Supplemental data 1 220

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1 Supplemental data Chemicals and reagents MTX (00 mg/ml Emthexate PF) was from Pharmachemie (Haarlem, The Netherlands), [ H]FEX was custom-made by GE Healthcare/Amersham Biosciences (UK), FEX, rifampicin, and ascorbate were from Sigma (St. Louis, USA), methoxyflurane (Metofane) from Medical Developments Australia (Springvale, Australia) and heparin (5,000 IE/ml) from Leo Pharma BV (Breda, The Netherlands). The Oatp antibodies M- (sc-846) and K-7 (sc-4770) were from Santa Cruz Biotechnology, Inc (Santa Cruz, USA). M III-5 and M 4 I-80 were kind gifts of Dr. G.L. Scheffer (Free University Hospital, Amsterdam, The Netherlands), M -8 was a kind gift of the group of Dr. P. Borst in our institute. BXP-5 was described before (Proc Natl Acad Sci 99: (00)). RNA isolation, cdna synthesis and RT-PCR DNA isolation from mouse liver, kidney, and small intestine and subsequent cdna synthesis and RT-PCR were performed as described (Mol Pharmacol 7:09-06 (008)). Specific primers (QIAGEN, Hilden, Germany) were used to detect expression levels of the following mouse genes: Slcoa, Slcoa4-6, Slcob, Slcob, Slc0a, Slca-, Slca6-0, Slca, Abcc-4, Abcba, Abcbb, Abcg, Aox, Aox, and Ugta. Western blot analysis Isolation of crude membrane fractions from liver, kidney and small intestine, and Western blotting were performed as described previously (Biochem Biophys Res Commun 0: (996)). Equal protein loading was confirmed by Ponceau S staining of the membranes after transfer. Oatpa4 and Oatpb were detected with respectively OATP (M-; sc-846) (dilution :00) and OATP4 antibodies (K-7; sc-4770) (dilution :00). For the detection of Abcc, Abcc, Abcc4 and Abcg the primary antibodies M III-5 (dilution :000), M -8 (dilution :5), M 4 I-80 (dilution :400) and BXP-5 (dilution :000) were used, respectively. Clinical-chemical analysis of plasma and urine and hematological analysis of blood Standard clinical-chemical analyses on EDTA plasma were performed on a Roche Hitachi 97 analyzer to determine levels of total and conjugated bilirubin, alkaline phosphatase, aspartate aminotransaminase, alanine aminotransaminase, γ-glutamyl transferase, lactate dehydrogenase, creatinine, urea, Na +, K +, Ca +, total protein, albumin, uric acid, cholesterol and triglyceride. Standard clinical-chemical analyses were also performed on urine (collected using Ruco Type M/ stainless steel metabolic cages [Valkenswaard, The Netherlands]) to determine the levels of

2 creatinine, glucose, Na +, K +, Ca +, urea, uric acid and total protein. Hemoglobin, hematocrit, mean corpuscular volume, red and white blood cells, and platelets were analyzed in peripheral EDTA blood on a Beckman Coulter Ac T Diff analyzer (Beckman Coulter, Fullerton, CA). Histological analysis Tissues were fixed in 4% phosphate-buffered formalin, embedded in paraffin, sectioned at 4 µm, and stained with hematoxylin and eosin according to standard procedures. Construction of targeting vectors for generation of mice. The mouse Slcoa and -b genes were mapped using data from the ENSEMBL database ( Total RPCI- female (9S6/SvEvTac) mouse PAC library-derived DNA was used as a template for the construction of suitable gene targeting vectors. For both the centromeric and telomeric side of the Slcoa/b cluster, targeting vectors were constructed allowing insertion of loxp sequences at the cluster flanks (i.e. Slcob and Slcoa5). For the telomeric side of the cluster, a targeting vector was made in which a.-kb fragment containing exon and 4 of Slcoa5 (according to ENSEMBL release 5, corresponding to the two exons after the exon containing the start codon) was replaced by a -kb Pgk-neomycin cassette in reverse transcriptional orientation with LoxP sequences. PCR primers used for generation of the Slcoa5 targeting construct were 5 - GCCTCTATCACATTGCCCTGTG- (forward) and 5 -GCTAGTGTATGCAATGGTGTC- (reverse). A 0.-kb ApaI/SacI (located in vector polylinker) linearized DNA fragment was used for electroporation into ES cells. For the centromeric side of the Slcoa/b cluster, a targeting vector was made in which a ~5.9-kb fragment containing exon 4 of Slcob (according to ENSEMBL release 5, corresponding to the first exon after the exon containing the start codon) was replaced by a ~5-kb Pgk-hygromycin cassette with LoxP sequences and a Pgk-thymidine kinase cassette, both in transcriptional orientation. PCR primers used for generation of the Slcob targeting construct were 5 -CAACCACTCTGGAAATCGGTCTG- (forward) and 5 - GGCTTCCACAGGATTGGCATAC- (reverse). A.9-kb PmeI/SfiI (located in vector polylinker) linearized DNA fragment was used for electroporation into targeted ES cells. Electroporation and selection for Slco-recombinant ES cells. 9/Ola-derived E4 embryonic stem (ES) cells were cultured as described before (Mol Cell Biol : (00)). Electroporation with linearized DNA of Slcob and Slcoa5 targeting vectors, or with circular DNA encoding Cre recombinase/puromycin selection genes, and subsequent selection were performed as described previously (Mol Cell Biol : (00)).

3 PCR and Southern blot analysis of Slco-recombinant ES cells. Correct homologous recombination of the Slcoa5 targeting construct was confirmed by Southern blot analysis. Hybridization of XbaI-digested genomic DNA with the Slcoa5 probe (Figure A) yielded a band of.0 kb and a targeted band of 4.9 kb, and hybridization with the 5 Slcoa5 probe (Figure A) resulted in a band of.0 kb and a targeted band of 5 kb. Absence of additional Slcoa5 targeting construct integrations was confirmed with a neomycin-specific probe. An ES cell clone with correctly inserted loxp-neomycin into Slcoa5, and with the correct karyotype was electroporated with the loxp-hygromycin Slcob targeting construct. Correct homologous recombination of the Slcob targeting construct was confirmed by hybridization with the Slcob probe (Figure A) yielding a band of 8.9 kb and a targeted band of 8. kb, and hybridization with the 5 Slcob probe (Figure A) resulted in a band of 0.9 kb and a targeted band of 9. kb. Absence of additional Slcob targeting construct integrations was confirmed with a hygromycin-specific probe. Clones with correctly integrated loxp sites at both flanks of the cluster were cotransfected with Pgk-Cre recombinase and Pgkpuromycin expression plasmids in order to excise the cluster. After selection with puromycin, surviving ES cell clones were screened for correct Cre recombinase-mediated excision of the Slcoa/b cluster by PCR, using primers at the Slcob flank (5 -GCATTCTTGGCACTTGCC- ) and at the Slcoa5 flank (5 -CAGCACTTGTCCTGCAGG- ). Generation of mice. Chimeric mice were generated by micro-injection of independently targeted ES clones with the Slcoa/b cluster deleted (and with correct karyotype) into blastocysts derived from C57BL/6J mice. Subsequently, these blastocysts were implanted into the oviducts of pseudopregnant F fosters (C57BL/6J), which carried them to term. Crossbreeding of resulting mice yielded independent mouse lines. PCR analysis of mice. founder lines were detected by PCR. DNA was extracted from ear snips or tail tips of mice. Forward 5 -GCATTCTTGGCACTTGCC- (F) and reverse 5 -CAGCACTTGTCCTGCAGG- (R) specific primers were used for the detection of the Slcoa/b-deleted cluster allele, which resulted in a 88-bp band (Figure A). For the detection of the cluster allele, forward 5 -GCATAATGCAGGACATGAGG- (F) and reverse 5 -CAGCACTTGTCCTGCAGG- (R) specific primers were used, yielding a 54- bp band (Figure A). Southern blot analysis of mice. Slcoa* and Slcob probes to demonstrate absence of Slcoa/b genes in mice by Southern blot analysis were generated by PCR from liver cdna. Primers used for this PCR reaction were 5 -CCTCATTTCCTCATGGGC-

4 (forward) and 5 -GGATGCTGGTCAGGATATTC- (reverse) for Slcoa* and 5 - CCTGACTGGTTTTCTATGG- (forward) and 5 -CTATGTGAGAGTCCACTGGG- (reverse) for the Slcob probe. Sequences of these probes were verified and revealed sequence identity of the Slcoa* probe with Slcoa genes (and not with Slcob, -c or -b) and of the Slcob probe with Slcob (and not with Slcoa, -c or -b). Genomic DNA from tail tips of founders was digested with Asp78 and probed with either Slcoa* or Slcob probe. Detection of BMG, BDG, and UCB in plasma and urine. The protocol was adapted from the method described by Spivak and Carey (Biochem J 5: (985)). In brief, urine and plasma samples were deproteinized with volumes of MeOH after the addition of KOH (final concentration 5 µm). Following centrifugation for minutes at 4000 rpm, the supernatant was injected. 00 µl was applied to a Pursuit C8, 5 µm, 0 cm HPLC column (Varian, Middelburg, The Netherlands). Starting eluent consisted of 50% MeOH/ 50% ammonium acetate (%, ph 4.5), followed by a linear gradient to 00% MeOH in 0 minutes. BDG, BMG and UCB eluted from the column at retention times of 8, and min, respectively. Detection of bilirubin was performed at 450 nm. Quantification of BDG, BMG and UCB was done by using a calibration curve of UCB. Determination of total bile acid pool. To determine the total bile acid pool, the protocol described by Pawlikowska et al (Hum Mol Genet :88-89 (004)) was slightly adapted. In brief, wildtype and mice were i.v. injected with 0.5 µci [ H]taurocholate and after 5 hours bile was collected for 0 min by gall bladder cannulation. Total radioactivity was analyzed by liquid scintillation counting and total bile acids as described (J Inherit Metab Dis :07-0 (999)). The obtained specific radioactivity was used to calculate the total bile acid pool size from the total radioactivity that was injected.

5 Supplemental data Overview of Ct values of the RT-PCR analysis to investigate expression of several endogenous uptake and efflux transporters in liver, kidney and small intestine of male and mice (n = ; each sample was assayed in duplicate). Part of these data are also shown in Figure C. Analysis of the results was done by comparative Ct method. Quantification of the target cdnas in all samples was normalized against the endogenous control β-actin (Ct target Ct β- actin = Ct). Accordingly, the lower the value, the higher the expression level. Liver Wild-type Slcoa (Oatpa) 0.76 ± ±.65 C Slcoa4 (Oatpa4). ± ±.79 C Slcoa5 (Oatpa5) 5.8 ± ± 0.90 Slcoa6 (Oatpa6) 6.9 ± ± 0.99 Slcob (Oatpb) -9 ± ±.4 C Slcob (Oatpb) 4.46 ± ± 0.50 Slca (Oct).48 ± ± 0.4 Slca (Oct). ±.5.6 ± 0.9 Slca7 (Oat).5 ± ±.9 Slc0a (Ntcp) 0.99 ± ± 0.5 Abcba (Mdra) 0. ± ± 0.5 A Abcbb (Mdrb) 0. ± ±.7 Abcb (Bsep).06 ± ± 0.84 Abcc (Mrp).6 ± ± 0.74 Abcc (Mrp) 7. ± ± 0.5 Abcc4 (Mrp4) 0.9 ± 0.7. ± 0.70 Abcg (Bcrp) 5.8 ± ± 0.78 Aox 6.67 ± ± 0.6 Aox.7 ± ± 0.68 Ugta.49 ± ± 0.5

6 Kidney Wild-type Slcoa (Oatpa).6 ± ±.97 C Slcoa4 (Oatpa4) 0.7 ± 0..9 ±.69 B Slcoa5 (Oatpa5) ± ±.5 Slcoa6 (Oatpa6).0 ± ± 0.87 C Slcob (Oatpb) 4.8 ± ±.59 B Slcob (Oatpb) 7.0 ± ± 0. Slca (Oct).00 ± ± 0.7 Slca (Oct) 4.0 ± ± 0.8 Slca (Oct) 4.4 ± ± 0.64 Slca6 (Oat) 0.94 ± ± 0.8 Slca7 (Oat) 9.0 ± ± 0.86 Slca8 (Oat).90 ± ± 9 Slca9 (Oat5) 6.05 ± ± 0.4 Slca (Urat-).44 ± 0..7 ± 0. Abcba (Mdra) 9.88 ± ± 0. Abcbb (Mdrb) 8. ± ±.8 Abcc (Mrp) 4.8 ± ± 0. Abcc (Mrp).9 ± ± 0.5 Abcc4 (Mrp4) 6.67 ± ± 0.8 Abcg (Bcrp).4 ± ± 0.6 Small intestine Wild-type Slcoa (Oatpa) 7.7 ± ± 0.6 Slcoa4 (Oatpa4) 0.6 ±.56.9 ±.70 B Slcoa5 (Oatpa5) ±.47. ±.70 Slcoa6 (Oatpa6) 8.8 ± ±.6 B Slcob (Oatpb) 5.5 ± ±.57 Slcob (Oatpb) 9.47 ± ± 0. Slc0a (Asbt).9 ±.45.4 ± 0.98 Slca (Oct) 9.5 ± ± 0.67 Slca (Oct) 5.4 ± ± 0.57 Abcba (Mdra) 7.9 ± ± 0. Abcbb (Mdrb) 4.4 ± ± 0.54 Abcc (Mrp) 7.50 ± ± 0. Abcc (Mrp).7 ± ± 0. Abcc4 (Mrp4).4 ± ± 0.6 Abcg (Bcrp) 7.60 ± ± 0.0 Ostα 8.4 ± ±.0 Ostβ 7.6 ± ± 0.79 Note: All data are presented as means ± S.D. (n =, male). A P < 5; B P < ; C P < 0 when compared with.

7 A 4 cholic acid B.5 taurocholic acid * C 0. ursodeoxycholic acid * D 0. tauro-ursodeoxycholic acid 0. E 0. chenodeoxycholic acid F 0. tauro-chenodeoxycholic acid 0. G α-muri-cholic acid H 4 tauro-α-muri-cholic acid 0 - I 5 deoxycholic acid 4 0 Supplemental data. Levels of individual bile acids in plasma of male and mice (A-I). Data are presented as means ± S.D. (n = 5-7; *, P < 5; **, P < ;, P < 0 when compared with ). The logarithm of the data was determined prior to assess the statistical significance of the data by two-sided unpaired Student s t test., lower limit of detection. Detection limit was 0. µm for all bile acids, except for cholic acid and α-muri-cholic acid, for which it was µm.

8 A B Liver MTX (% of dose) Liver [ H]FEX (% of dose) Wild-type * ** ** Time (min) Time (min) Supplemental data 4. Liver accumulation (% of dose) after oral dosing of MTX (0 mg/kg) (A) and [ H]FEX ( mg/kg) (B) to and mice. All data are presented as means ± S.D. (n = 4-8; *, P < 5; **, P < ;, P < 0 when compared with ).

9 Supplemental data 5 Plasma AUCs of MTX and [ H]FEX in the portal vein (AUC PV ) and systemic circulation (AUC SC ) after oral administration of, respectively, MTX (0 mg/kg) and FEX ( mg/kg). MTX [ H]FEX AUC PV AUC SC AUC PV AUC SC (A) Wild-type 49.6 ±. 4.4 ± ± ± (B) 94. ± 4.6 B 54.5 ±.9 A. ± 0. A.90 ± 0. B Difference (B) (A) ~44.5 ~40. ~.0 ~.5 Note: AUCs are represented as min µg/ml. All values represent means ± S.E. (n = 4-8). A P < 5; B P < when compared with.