Functional Coding Variants in SLC6A15, a Possible Risk Gene for Major Depression

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Quast, Carina ^a   Cuboni, Serena ^a   Bader, Daniel ^a   Altmann, André ^a,b   Weber, Peter ^a   Arloth, Janine ^a   Röh, Simone ^a   Brückl, Tanja ^a   Ising, Marcus ^a   Kopczak, Anna ^a   Erhardt, Angelika ^a   Hausch, Felix ^a   Lucae, Susanne ^a   Binder, Elisabeth B ^a  

^a MAX PLANCK INSTITUTE OF PSYCHIATRY   (Germany)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; PROTEIN SLC6A15; UNCLASSIFIED DRUG;

ADULT; AMINO ACID SEQUENCE; ARTICLE; CASE CONTROL STUDY; CELL TRANSPORT; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MAJOR DEPRESSION; MALE; PROTEIN FUNCTION; SLC6A15 GENE;

EID: 84880762118     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068645     Document Type: Article

References (51)

1. Broer A, Tietze N, Kowalczuk S, Chubb S, Munzinger M, et al. (2006) The orphan transporter v7-3 (slc6a15) is a Na+-dependent neutral amino acid transporter (B(0)AT2). Biochemical Journal 393: 421-430.
2. Farmer MK, Robbins MJ, Medhurst AD, Campbell DA, Ellington K, et al. (2000) Cloning and characterization of human NTT5 and v7-3: Two orphan transporters of the Na+/Cl-dependent neurotransmitter transporter gene family. Genomics 70: 241-252.
3. Tapiero H, Mathe G, Couvreur P, Tew KD, (2002) Dossier: Free amino acids in human health and pathologies- II. Glutamine and glutamate. Biomedicine & Pharmacotherapy 56: 446-457.
4. Kohli MA, Lucae S, Saemann PG, Schmidt MV, Demirkan A, et al. (2011) The Neuronal Transporter Gene SLC6A15 Confers Risk to Major Depression. Neuron 70: 252-265.
5. Holsboer F, (2000) The corticosteroid receptor hypothesis of depression. Neuropsychopharmacology 23: 477-501.
6. Schuhmacher A, Lennertz L, Wagner M, Hoefels S, Pfeiffer U, et al. (2013) A variant of the neuronal amino acid transporter SLC6A15 is associated with ACTH and cortisol responses and cognitive performance in unipolar depression. International Journal of Neuropsychopharmacology 16: 83-90.
7. Drgonova J, Liu Q-R, Hall FS, Krieger RM, Uhl GR, (2007) Deletion of v7-3 (SLC6A15) transporter allows assessment of its roles in synaptosomal proline uptake, leucine uptake and behaviors. Brain Research 1183: 10-20.
8. Zhou Z, Zhen J, Karpowich NK, Goetz RM, Law CJ, et al. (2007) LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317: 1390-1393.
9. Hennings JM, Owashi T, Binder EB, Horstmann S, Menke A, et al. (2008) Clinical characteristics and treatment outcome in a representative sample of depressed inpatients- Findings from the Munich Antidepressant Response Signature (MARS) project. Journal of Psychiatric Research 43: 215-229.
10. Ising M, Lucae S, Binder EB, Bettecken T, Uhr M, et al. (2009) A Genomewide Association Study Points to Multiple Loci That Predict Antidepressant Drug Treatment Outcome in Depression. Archives of General Psychiatry 66: 966-975.
11. Hamilton M, (1959) The assessment of anxiety-states by rating. British Journal of Medical Psychology 32: 50-55.
12. Hamilton M, (1960) A rating scale for depression. Journal of Neurology Neurosurgery and Psychiatry 23: 56-62.
13. Erhardt A, Czibere L, Roeske D, Lucae S, Unschuld PG, et al. (2011) TMEM132D, a new candidate for anxiety phenotypes: evidence from human and mouse studies. Molecular Psychiatry 16: 647-663.
14. Lucae S, Salyakina D, Barden N, Harvey M, Gagne B, et al. (2006) P2RX7, a gene coding for a purinergic ligand-gated ion channel, is associated with major depressive disorder. Human Molecular Genetics 15: 2438-2445.
15. Muglia P, Tozzi F, Galwey NW, Francks C, Upmanyu R, et al. (2010) Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts. Molecular Psychiatry 15: 589-601.
16. Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, et al. (2011) vipR: variant identification in pooled DNA using R. Bioinformatics. 27: I77-I84.
17. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
18. David M, Dzamba M, Lister D, Ilie L, Brudno M, (2011) SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinformatics 27: 1011-1012.
19. Quast C, Altmann A, Weber P, Arloth J, Bader D, et al. (2012) Rare Variants in TMEM132D in a Case-Control Sample for Panic Disorder. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics 159B: 896-907.
20. Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38.
21. Gauderman W, Morrison J (2006) QUANTO 1.1: A computer program for power and sample size calculations for genetic-epidemiology studies.
22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81: 559-575.
23. Morgenthaler S, Thilly WG (2007) A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST). Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 615.
24. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
25. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4: 1073-1082.
26. Thomas PD, Campbell MJ, Kejariwal A, Mi HY, Karlak B, et al. (2003) PANTHER: A library of protein families and subfamilies indexed by function. Genome Research 13: 2129-2141.
27. Adzhubei I, Jordan DM, Sunyaev SR, (2013) Predicting functional effect of human missense mutations using PolyPhen-2. Current protocols in human genetics/editorial board, Jonathan L Haines [et al] Chapter 7: Unit7.20-Unit27.20.
28. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, et al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
29. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, et al. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Research 15: 901-913.
30. Yuan H-Y, Chiou J-J, Tseng W-H, Liu C-H, Liu C-K, et al. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Research 34: W635-W641.
31. Botstein D, Risch N, (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nature Genetics 33: 228-237.
32. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, et al. (2012) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science 337: 1190-1195.
33. Gibson G, (2012) Rare and common variants: twenty arguments. Nature Reviews Genetics 13: 135-145.
34. Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
35. Cooper GM, Shendure J, (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics 12: 628-640.
36. Miller MP, Kumar S, (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 10: 2319-2328.
37. Sunyaev S, Ramensky V, Bork P, (2000) Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends in Genetics 16: 198-200.
38. Chasman D, Adams RM, (2001) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation. Journal of Molecular Biology 307: 683-706.
39. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, et al. (2005) The universal protein resource (UniProt). Nucleic Acids Research 33: D154-D159.
40. Bao L, Cui Y, (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics 21: 2185-2190.
41. Dobson RJ, Munroe PB, Caulfield MJ, Saqi MAS (2006) Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. Bmc Bioinformatics 7.
42. Wyse ATS, Netto CA, (2011) Behavioral and neurochemical effects of proline. Metabolic Brain Disease 26: 159-172.
43. Papakostas GI, (2009) Evidence for S-Adenosyl-L-Methionine (SAM-e) for the Treatment of Major Depressive Disorder. Journal of Clinical Psychiatry 70: 18-22.
44. Yudkoff M, Daikhin Y, Grunstein L, Nissim I, Stern J, et al. (1996) Astrocyte leucine metabolism: Significance of branched-chain amino acid transamination. Journal of Neurochemistry 66: 378-385.
45. Javitt DC, (2004) Glutamate as a therapeutic target in psychiatric disorders. Molecular Psychiatry 9: 984-997.
46. Hägglund MGA, Roshanbin S, Löfqvist E, Hellsten SV, Nilsson VCO, et al. (2013) B0AT2 (SLC6A15) Is Localized to Neurons and Astrocytes, and Is Involved in Mediating the Effect of Leucine in the Brain. PLoS ONE 8: e58651.
47. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, et al. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research 17: 760-774.
48. Cooper GM, Brown CD, (2008) Qualifying the relationship between sequence conservation and molecular function. Genome Research 18: 201-205.
49. Bansal V, Libiger O, Torkamani A, Schork NJ, (2010) Statistical analysis strategies for association studies involving rare variants. Nature Reviews Genetics 11: 773-785.
50. Zoellner S, (2012) Sampling strategies for rare variant tests in case-control studies. European Journal of Human Genetics 20: 1085-1091.
51. Raychaudhuri S, (2011) Mapping Rare and Common Causal Alleles for Complex Human Diseases. Cell 147: 57-69.