| Literature DB >> 25606452 |
Mayumi Toda1, Yasuna Kobayashi1, Tomotake Koizumi2, Koji Saito3, Masayuki Ohbayashi1, Noriko Kohyama1, Takeshi Aoki2, Masahiko Murakami2, Hajime Yasuhara4, Toshinori Yamamoto1.
Abstract
Human organic solute carrier protein 1 (hOSCP1) is a Na(+)-independent multispecific organic solute transporter. To date, several studies have revealed that gene mutations of the transporters are likely to be associated with some diseases; however, there are no data concerning the genetic polymorphism of the hOSCP1 gene in Japanese patients with non-viral liver carcinoma (LC). In the present study, we isolated genomic DNA from a normal portion of LC, and analyzed 41 single nucleotide polymorphisms (SNPs) chosen from a database of SNPs (dbSNPs). We found genotype frequencies for 2 non-synonymous SNPs [rs34409118 (Thr(131) → Ala) and rs1416840 (Ile(219) → Thr)] and 1 synonymous SNP [rs16822954 (Ser(193) → Ser)] to be statistically significant when compared with dbSNPs. No statistical significance was observed in rs2275477 (Gly(307) → Arg) in the hOSCP1 gene. With respect to the allele frequency, we also observed rs34409118 to be statistically significant. Interestingly, we found that non-viral LC patients do not carry heterozygous mutations in rs1416840 (A/G) and rs16822954 (A/G), suggesting that a non-carrier of heterozygous mutations in these two SNPs might be a biomarker for susceptibility for non-viral LC in Japanese. Further analyses of patients with hOSCP1 variants may elucidate the relationship between the hOSCP1 gene and susceptibility of non-viral LC in Japanese patients.Entities:
Keywords: AGC2, aspartate glutamate carrier 2; ALT, alanine aminotransferase; AST, aspartate aminotransferase; DNA, deoxyribonucleic acid; Genetic polymorphism; HCC, hepatocellular carcinoma; HCV, hepatitis C virus; HWE, Hardy–Weinberg equilibrium; ICC, intrahepatic cholangiocarcinoma; ICG, indocyanine green test; LC, liver carcinoma; LDH, lactate dehydrogenase; MDR1, multidrug-resistance 1; NAFLD, non-alcoholic fatty liver disease; Non-viral liver carcinoma; OAT, organic anion transporter; OATP, organic anion transporting polypeptide; PCR, polymerase chain reaction; SLC/Slc, solute carrier; SNPs, single nucleotide polymorphisms; Transporter; cSNPs, coding single nucleotide polymorphisms; hOSCP1; hOSCP1, human organic solute carrier protein 1; hURAT1, urate transporter 1; γ-GTP, γ-glutamyltranspeptidase
Year: 2014 PMID: 25606452 PMCID: PMC4287821 DOI: 10.1016/j.mgene.2014.09.002
Source DB: PubMed Journal: Meta Gene ISSN: 2214-5400
Primer sequences and PCR conditions used for genotyping of the hOSCP1 gene.
| dbSNP or oligo name | Allele change | Amino Acid Change | Forward primer | Reverse primer | Length (bp) | Annealing temperature (°C) |
|---|---|---|---|---|---|---|
| rs17851613☨ | A → G | Leu82Leu | TCATGTGACCCCAGTCTATGAT | AAGAAGGCCCTGAGGACTGT | 156 | 57 |
| rs34409118 | A → G | Thr131Ala | GACCTGATGACCATGGCTTT | ATGGACACGGATTGCTTTTC | 313 | 57 |
| rs16822954 | A → G | Ser193Ser | TTTCCTAGCACCCCAAACAT | AATAACGGTCGCTTTGTGTTG | 116 | 60 |
| rs61308377 | A → G | Tyr209His | CTTTGTCCATGGAAGGGAAA | GCCCAGCCAAAATAAAACAA | 417 | 57 |
| rs1416840 | A → G | Ile219Thr | GTTTCAGGACTCGGTCTCCA | CCCAGTTCCCCAGGACTAAT | 388 | 57 |
| rs2359016 | C → T | Lys222Glu | TCAGGACTCGGTCTCCATAAA | AGCCTCCAGGACTACCTAAG | 510 | 60 |
| rs17442970 | A → C | Val253Leu | CAGGGGAAATGTTGGCTAGA | AACGCCAAACATAAGGCAAC | 557 | 57 |
| rs2275477 | C → T | Gly307Arg | TGGAAGATTCAGGCCATTTC | ATGTGATTGCCTTCATGTGG | 363 | 58 |
| rs17851612 | C → T | Ser367Gly | CACCATCCAGCAGCCTCT | TCCCTCATAGGACCAGCAAC | 176 | 53 |
Positions are relative to the ATG start site and are based on the cDNA sequence from GenBank accession number AB079075.
rs17851613 has merged into rs6978099.
clinical characteristics of patients with non-viral liver carcinoma.
| Characteristics | |
|---|---|
| Gender (male/female) | 12/6 |
| Age (years) | 69.1 (49–83) |
| Primary or metastatic | |
| Primary | 9 |
| Metastatic | 9 |
| Child–Pugh (A/B/C) | 17/1/0 |
| AST (IU/L) | 30.1 (17–52) |
| ALT (IU/L) | 24.4 (11–55) |
| LDH (IU/L) | 287.1 (137–1284) |
| Cholinesterase (IU/L) | 224.8 (110–285) |
| γ-GTP (IU/L) | 90.8 (14–268) |
| Total protein (g/dL) | 6.8 (2.0–8.2) |
| Albumin (g/dL) | 3.8 (2.8–4.5) |
| Total bilirubin (mg/dL) | 0.7 (0.4–0.9) |
| Platelet (× 104/μL) | 20.9 (7.6–26.6) |
| Prothrombin time (%) | 95.5 (75–100) |
| ICG at 15 min (%) | 17 (5–39) |
| Alcohol (yes/no/unknown) | 9/6/3 |
| Smoking (+/−/unknown) | 6/9/3 |
AST, aspartate aminotransferase; ALT, alanine aminotransferase; LDH, lactate dehydrogenase; γ-GTP, γ-glutamyltranspeptidase; ICG, indocyanine green test.
Genotype and allele frequencies of hOSCP1 variants.
| dbSNP | Genotype | Allele | |||
|---|---|---|---|---|---|
| w/w | w/m | m/m | w | m | |
| rs77019703 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs140615314 | G/G (1.000) | G/T (0.000) | T/T (0.000) | G (1.000) | T (0.000) |
| rs142047873 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| T/T (1.000) | T/C (0.000) | C/C (0.000) | T (1.000) | C (0.000) | |
| A/A (0.444) | A/G (0.167) | G/G (0.389) | A (0.528) | G (0.472) | |
| rs146099595 | T/T (1.000) | T/C (0.000) | C/C (0.000) | T (1.000) | C (0.000) |
| rs142000188 | C/C (1.000) | C/G (0.000) | G/G (0.000) | C (1.000) | G (0.000) |
| rs139145594 | A/A (1.000) | A/G (0.000) | G/G (0.000) | A (1.000) | G (0.000) |
| rs115388124 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| A/A (0.722) | A/G (0.167) | G/G (0.111) | A (0.806) | G (0.194) | |
| rs138115239 | T/T (1.000) | T/C (0.000) | C/C (0.000) | T (1.000) | C (0.000) |
| C/C (1.000) | C/A (0.000) | A/A (0.000) | C (1.000) | A (0.000) | |
| T/T (1.000) | T/C (0.000) | C/C (0.000) | T (1.000) | C (0.000) | |
| A/A (0.667) | A/G (0.000) | G/G (0.333) | A (0.667) | G (0.333) | |
| A/A (0.111) | A/G (0.000) | G/G (0.889) | A (0.111) | G (0.889) | |
| rs151311655 | G/G (1.000) | G/T (0.000) | T/T (0.000) | G (1.000) | T (0.000) |
| rs151147935 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs148820896 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs148013964 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs150459319 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| C/C (1.000) | C/A (0.000) | A/A (0.000) | C (1.000) | A (0.000) | |
| rs144130136 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs144226900 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs14521649 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs146088740 | T/T (1.000) | T/A (0.000) | A/A (0.000) | T (1.000) | A (0.000) |
| rs114554640 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs150491917 | C/C (1.000) | C/G (0.000) | G/G (0.000) | C (1.000) | G (0.000) |
| rs146439686 | C/C (1.000) | C/G (0.000) | G/G (0.000) | C (1.000) | G (0.000) |
| rs149060854 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs138506112 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs148484503 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs11547025 | C/C (1.000) | C/A (0.000) | A/A (0.000) | C (1.000) | A (0.000) |
| rs141201826 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs138864592 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| C/C (0.445) | C/T (0.444) | T/T (0.111) | C (0.667) | T (0.333) | |
| rs140749623 | T/T (1.000) | T/A (0.000) | A/A (0.000) | T (1.000) | A (0.000) |
| rs139567315 | G/G (1.000) | G/A (0.000) | A/A (0.000) | G (1.000) | A (0.000) |
| rs182337804 | T/T (1.000) | T/C (0.000) | C/C (0.000) | T (1.000) | C (0.000) |
| rs186694883 | G/G (1.000) | G/C (0.000) | C/C (0.000) | G (1.000) | C (0.000) |
| rs150943653 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
| rs144344454 | C/C (1.000) | C/T (0.000) | T/T (0.000) | C (1.000) | T (0.000) |
Bold, PCR primer SNPs.
Synonymous.
Non-synonymous.
Stop codon.
Genotype and allele frequencies of rs34409118, rs61308377, rs1614840, rs16822954, and rs2275477 in the hOSCP1 gene.
| SNP ID | Genotype | This study | dbSNPs | p-Value | Allele | This study | dbSNPs | p-Value |
|---|---|---|---|---|---|---|---|---|
| rs34409118 | A/A | 0.444 (8) | 0.578 (52) | < 0.01 | A | 0.528 (19) | 0.744 (67) | 0.022 |
| A/G | 0.167 (3) | 0.333 (30) | G | 0.472 (17) | 0.256 (23) | |||
| G/G | 0.389 (7) | 0.089 (8) | ||||||
| rs61308377 | A/A | 0.722 (13) | – | N.D. | A | 0.806 (29) | 0.733 (88) | 0.511 |
| A/G | 0.167 (3) | – | G | 0.164 (7) | 0.267 (32) | |||
| G/G | 0.111 (2) | – | ||||||
| A/A | 0.667 (12) | 0.546 (94) | < 0.01 | A | 0.667 (24) | 0.756 (130) | 0.298 | |
| rs1416840 | A/G | 0.000 (0) | 0.419 (72) | G | 0.333 (12) | 0.244 (42) | ||
| G/G | 0.333 (6) | 0.035 (6) | ||||||
| A/A | 0.111 (2) | 0.047 (4) | < 0.01 | A | 0.111 (4) | 0.223 (19) | 0.207 | |
| rs16822954 | A/G | 0.000 (0) | 0.372 (32) | G | 0.889 (32) | 0.767 (66) | ||
| G/G | 0.889 (16) | 0.581 (50) | ||||||
| rs2275477 | C/C | 0.445 (8) | 0.547 (94) | N.S. | C | 0.667 (24) | 0.750 (129) | 0.305 |
| C/T | 0.444 (8) | 0.407 (70) | T | 0.333 (12) | 0.250 (43) | |||
| T/T | 0.111 (2) | 0.046 (8) |
SNPs, single nucleotide polymorphisms. In parentheses are the numbers of subject. N.D., not determined; N.S., not significant.
Chi-square test.
Fisher's exact test. dbSNPs, database of SNPs (http://www.ncbi.nlm.nih.gov/snp/).
HapMap-JPT.
Pilot 1 CHB + JPT low coverage panel.