A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response.

One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (γH2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6-3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis.

The mucosal adhesion receptor alpha4beta7 integrin is selectively increased in lymphocytes stimulated with beta-lactoglobulin in children allergic to cow's milk.

BACKGROUND: It has been shown in mice that the integrin alpha4beta7 directs the migration of memory T cells into the gut-associated lymphoid tissue. However, little is known about T-cell homing mechanisms in children with food allergies. OBJECTIVE: We investigated the expression of this and other integrins in children with different manifestations of cow's milk allergy (urticaria, atopic dermatitis, and wheezing). METHODS: PBMCs were stimulated with beta-lactoglobulin, 1 of the major allergenic proteins in cow's milk, and tetanus toxoid. Integrin expression was studied by flow cytometric analysis after 1 week of culture. RESULTS: We found significantly higher expression of the alpha4beta7 integrin in cells from patients compared with control subjects with no allergies (P =. 005) when beta-lactoglobulin was used to stimulate the cells. alpha4beta7 integrin was also expressed at significantly higher levels in beta-lactoglobulin-stimulated cells than in tetanus toxoid-stimulated cells (P =.005). The alphaEbeta7 and the alpha4beta1 integrins were not upregulated by allergen stimulation. Most alpha4beta7 integrin-expressing cells were identified as CD4(+) T cells. CONCLUSION: These results show that alpha4beta7 integrin expression after stimulation with beta-lactoglobulin correlates with the presumptive site of cow's milk sensitization (ie, the gut-associated lymphoid tissue but not with the site of symptoms of cow's milk allergy).