Recurrent recessive mutation in deoxyguanosine kinase causes idiopathic noncirrhotic portal hypertension

Abstract

Despite advances in the diagnosis and management of idiopathic noncirrhotic portal hypertension, its pathogenesis remains elusive. Insight may be gained from study of early-onset familial idiopathic noncirrhotic portal hypertension, in which Mendelian mutations may account for disease. We performed exome sequencing of eight subjects from six kindreds with onset of portal hypertension of indeterminate etiology during infancy or childhood. Three subjects from two consanguineous families shared the identical rare homozygous p.N46S mutation in DGUOK, a deoxyguanosine kinase required for mitochondrial DNA replication; haplotype sharing demonstrated that the mutation in the two families was inherited from a remote common ancestor. All three affected subjects had stable portal hypertension with noncirrhotic liver disease for 6-16 years of follow-up. This mutation impairs adenosine triphosphate binding and reduces catalytic activity. Loss-of-function mutations in DGUOK have previously been implicated in cirrhosis and liver failure but not in isolated portal hypertension. Interestingly, treatment of patients with human immunodeficiency viral infection with the nucleoside analogue didanosine is known to cause portal hypertension in a subset of patients and lowers deoxyguanosine kinase levels in vitro; the current findings implicate these effects on deoxyguanosine kinase in the causal mechanism.

Conclusion: Our findings provide new insight into the mechanisms mediating inherited and acquired noncirrhotic portal hypertension, expand the phenotypic spectrum of DGUOK deficiency, and provide a new genetic test for a specific cause of idiopathic noncirrhotic portal hypertension. (Hepatology 2016;63:1977-1986).

Figure 1

Kindreds with non-cirrhotic portal hypertension with recurrent homozygous p.N46S DGUOK mutation are shown. Studied subjects with non-cirrhotic portal hypertension are shown as black filled symbols. Corresponding Sanger sequencing of the three index cases and their parents are depicted and labeled. Mutations are homozygous in affected subjects and heterozygous in unaffected parents.

Figure 2

Principal component analysis of the three index cases with recurrent p.N46S mutation in DGUOK (red filled circles) shows they cluster with people of European ancestry from the HapMap project (green circles).

Figure 3

Shared haplotypes among subjects with homozygous DGUOK mutation. Homozygous SNPs (filled symbols) and heterozygous SNPs (unfilled symbols) are shown across the segment of chromosome 2 containing DGUOK in the affected members of kindreds 1 and 2. The segment in which SNP genotypes are identical among all three subjects is shaded in gray. This haplotype identity establishes that the DGUOK mutation is inherited from a remote common ancestor in these families. The minimum identical homozygous segment spans 27 SNPs and 1.8 Mb (shaded in gray). rs numbers for SNPs are indicated (see also Supplementary Table 2).

Figure 4

Conservation and role of p.N46 in DGUOK. (A) Conservation of N-46 in DGUOK orthologs and related kinases (deoxycitidine kinase and thymidine kinase 2). The amino acid sequences of a segment including the P-loop of deoxyguanosine kinase, deoxycitidine kinase and thymidine kinase 2 are shown, demonstrating that asparagine is completely conserved at the homologous position across all vertebrate species. (B) Ribbon diagram of the crystal structure of deoxyguanosine kinase with bound dATP (PDB accession code 2OCP (22)). The P-loop of the kinase is shown in pink, and the positions of Asn-46 and its hydrogen-bonding partner Leu-219 are indicated by arrows.