Association study of 15 novel single-nucleotide polymorphisms of the T-bet locus among Finnish asthma families E. Ylikoski*, R. Kinos*, N. Sirkkanenw, M. Pyka¨la¨inen*, J. Savolainenz, L. A. Laitinen§, J. Kerez k , T. Laitinenz and R. Lahesmaa* *Centre for Biotechnology, University of Turku and A ˚ bo Akademi University, Finland, wDepartment of Clinical Genetics, Turku University Central Hospital, Finland, zDepartment of Pulmonary Diseases and Clinical Allergology, Turku University Central Hospital, Finland, §Department of Pulmonary Medicine, Helsinki University Central Hospital, Finland, zDepartment of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Finland and k Department of Biosciences at Novum and Clinical Reseach Centre, Karolinska Institute, Stockholm, Sweden Summary Objective T-box expressed in T cells (T-bet) is a transcription factor regulating the commitment of T helper (Th) cells by driving the cells into the Th1 direction. Abnormal Th1/Th2 balance may lead to complex disorders like asthma or autoimmune diseases. Recent studies have suggested that T-bet might be a candidate gene for asthma. This led us to screen 23 Finnish individuals for single- nucleotide polymorphisms (SNPs) in the T-bet locus and study the association between the SNPs and high serum IgE level and asthma. Methods We screened all six exons, adjacent intronic areas and 2kb of the 5 0 -flanking region from 23 individuals utilizing WAVE TM technology. To explore whether T-bet is associated in serum IgE regulation or asthma we genotyped the SNPs in a Finnish asthmatic founder population. The association analyses were made using haplotype pattern mining. Results Fifteen novel SNPs were found in the T-bet gene. Within the Finnish asthmatic founder population, there was no association between T-bet SNPs and high serum IgE level or asthma. Conclusions The genetic variability in the T-bet gene does not play a role in the pathogenesis of human asthma. Our results provide a novel panel of SNPs in T-bet and will help determine whether the SNPs have a functional role in other T cell-mediated diseases. Keywords asthma, human, SNP, T-bet, Th1/Th2 cells, transcription factors Submitted 30 June 2003; revised 11 November 2003; accepted 16 March 2004 Introduction Allergic asthma and other atopic diseases are characterized by T helper (Th)2-mediated inflammation. Although environ- mental factors contribute to the development of asthma and atopy, a strong genetic component is evident. Several chromosomal regions have been linked to asthma-related traits [1–5]. Asthma is a multi-factorial disease and, therefore, identification of candidate genes has been difficult. T-box expressed in T cells (T-bet) (also known as Tbx21 and TBLYM), located in 17q21.32, is a T cell-specific transcription factor regulating in part the differentiation of Th cells. T-bet promotes the differentiation of CD4 1 T cells to the Th1 direction. Expression of T-bet is up-regulated in response to IFN-g and activation of the cells through the T- cell receptor (TCR). Up-regulation of T-bet results in enhanced IFN-g transcription and IL-12Rb2 expression, thus sensitizing the cells for IL-12/STAT4 signalling [6–8]. Th1 cytokines are known to inhibit allergic responses [9, 10]. In a recent study, Finotto et al. [11] observed a reduced expression of T-bet in human asthmatic airways. In the same study, they demonstrated that T-bet-deficient mice exhibit a phenotype reminiscent of human asthma, even in the absence of allergen exposure. These findings suggest that T-bet might protect from asthma by predisposing the cells to differentiate to the Th1 rather than Th2 direction and further establishing and maintaining the Th1 phenotype. In addition, in one of the several genome-wide screens by Dizier et al. [12] linkage for asthma and asthma-related phenotypes was investigated. In the screen they found linkage to HOX2B gene, which is loca- ted close to T-bet in 17q21.32. Taken together these findings suggest that T-bet might be a candidate gene for asthma. To elucidate the role of T-bet in asthma genetics, we searched for single-nucleotide polymorphisms (SNPs) within the gene in 46 chromosomes. Furthermore, these markers were screened for an association with high levels of serum IgE in asthmatic individuals and controls from a Finnish founder population. Materials and methods Patients screened for genetic variation in T-bet To screen genetic variation in T-bet, we studied two patient groups. Ten patients had the history of allergic asthma (mean Correspondence: Emmi Ylikoski, Centre for Biotechnology, University of Turku and A ˚ bo Akademi, PO Box 123, FIN-20520, Turku, Finland. E-mail: emmi.ylikoski@btk.utu.fi Clin Exp Allergy 2004; 34:1049–1055 doi:10.1111/j.1365-2222.2004.01995.x r 2004 Blackwell Publishing Ltd 1049