Clinical and molecular study of a pediatric patient with sodium taurocholate cotransporting polypeptide deficiency

Abstract

The human solute carrier family 10 member 1 (SLC10A1) gene encodes sodium taurocholate cotransporting polypeptide (NTCP), the principal transporter of conjugated bile salts from the plasma into hepatocytes. Although the function of NTCP has been studied extensively and a number of SLC10A1 variations have been identified in humans, information regarding NTCP deficiency is limited. To date, only one patient with NTCP deficiency has been described; however, in the present study a pediatric patient who experienced intractable and striking hypercholanemia is presented. Analysis of the SLC10A1 gene in the patient revealed a homozygous p.Ser267Phe (c.800C>T) variation, which proved to be a single-nucleotide polymorphism (SNP) in the allele frequency of 4.7% of healthy controls. This variation involved a conserved amino acid residue on the orthologous alignment that was predicted to be 'disease-causing' by functional analysis using a number of bioinformatic tools. Next generation sequencing was performed; however, no other genetic causes were identified that would affect the bile acid homeostasis in the patient. Moreover, an adult, with the same genotype as the pediatric patient, was identified for the first time as experiencing mild hypercholanemia. The molecular and clinical findings in the present study suggest, for the first time, that there is an association between p.Ser267Phe SNP and hypercholanemia, and this information may be used to clinically identify NTCP deficiency worldwide.

Keywords: cholestasis; dysfunctional polymorphism; hypercholanemia; sodium taurocholate cotransporting polypeptide; solute carrier family 10 member 1 gene.

Figure 1.

Solute carrier family 10 member 1 (SLC10A1) genotypes in the family of the pediatric patient and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol for variation screening. (A) Sanger sequencing revealing that the pediatric patient is a homozygote whose parents are both carriers of the c.800C>T (p.Ser267Phe) variation. The SLC10A1 genotypes in the family were further confirmed by (B) gel electrophoresis using a newly-developed PCR-RFLP protocol, (C) the schematic diagram of which is illustrated. The variation generated a new digestive site for the restriction enzyme HphI, producing fragments of 65 and 164 bp from the 229 bp fragment from enzymatic digestion. bp, base pairs.

Figure 2.

Alignment of homologous peptides in a diversity of species. With the exception of armadillo, turkey and zebrafish, all the remaining 37 species, including primates, rodents, laurasiatheria, placental mammals, sauropsida, fish and marine chordate, have the same serine residue as highlighted in green This indicates that the p.Ser267Phe variation affected a number of conserved amino acid residues among species. NTCP, sodium taurocholate cotransporting polypeptide; ASBT, apical sodium-dependent bile acid transporter.