et al., 2003, Smith et al., 2000, Stover et al., 2002). Mutations in the SLC4A1 gene encoding the human AE1 have been associated with either AD or AR dRTA (Batlle and Haque, 2012, Sinha et al., 2013).

Additionally, the presence of sensorineural hearing loss (SNHL) in a patient who showed no mutation in ATP6V1B1 and ATP6V0A4 genes do not excluding a priori the possibility of a dRTA form related to a mutation in the SLC4A1 gene (Palazzo et al., 2017). The development of SNHL may also occur due to the consequences raised from non-genetic factors, such as ototoxic agents, neonatal distress and electrolyte disequilibrium.

Genetic analysis is required to further support the phenotype-genotype correlation in dRTA patients (Gao et al., 2014). Recent advances in genomics allowed mutation screening of enriched coding regions of the human genome in combination with next-generation sequencing to identify novel disease genes (Ng et al., 2010, Sanders, 2011, Walsh et al., 2010).

In this study, we initially screened ATP6V1B1 and ATP6V0A4 genes by direct sequencing in a young dRTA patient and then performed Whole Exome Sequencing (WES) to screen for mutations or large genomic rearrangements occurring in dRTA related or other genes. We reported two novel heterozygous mutations, one in each of the ATP6V1B1 and ATP6V0A4 genes in a Libyan dRTA patient with SNHL. Results highlight the possibility of digenic inheritance in dRTA, which in turn must be accounted in genetic counseling of individuals originating from Libya.

Section snippets

Patients

A two and a half years old patient from the North West of Libya, with its parents being first-cousins (third degree relatives), had severe clinical features in the first month after birth. The disease presented with hyperchloremia over 110 mmol/l, hypocalcaemia and normal plasma anion gap. This patient also showed digestive problems for several weeks, followed by fluid diarrhea and vomiting. Urinary tests showed a consistently higher urinary pH (8.3) and hypercalciuria. Radiologically, the

Results

Genetic analysis of one dRTA patient with additional SNHL, revealed two mutations in two different genes, ATP6V1B1 and ATP6V0A4, both previously associated with the trait, and the patient was heterozygous for both mutations.

Based on clinical data and since the patient presented with early bilateral deafness, molecular analysis commenced by the screening of ATP6V1B1. A novel variation (NM_001692.3: c.437A > G) was found in exon 5 in the heterozygous state. An aspartic acid residue (Asp, family

Discussion

This study is, to our knowledge, the first Libyan dRTA case that has been genetically studied. Reportedly, we identified two novel ATP6V1B1 and ATP6V0A4 in a single dRTA patient. This patient was heterozygous for a ATP6V1B1 missense mutation (p.Asp146Gly) and also heterozygous for p.Thr140Met in the ATP6V0A4 gene. It is postulated that the above variants, might be associated with the dRTA phenotype and it is remarkable in both cases the wild type acidic and polar residues respectively were

Conclusion

To our knowledge, this is the first study reporting the molecular investigation of a dRTA patient originating from Libya. Previous knowledge of a patient's ethnic background is essential in performing molecular diagnostics and must be taken into consideration for dRTA and other Mendelian diseases. The evidence shows that a novel heterozygous missense variant in ATP6V1B1, either paternal (unavailable) or spontaneous, and a previously reported heterozygous rare variant in ATP6V0A4 inherited from

Funding

This work was supported by the Tunisian Ministry of Public Health and the Ministry of Higher Education and Scientific Research (LR11IPT05), GENOMEDIKA FP7 project (Grant agreement No. 295097) and partly by a grant co-funded by the European Regional Development Fund and the Republic of Cyprus through the Research Promotion Foundation (Strategic Infrastructure Project NEW INFRASTRUCTURE/STRATEGIC/0308/24) to CD.

Conflict of interest

The authors declare no conflicts of interest.

Acknowledgements

We are grateful to the family members for their participation in this study.

References (37)

  • C. Landolt-Marticorena et al.

    Evidence that the NH2 terminus of vph1p, an integral subunit of the V0 sector of the yeast V-ATPase, interacts directly with the Vma1p and Vma13p subunits of the V1 sector

    J. Biol. Chem.

    (2000)
  • V. Palazzo et al.

    The genetic and clinical spectrum of a large cohort of patients with distal renal tubular acidosis

    Kidney Int.

    (2017)
  • D. Batlle et al.

    Genetic causes and mechanisms of distal renal tubular acidosis. Nephrology, dialysis, transplantation

    Official Publ. Eur. Dialysis Transpl. Assoc. - Eur. Ren. Assoc.

    (2012)
  • D. Chivian et al.

    Automated prediction of CASP-5 structures using the Robetta server

    Proteins

    (2003)
  • C. Deltas et al.

    Cystic diseases of the kidney: molecular biology and genetics

    Archives pathology laboratory Med.

    (2010)
  • M.A. DePristo et al.

    A framework for variation discovery and genotyping using next-generation DNA sequencing data

    Nat. Genet.

    (2011)
  • D. Elhayek et al.

    Molecular diagnosis of distal renal tubular acidosis in Tunisian patients: proposed algorithm for Northern Africa populations for the ATP6V1B1, ATP6V0A4 and SCL4A1 genes

    BMC Med. Genet.

    (2013)
  • M. Forgac

    Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology

    Nat. Rev. Mol. Cell Biol.

    (2007)
  • X. Gao et al.

    Deletion of hensin/DMBT1 blocks conversion of beta- to alpha-intercalated cells and induces distal renal tubular acidosis

    Proc. Natl. Acad. Sci. U. S. A.

    (2010)
  • Y. Gao et al.

    Mutation analysis and audiologic assessment in six Chinese children with primary distal renal tubular acidosis

    Ren. Fail.

    (2014)
  • M.A. Garcia-Gonzalez et al.

    Genetic interaction studies link autosomal dominant and recessive polycystic kidney disease in a common pathway

    Hum. Mol. Genet.

    (2007)
  • J. Gomez et al.

    Primary distal renal tubular acidosis: novel findings in patients studied by next-generation sequencing

    Pediatr. Res.

    (2016)
  • J. Hoefele et al.

    Mutational analysis of the NPHP4 gene in 250 patients with nephronophthisis

    Hum. Mutat.

    (2005)
  • F.E. Karet

    Mechanisms in hyperkalemic renal tubular acidosis

    J. Am. Soc. Nephrol. JASN

    (2009)
  • F.E. Karet et al.

    Mutations in the gene encoding B1 subunit of H+-ATPase cause renal tubular acidosis with sensorineural deafness

    Nat. Genet.

    (1999)
  • E. Kose et al.

    Val2Ala mutation in the Atp6v0a4 gene causes early-onset sensorineural hearing loss in children with recessive distal renal tubular acidosis: a case report

    Ren. Fail.

    (2014)
  • H. Li et al.

    Fast and accurate short read alignment with Burrows-Wheeler transform

    Bioinformatics

    (2009)
  • H. Li et al.

    The sequence alignment/map format and SAMtools

    Bioinformatics

    (2009)
  • View full text