Screening of tumor necrosis factor receptor-associated factor 6 as a candidate gene for inflammatory bowel disease.
OBJECTIVE
The two forms of inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC), are thought to arise because of an interplay of unfavorable genetic and exogenous factors. During a genome-wide linkage study of IBD, we observed a nominal linkage to chromosome 11p12-q13 that was further confirmed upon fine density mapping. This chromosomal region contains a functional IBD candidate gene coding for tumor necrosis factor receptor-associated factor 6 (TRAF6), a signal transducer regulating innate and adaptive immunity as well as bone homeostasis.


METHODS
Using denaturing high-performance liquid chromatography (dHPLC) and DNA sequencing, all exons and exon-intron boundaries of the TRAF6 gene in probands of 95 IBD families were initially screened; this material comprised 20 CD, 39 UC and 36 mixed families.


RESULTS
No nucleotide changes in the coding sequence of TRAF6 were detected, but a single-base insertion/deletion polymorphism in a polythymine stretch (containing 8 or 7 thymines, respectively) in intron 3 was identified. However, examination of an extended material of 290 unrelated CD patients, 416 UC patients and 320 healthy blood donors failed to show any association with this 7T/8T variation and IBD, nor was this polymorphism related to specific clinical features in IBD.


CONCLUSIONS
Our study tends to exclude a good positional and functional candidate gene, TRAF6, as an IBD predisposing gene and lends support to the idea that the function of TRAF6 is important enough not to permit structural alterations of this mediator.
Lappalainen
Maarit
M
Research Program in Molecular Medicine, Biomedicum Helsinki, Helsinki, Finland.
Paavola-Sakki
Paulina
P
Halme
Leena
L
Turunen
Ulla
U
Heliö
Tiina
T
Färkkilä
Martti
M
Kontula
Kimmo
K
D002851:Chromatography, High Pressure Liquid; D002880:Chromosomes, Human, Pair 11; D003093:Colitis, Ulcerative / Q000235:genetics*; D003424:Crohn Disease / Q000235:genetics*; D005260:Female; D008040:Genetic Linkage; D006801:Humans; D008297:Male; D008875:Middle Aged; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D048029:TNF Receptor-Associated Factor 6 / Q000235:genetics*
D048029:TNF Receptor-Associated Factor 6