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Global genetic analyses reveal strong inter-ethnic variability in the loss of activity of the organic cation transporter OCT1.

Seitz T, Stalmann R, Dalila N, Chen J, Pojar S, Dos Santos Pereira JN, Krätzner R, Brockmöller J, Tzvetkov MV - Genome Med (2015)

Bottom Line: In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima's D = -1.64, P < 0.01).Comprehensive genetic analyses showed strong global variations in the frequency of loss of OCT1 activity with selection pressure for maintaining OCT1 activity in East Asia and Oceania.These results not only enable pharmacogenetically-based optimization of drug treatment worldwide, but may help elucidate the functional role of human OCT1.

View Article: PubMed Central - PubMed

Affiliation: Institute of Clinical Pharmacology, University Medical Center Göttingen, Robert-Koch-Str. 40, DE-37075 Göttingen, Germany.

ABSTRACT

Background: The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-function polymorphisms in OCT1 gene. Here we analyzed the global genetic variability in OCT1 to estimate the therapeutic relevance of OCT1 polymorphisms in populations beyond Caucasians and to identify evolutionary patterns of the common loss of OCT1 activity in humans.

Methods: We applied massively parallel sequencing to screen for coding polymorphisms in 1,079 unrelated individuals from 53 populations worldwide. The obtained data was combined with the existing 1000 Genomes data comprising an additional 1,092 individuals from 14 populations. The identified OCT1 variants were characterized in vitro regarding their cellular localization and their ability to transport 10 known OCT1 substrates. Both the population genetics data and transport data were used in tandem to generate a world map of loss of OCT1 activity.

Results: We identified 16 amino acid substitutions potentially causing loss of OCT1 function and analyzed them together with five amino acid substitutions that were not expected to affect OCT1 function. The variants constituted 16 major alleles and 14 sub-alleles. Six major alleles showed improper subcellular localization leading to substrate-wide loss in activity. Five major alleles showed correct subcellular localization, but substrate-specific loss of activity. Striking differences were observed in the frequency of loss of OCT1 activity worldwide. While most East Asian and Oceanian individuals had completely functional OCT1, 80 % of native South American Indians lacked functional OCT1 alleles. In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima's D = -1.64, P < 0.01).

Conclusions: Comprehensive genetic analyses showed strong global variations in the frequency of loss of OCT1 activity with selection pressure for maintaining OCT1 activity in East Asia and Oceania. These results not only enable pharmacogenetically-based optimization of drug treatment worldwide, but may help elucidate the functional role of human OCT1.

No MeSH data available.


Related in: MedlinePlus

Non-synonymous OCT1 polymorphisms causing potentially functional amino acid substitutions, and their distribution in different world regions. a The localization of the 21 polymorphisms analyzed in details in this study. Substitutions previously reported in the literature to have strong functional effects on OCT1 activity are shown in black (reported loss of function), substitutions predicted to affect OCT1 activity are shown in gray (predicted loss-of-function), and substitutions previously reported to not affect or to cause less than 50 % reduction of OCT1 activity are shown in white (reported to lack strong effects). The polymorphisms are designated with the amino acid substitutions that they cause and the codon that is affected. Their rs-number in the dbSNP database (if available) and their location on chromosome 6 according to the human genome assembly hg19 are also given. b Minor allele frequencies of the 16 known or predicted loss-of-function OCT1 polymorphisms. Shown are 39 populations from Sub-Saharan Africa, North Africa and the Middle East, Central Asia, Europe, and America. The 39 populations shown include 35 populations from the CEPH human genome diversity panel and five from the 1000 Genome Project [24] (designated with 1 K). The populations CEU, ASW, MXL, PUR, and CLM from the 1000 Genomes Project were omitted from these analyses due to their highly admixed structure and/or inability to be allocated to a defined world region
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Fig2: Non-synonymous OCT1 polymorphisms causing potentially functional amino acid substitutions, and their distribution in different world regions. a The localization of the 21 polymorphisms analyzed in details in this study. Substitutions previously reported in the literature to have strong functional effects on OCT1 activity are shown in black (reported loss of function), substitutions predicted to affect OCT1 activity are shown in gray (predicted loss-of-function), and substitutions previously reported to not affect or to cause less than 50 % reduction of OCT1 activity are shown in white (reported to lack strong effects). The polymorphisms are designated with the amino acid substitutions that they cause and the codon that is affected. Their rs-number in the dbSNP database (if available) and their location on chromosome 6 according to the human genome assembly hg19 are also given. b Minor allele frequencies of the 16 known or predicted loss-of-function OCT1 polymorphisms. Shown are 39 populations from Sub-Saharan Africa, North Africa and the Middle East, Central Asia, Europe, and America. The 39 populations shown include 35 populations from the CEPH human genome diversity panel and five from the 1000 Genome Project [24] (designated with 1 K). The populations CEU, ASW, MXL, PUR, and CLM from the 1000 Genomes Project were omitted from these analyses due to their highly admixed structure and/or inability to be allocated to a defined world region

Mentions: We identified a total of 85 variants (a detailed list of all variants is available in Additional file 5). Thereof 44 variants were within the coding region of OCT1 and 29 of them caused amino acid substitutions. We selected 21 amino acid substitution variants for our subsequent analyses (see Fig. 1b for the selection strategy). Included were 14 amino acid substitutions that may affect OCT1 activity (Fig. 2a): nine variants previously known to cause loss of OCT1 activity (Ser14Phe, Arg61Cys, Cys88Arg, Pro117Leu, Ser189Leu, Arg206Cys, Gly401Ser, Met420-deletion, Gly465Arg) [2–5, 7, 10, 11, 17] and five variants predicted to cause loss of OCT1 function (Ser29Leu, Thr245Met, Glu284Lys, Gly414Ala, Ile449Thr). To predict loss of OCT1 function we used eight independent prediction tools. Variants that were predicted to be deleterious by at least five of the eight prediction tools were regarded as potential loss-of-function variants (Additional file 6). We also genotyped two variants, Gln97Lys and Gly220Val, which were not identified in our population by massively parallel sequencing. However, Gln97Lys was previously reported in the literature to strongly affect OCT1 activity [17], while Gly220Val was observed in the 1000 Genomes project and was predicted to be deleterious (Additional file 6). Furthermore, we analyzed five amino acid substitutions (Leu160Phe, Pro341Leu, Arg342His, Met408Val, and Arg488Met) that were known to either not affect or to cause less than 50 % reduction in OCT1 activity [2, 10, 11, 20, 21]. We included these variants for two reasons. First, we wanted to obtain information about the effects of these variants on the uptake of a much broader spectrum of substrates than previously tested. Second, we aimed to identify common amino acid substitutions that do not affect OCT1 activity as a control in our population genetic analyses.Fig. 2


Global genetic analyses reveal strong inter-ethnic variability in the loss of activity of the organic cation transporter OCT1.

Seitz T, Stalmann R, Dalila N, Chen J, Pojar S, Dos Santos Pereira JN, Krätzner R, Brockmöller J, Tzvetkov MV - Genome Med (2015)

Non-synonymous OCT1 polymorphisms causing potentially functional amino acid substitutions, and their distribution in different world regions. a The localization of the 21 polymorphisms analyzed in details in this study. Substitutions previously reported in the literature to have strong functional effects on OCT1 activity are shown in black (reported loss of function), substitutions predicted to affect OCT1 activity are shown in gray (predicted loss-of-function), and substitutions previously reported to not affect or to cause less than 50 % reduction of OCT1 activity are shown in white (reported to lack strong effects). The polymorphisms are designated with the amino acid substitutions that they cause and the codon that is affected. Their rs-number in the dbSNP database (if available) and their location on chromosome 6 according to the human genome assembly hg19 are also given. b Minor allele frequencies of the 16 known or predicted loss-of-function OCT1 polymorphisms. Shown are 39 populations from Sub-Saharan Africa, North Africa and the Middle East, Central Asia, Europe, and America. The 39 populations shown include 35 populations from the CEPH human genome diversity panel and five from the 1000 Genome Project [24] (designated with 1 K). The populations CEU, ASW, MXL, PUR, and CLM from the 1000 Genomes Project were omitted from these analyses due to their highly admixed structure and/or inability to be allocated to a defined world region
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Fig2: Non-synonymous OCT1 polymorphisms causing potentially functional amino acid substitutions, and their distribution in different world regions. a The localization of the 21 polymorphisms analyzed in details in this study. Substitutions previously reported in the literature to have strong functional effects on OCT1 activity are shown in black (reported loss of function), substitutions predicted to affect OCT1 activity are shown in gray (predicted loss-of-function), and substitutions previously reported to not affect or to cause less than 50 % reduction of OCT1 activity are shown in white (reported to lack strong effects). The polymorphisms are designated with the amino acid substitutions that they cause and the codon that is affected. Their rs-number in the dbSNP database (if available) and their location on chromosome 6 according to the human genome assembly hg19 are also given. b Minor allele frequencies of the 16 known or predicted loss-of-function OCT1 polymorphisms. Shown are 39 populations from Sub-Saharan Africa, North Africa and the Middle East, Central Asia, Europe, and America. The 39 populations shown include 35 populations from the CEPH human genome diversity panel and five from the 1000 Genome Project [24] (designated with 1 K). The populations CEU, ASW, MXL, PUR, and CLM from the 1000 Genomes Project were omitted from these analyses due to their highly admixed structure and/or inability to be allocated to a defined world region
Mentions: We identified a total of 85 variants (a detailed list of all variants is available in Additional file 5). Thereof 44 variants were within the coding region of OCT1 and 29 of them caused amino acid substitutions. We selected 21 amino acid substitution variants for our subsequent analyses (see Fig. 1b for the selection strategy). Included were 14 amino acid substitutions that may affect OCT1 activity (Fig. 2a): nine variants previously known to cause loss of OCT1 activity (Ser14Phe, Arg61Cys, Cys88Arg, Pro117Leu, Ser189Leu, Arg206Cys, Gly401Ser, Met420-deletion, Gly465Arg) [2–5, 7, 10, 11, 17] and five variants predicted to cause loss of OCT1 function (Ser29Leu, Thr245Met, Glu284Lys, Gly414Ala, Ile449Thr). To predict loss of OCT1 function we used eight independent prediction tools. Variants that were predicted to be deleterious by at least five of the eight prediction tools were regarded as potential loss-of-function variants (Additional file 6). We also genotyped two variants, Gln97Lys and Gly220Val, which were not identified in our population by massively parallel sequencing. However, Gln97Lys was previously reported in the literature to strongly affect OCT1 activity [17], while Gly220Val was observed in the 1000 Genomes project and was predicted to be deleterious (Additional file 6). Furthermore, we analyzed five amino acid substitutions (Leu160Phe, Pro341Leu, Arg342His, Met408Val, and Arg488Met) that were known to either not affect or to cause less than 50 % reduction in OCT1 activity [2, 10, 11, 20, 21]. We included these variants for two reasons. First, we wanted to obtain information about the effects of these variants on the uptake of a much broader spectrum of substrates than previously tested. Second, we aimed to identify common amino acid substitutions that do not affect OCT1 activity as a control in our population genetic analyses.Fig. 2

Bottom Line: In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima's D = -1.64, P < 0.01).Comprehensive genetic analyses showed strong global variations in the frequency of loss of OCT1 activity with selection pressure for maintaining OCT1 activity in East Asia and Oceania.These results not only enable pharmacogenetically-based optimization of drug treatment worldwide, but may help elucidate the functional role of human OCT1.

View Article: PubMed Central - PubMed

Affiliation: Institute of Clinical Pharmacology, University Medical Center Göttingen, Robert-Koch-Str. 40, DE-37075 Göttingen, Germany.

ABSTRACT

Background: The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-function polymorphisms in OCT1 gene. Here we analyzed the global genetic variability in OCT1 to estimate the therapeutic relevance of OCT1 polymorphisms in populations beyond Caucasians and to identify evolutionary patterns of the common loss of OCT1 activity in humans.

Methods: We applied massively parallel sequencing to screen for coding polymorphisms in 1,079 unrelated individuals from 53 populations worldwide. The obtained data was combined with the existing 1000 Genomes data comprising an additional 1,092 individuals from 14 populations. The identified OCT1 variants were characterized in vitro regarding their cellular localization and their ability to transport 10 known OCT1 substrates. Both the population genetics data and transport data were used in tandem to generate a world map of loss of OCT1 activity.

Results: We identified 16 amino acid substitutions potentially causing loss of OCT1 function and analyzed them together with five amino acid substitutions that were not expected to affect OCT1 function. The variants constituted 16 major alleles and 14 sub-alleles. Six major alleles showed improper subcellular localization leading to substrate-wide loss in activity. Five major alleles showed correct subcellular localization, but substrate-specific loss of activity. Striking differences were observed in the frequency of loss of OCT1 activity worldwide. While most East Asian and Oceanian individuals had completely functional OCT1, 80 % of native South American Indians lacked functional OCT1 alleles. In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima's D = -1.64, P < 0.01).

Conclusions: Comprehensive genetic analyses showed strong global variations in the frequency of loss of OCT1 activity with selection pressure for maintaining OCT1 activity in East Asia and Oceania. These results not only enable pharmacogenetically-based optimization of drug treatment worldwide, but may help elucidate the functional role of human OCT1.

No MeSH data available.


Related in: MedlinePlus