An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

Genes and Immunity

Volumn 10, Issue 6, 2009, Pages 566-578

  Sazzini, M ^a   Zuntini, R ^b   Farjadian, S ^c   Quinti, I ^d   Ricci, G ^a   Romeo, G ^b   Ferrari, S ^b   Calafell, F ^e,f   Luiselli, D ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^d SAPIENZA UNIVERSITY OF ROME   (Italy)

^e UNIVERSITAT POMPEU FABRA   (Spain)

^f CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSMEMBRANE ACTIVATOR AND CAML INTERACTOR;

ADAPTIVE IMMUNITY; ARTICLE; CHIMPANZEE; CHROMOSOME ANALYSIS; COMMON VARIABLE IMMUNODEFICIENCY; CONTROLLED STUDY; DNA FLANKING REGION; EVOLUTIONARY ADAPTATION; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHY; HAPLOTYPE; HUMAN; IMMUNOGLOBULIN A DEFICIENCY; INNATE IMMUNITY; ITALY; MAJOR CLINICAL STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CASE-CONTROL STUDIES; COMMON VARIABLE IMMUNODEFICIENCY; EVOLUTION; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MUTATION; PAN TROGLODYTES; PHENOTYPE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSMEMBRANE ACTIVATOR AND CAML INTERACTOR PROTEIN; WORLD HEALTH;

EID: 69949119995     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2009.43     Document Type: Article

References (59)

1. Ng LG, Sutherland AP, Newton R, Qian F, Cachero TG, Scott ML et al B cell-activating factor belonging to the TNF family (BAFF)-R is the principal BAFF receptor facilitating BAFF costimulation of circulating T and B cells. J Immunol 2004; 173: 807-817.
2. Novak AJ, Darce JR, Arendt BK, Harder B, Henderson K, Kindsvogel W et al. Expression of BCMA, TACI, and BAFF-R in multiple myeloma: A mechanism for growth and survival. Blood 2004; 103: 689-694.
3. Mackay F, Schneider P. TACI, an enigmatic BAFF/APRIL receptor, with new unappreciated biochemical and biological properties. Cytokine Growth Factor Rev 2008; 19: 263-276.
4. Salzer U, Grimbacher B. Common variable immunodeficiency: The power of costimulation. Semin Immunol 2006; 18: 337-346.
5. Castigli E, Wilson SA, Garibyan L, Rachid R, Bonilla F, Schneider L et al. TACI is mutant in common variable immunodeficiency and IgA deficiency. Nat Genet 2005; 37: 829-834.
6. Salzer U, Chapel HM,Webster AD, Hammarstrom Q, Schmitt-Graeff A, Schlesier M et al. Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans. Nat Genet 2005; 37: 820-828.
7. Castigli E, Wilson SA, Garibyan L, Rachid R, Bonilla F, Schneider L et al. Reexamining the role of TACI coding variants in common variable immunodeficiency and selective IgA deficiency. Nat Genet 2007; 39: 430-431.
8. Pan-Hammarström Q, Salzer U, Du L, Björkander J, Cunningham-Rundles C, Nelson DL et al. Reexamining the role of TACI coding variants in common variable immunodeficiency and selective IgA deficiency. Nat Genet 2007; 39: 429-430.
9. Lee JJ, Ozcan E, Rauter I, Geha RS. Transmembrane activator and calcium-modulator and cyclophilin ligand interactor mutations in common variable immunodeficiency. Curr Opin Allergy Clin Immunol 2008; 8: 520-526.
10. Salzer U, Bacchelli C, Buckridge S, Pan-Hammarstrom Q, Jennings S, Lougaris V et al. Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes. Blood 2009; 113: 1967-1976.
11. Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet 2001; 29: 306-309.
12. Aldea A, Calafell F, Aróstegui JL, Lao O, Rius J, Plaza S et al The west side story: MEFV haplotype in Spanish FMF patients and controls, and evidence of high LD and a recombination 'hot-spot' at the MEFV locus. Hum Mutat 2004; 23: 399-406.
13. Sabater-Lleal M, Soria JM, Bertranpetit J, Almasy L, Blangero J, Fontcuberta J et al. Human F7 sequence is split into three deep clades that are related to FVII plasma levels. Hum Genet 2006; 118: 741-751.
14. Soldevila M, Andrés AM, Ramírez-Soriano A, Marquès-Bonet T, Calafell F, Navarro A et al. The prion protein gene in humans revisited: Lessons from a worldwide resequencing study. Genome Res 2006; 16: 231-239.
15. Bamshad M,Wooding SP. Signatures of natural selection in the human genome. Nat Genet 2003; 4: 99-111.
16. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE et al. Haplotype variation and linkage disequilibrium in 313 human genes. Science 2001; 293: 489-493.
17. Ferrer-Admetlla A, Bosch E, Sikora M, Marquès-Bonet T, Ramírez-Soriano A, Muntasell A et al. Balancing selection is the main force shaping the evolution of innate immunity genes. J Immunol 2008; 181: 1315-1322.
18. Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K et al Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 1996; 271: 1380-1387.
19. Calafell F, Shuster A, Speed WC, Kidd JR, Kidd KK. Short tandem repeat polymorphism evolution in humans. Eur J Hum Genet 1998; 6: 38-49.
20. Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B et al. A global haplotype analysis of the myotonic dystrophy locus: Implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am J Hum Genet 1998; 62 1389-1402.
21. Mateu E, Calafell F, Lao O, Bonné-Tamir B, Kidd JR, Pakstis A et al. Worldwide genetic analysis of the CFTR region. Am J Hum Genet 2001; 68: 103-117.
22. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005; 437: 69-87.
23. Tjandra N. Establishing a degree of order: Obtaining high-resolution NMR structures from molecular alignment. Structure 1999; 7: R205-R211.
24. Garibyan L, Lobito AA, Siegel RM, Call ME, Wucherpfennig KW, Geha RS. Dominant-negative effect of the heterozygous C104R TACI mutation in common variable immunodeficiency (CVID). J Clin Invest 2007; 117: 1550-1557.
25. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL. An apportionment of human DNA diversity. Proc Natl Acad Sci USA 1997; 94: 4516-4519.
26. Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST et al. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 2002; 12 602-612.
27. Moreno-Estrada A, Casals F, Ramírez-Soriano A, Oliva B, Calafell F, Bertranpetit J et al. Signatures of selection in the human olfactory receptor OR5I1 gene. Mol Biol Evol 2008; 25: 144-154.
28. Calafell F, Roubinet F, Ramírez-Soriano A, Saitou N, Bertranpetit J, Blancher A. Evolutionary dynamics of the human ABO gene. Hum Genet 2008; 124: 123-135.
29. Ramos-Onsis SE, Rozas J. Statistical properties of new neutrality tests against population growth. Mol Biol Evol 2002; 19: 2092-2100.
30. Ramírez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics 2008; 179: 555-567.
31. Nachman MW, Crowell SL. Contrasting evolutionary histories of two introns of the duchenne muscular dystrophy gene, Dmd, in humans. Genetics 2000; 155: 1855-1864.
32. Harding RM, Healy E, Ray AJ, Ellis NS, Flanagan N, Tood C et al. Evidence for variable selective pressures at MC1R. Am J Hum Genet 2000; 66: 1351-1361.
33. Salzer U, Birmelin J, Bacchelli C, Witte T, Buchegger-Podbielski U, Buckridge S et al. Sequence analysis of TNFRSF13b, encoding TACI, in patients with systemic lupus erythematosus. J Clin Immunol 2007; 4: 372-377.
34. Inoue K, Mineharu Y, Inoue S, Yamada S, Matsuda F, Nozaki K et al. Search on chromosome 17 centromere reveals TNFRSF13B as a susceptibility gene for intracranial aneurysm: A preliminary study. Circulation 2006; 113: 2002-2010.
35. Lee WI, Huang JL, Kuo ML, Lin SJ, Chen LC, Chen MT et al. Analysis of genetic defects in patients with the common variable immunodeficiency phenotype in a single Taiwanese tertiary care hospital. Ann Allergy Asthma Immunol 2007; 99: 433-442.
36. Stoneking M. Human origins. The molecular perspective. EMBO Rep 2008; 9: S46-S50.
37. Maglione PJ, Chan J. 2009. How B cells shape the immune response against Mycobacterium tuberculosis. Eur J Immunol 2009; 39: 676-686.
38. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O et al. Positive natural selection in the human lineage. Science 2006; 312: 1614-1620.
39. Groom JR, Fletcher CA, Walters SN, Grey ST, Watt SV, Sweet MJ et al BAFF and MyD88 signals promote a lupuslike disease independent of T cells. J Exp Med 2007; 204: 1959-1971.
40. Katsenelson N, Kanswal S, Puig M, Mostowski H, Verthelyi D, Akkoyunlu M. Synthetic CpG oligodeoxynucleotides augment BAFF- and APRIL-mediated immunoglobulin secretion. Eur J Immunol 2007; 37: 1785-1795.
41. Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet 2001; 17: 502-510.
42. Fearnhead NS, Winney B, Bodmer WF. Rare variant hypothesis for multifactorial inheritance: Susceptibility to colorectal adenomas as a model. Cell Cycle 2005; 4: 521-525.
43. Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinformatics Online 2005; 1: 47-50.
44. Stephens M, Smith NJ, Donnely P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68 978-989.
45. Stephens JC, Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 2005; 76: 449-462.
46. Graffelman J, Balding DJ, Gonzalez-Neira A, Bertranpetit J. Variation in estimated recombination rates across human populations. Hum Genet 2007; 122: 301-310.
47. Rozas J, Sánchez-Del Barrio JC, Messeguer X, Rozas R. DnaSp, DNA polymorphism analyses by the coalescent and others methods. Bioinformatics 2003; 19: 2496-2497.
48. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 2005; 21 263-265.
49. Bandelt HJ, Forster P, Sykes BC, Richards MB. Mitochondrial portraits of human populations using median networks. Genetics 1995; 141: 743-753.
50. Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 1992; 131 479-491.
51. Slatkin M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 1995; 139: 457-462.
52. Kruskal J. Nonmetric multidimensional scaling: A numerical method. Psychometrika 1964; 29: 28-42.
53. McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 1991; 351: 652-654.
54. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics 1987; 116: 153-159.
55. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989; 123: 585-595.
56. Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics 1993; 133: 693-709.
57. Fay JC, Wu CI. Hitchhiking under positive Darwinian selection. Genetics 2000; 155: 1405-1413.
58. Takahata N, Satta Y, Klein J. Divergence and population size in the lineage leading to modern humans. Theor Popul Biol 1995; 48: 198-221.
59. Myers S, Bottolo L, Freeman C, Mc Vean G, Donnely P. A finescale map of recombination rates and hotspots across the human genome. Science 2005; 310: 321-324.