Polymorphisms in the 3'-untranslated region of the CDH1 gene are a risk factor for primary gastric diffuse large B-cell lymphoma.

BACKGROUND: Primary gastric B-cell lymphomas arise from mucosa-associated lymphatic tissue (MALT) in patients with chronic Helicobacter pylori infection. We investigated whether germline variants in the CDH1 gene, coding for E-cadherin, genetically predispose patients to primary gastric B-cell lymphoma. DESIGN AND METHODS: Single marker analyses of the CDH1 gene were conducted in patients with primary gastric B-cell lymphoma (n=144), in patients with primary gastric high-grade lymphoma (n=61), and in healthy blood donors (n=361). Twelve single nucleotide polymorphisms were genotyped by TaqMan(®) technology. Allelic imbalance was tested by pyrosequencing and clone direct sequencing of heterozygote genomic and cDNA. Mutation detection was conducted around the poly-A signal of the CDH1 3'-untranslated region. The influence of the 3'-untranslated region on protein translation was determined by a luciferase reporter assay. RESULTS: Single marker analyses identified two single nucleotide polymorphisms in strong linkage disequilibrium located in the CDH1 3'-untranslated region. One of them was significantly associated with primary gastric diffuse large B-cell lymphomas after correction for multiple testing and this association was confirmed in an independent sample set. Patients homozygous for the rare T allele (rs1801026) had a 4.9-fold increased risk (95% CI: 1.5-15.9) of developing primary gastric diffuse large B-cell lymphoma. Allelic imbalance and reporter gene assays indicated a putative influence on mRNA stability and/or translational efficacy. CONCLUSIONS: We identified variants in CDH1 as the first potential genetic risk factors for the development of primary gastric diffuse large B-cell lymphomas. One of the potentially causative variants affects allelic CDH1 expression. These findings support the hypothesis that besides somatic alterations of B-cells, germline variants in the CDH1 gene contribute to a predisposition to the development of primary gastric diffuse large B-cell lymphomas.

NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease.

AIM: To investigate the frequency of NOD2, IL23R and ATG16L1 genetic variants in a case-control panel for inflammatory bowel disease (IBD) from Lithuania. METHODS: One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (UC)] and 186 healthy controls were genotyped for the following known genetic susceptibility variants: NOD2 - Arg702Trp (rs2066844), Gly908Arg (rs2066845) and Leu1007insC (rs2066847), as well as IL23R - Arg381Gln (rs11209026) and ATG16L1 - Thr300Ala (rs2241880). RESULTS: The effect that carriership of at least one NOD2 risk allele predisposes to CD was replicated in the Lithuanian population (41.1% CD vs 16.9% controls, P = 2 x 10(-4), OR = 3.48, 95% CI: 1.81-6.72). In the allelic single marker analysis, Leu1007insC was strongly associated with CD (21.4% CD vs 4.7% controls, P = 3.687 x 10(-8), OR = 5.54, 95% CI: 2.85-10.75). Neither the other two NOD2 variants, nor the known variants in IL23R and ATG16L1 were found to be risk factors for CD, UC or IBD. However, our relatively small study population was underpowered to demonstrate such weak to moderate disease associations. CONCLUSION: The results support a strong association between CD susceptibility and the Leu1007insC variant in NOD2 in the Lithuanian study population.

Allelic variation in BTNL2 and susceptibility to tuberculosis in a South African population.

Tuberculosis and sarcoidosis show phenotypic features of granulomatous disease. The bacterium Mycobacterium tuberculosis can induce the expression of the sarcoidosis susceptibility gene BTNL2 in monocyte-derived macrophages. BTNL2 was therefore investigated as a candidate gene for tuberculosis in a case-control association study in the South African Coloured population. We sequenced the coding regions of BTNL2 to detect known and novel polymorphisms and genotyped 18 SNPs in 432 pulmonary tuberculosis cases and 482 controls. We did not find a significant association between the truncating rs2076530 SNP, previously associated with sarcoidosis, and tuberculosis. No association was found between any of the other SNPs studied and disease and none of the estimated haplotypes showed any association with TB. Comparative analyses with the South African data from this study and published data on German and American populations revealed that, for a segment of BTNL2, the admixed, but not stratified, South African population resembles the African-Americans more than white populations.

Host susceptibility to tuberculosis: CARD15 polymorphisms in a South African population.

Tuberculosis (TB) is one of the leading causes of death worldwide. The nucleotide-binding oligomerisation domain 2 protein (NOD2) has recently been recognised as a non-redundant recognition mechanism of Mycobacterium tuberculosis. The caspase recruitment domain-containing protein 15 gene (CARD15), which encodes the NOD2 protein, is a susceptibility gene for Crohn's disease (CD), a granulomatous, chronic inflammatory disorder. CARD15 was therefore investigated as a candidate gene in TB. We genotyped the R702W, G908R and 1007fs variants, previously associated with CD, in TB cases and controls from the admixed South African Coloured population. No statistically significant differences between cases and controls were observed for these variants. We determined that the CD-associated mutations occur at very low frequencies in this population. Our results indicate that CARD15 is not a major susceptibility gene for TB in the South African Coloureds.

SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs.

Functional annotation of SNPs (as generated by HapMap (http://www.hapmap.org) for instance) is a major challenge. SNPs that lead to single amino acid substitutions, stop codons, or frameshift mutations can be readily interpreted, but these represent only a fraction of known SNPs. Many SNPs are located in sequences of splicing relevance-the canonical splice site consensus sequences, exonic and intronic splice enhancers or silencers (exonic splice enhancer [ESE], intronic splice enhancer [ISE], exonic splicing silencer [ESS], and intronic splicing silencer [ISS]), and others. We propose using sets of matching DNA and complementary DNA (cDNA) as a screening method to investigate the potential splice effects of SNPs in RT-PCR experiments with tissue material from genotyped sources. We have developed a software solution (SNPSplicer; http://www.ikmb.uni-kiel.de/snpsplicer) that aids in the rapid interpretation of such screening experiments. The utility of the approach is illustrated for SNPs affecting the donor splice sites (rs2076530:A>G, rs3816989:G>A) leading to the use of a cryptic splice site and exon skipping, respectively, and an exonic splice enhancer SNP (rs2274987:C/T), leading to inclusion of a new exon. We anticipate that this methodology may help in the functional annotation of SNPs in a more high-throughput fashion.