Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1

Abstract

The organic cation transporter, OCT1, is a major hepatic transporter that mediates the uptake of many organic cations from the blood into the liver where the compounds may be metabolized or secreted into the bile. Because OCT1 interacts with a variety of structurally diverse organic cations, including clinically used drugs as well as toxic substances (e.g., N-methylpyridinium, MPP ؉ ), it is an important determinant of systemic exposure to many xenobiotics. To understand the genetic basis of extensive interindividual differences in xenobiotic disposition, we functionally characterized 15 protein-altering variants of the human liver organic cation transporter, OCT1, in Xenopus oocytes. All variants that reduced or eliminated function (OCT1-R61C, OCT1-P341L, OCT1-G220V, OCT1-G401S, and OCT1-G465R) altered evolutionarily conserved amino acid residues. In general, variants with decreased function had amino acid substitutions that resulted in more radical chemical changes (higher Grantham values) and were less evolutionarily favorable (lower BLOSUM62 values) than variants that maintained function. A variant with increased function (OCT1-S14F) changed an amino acid residue such that the human protein matched the consensus of the OCT1 mammalian orthologs. Our results indicate that changes at evolutionarily conserved positions of OCT1 are strong predictors of decreased function and suggest that a combination of evolutionary conservation and chemical change might be a stronger predictor of function.

Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3)

“…8,16 In addition, Shu et al analyzed protein-altering variants of the organic cation transporter, OCT1, and found that combining evolutionary conservation with Grantham values was a stronger predictor of function. 17 Interestingly, TMD 8 of CNT3 has four glycines, including Gly367, which are conserved not only among mammals, but also in the other two human paralogs (CNT1 and CNT2), suggesting that these residues may be particularly important for the function of the concentrative nucleoside transporter family. A similar observation was also recently reported by Shu et al 17 for the organic cation transporter family, where all three of the nonfunctional variants of OCT1 altered evolutionarily conserved glycine residues.…”

“…Nonsynonymous variants of CNT3, as well as of ENT1 and CNT1, have less functional diversity than those of the xenobiotic transporter, OCT1. 7,17,23 A possible explanation for this phenomenon could be that transporters with a primary role in xenobiotic detoxification may be functionally less constrained compared to transporters, like CNT3, which though involved in xenobiotic disposition, function primarily to maintain homeostasis of endogenous compounds.…”

Transporters Involved in Metformin Pharmacokinetics and Treatment Response

“…Thus, transporters appear to play important roles in the absorption, distribution and elimination of metformin. Many studies have shown that metformin is a substrate of various polyspecific organic cation transporters, which are important determinants of pharmacokinetics, including OCT1 (SLC22A1), OCT2 (SLC22A2), OCT3 (SLC22A3), MATE1 (SLC47A1), MATE2 (SLC47A2), PMAT (SLC29A4), and OCTN1 (SLC22A4) [11][12][13][14][15][16] (Fig. 1.1, Table 1).…”

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster

“…Many previous studies of the breadth of human diversity of pharmacologically relevant genes have focused on exon re-sequencing and in vitro assays of protein function. 29,30 Such studies are likely to identify many functional variants, but may miss functional noncoding sequence variants, 31 as have already proved important for UGT1A1. 8,11,32 To focus on the regions of the entire UGT1A locus most likely to affect clinical phenotypes, we identified 29 kb of non-coding sequence highly conserved between humans and four mammalian species and resequenced these regions as well as over 8 kb of exon sequence in 72 individuals from three ethnic populations.…”