DNA ligase IV (LigIV) deficiency was identified as the molecular basis for a severe form of combined immunodeficiency in two microcephalic siblings with cellular radiosensitivity. In one patient the diagnosis was made directly after birth, allowing analysis of the role of LigIV in the development of specific immune cells. Absolute numbers of B cells were reduced 100-fold and αβ T cells 10-fold, whereas γδ T cells were normal. Spectratyping of all three cell populations showed a diverse repertoire, but sequencing of IgH V(D)J junctions revealed shorter CDR3 regions due to more extensive nucleotide deletions among D and J elements and fewer N nucleotide insertions. Clonal restriction of IgG-expressing, but not IgM-expressing, B cells and the lack of primary and secondary lymph node follicles indicated impaired class switch recombination. Observations in the older sibling showed that this rudimentary immune system was able to mount specific responses to infection. However, partial Ab responses and extensive amplification of γδ T cells could not prevent a life-threatening course of viral and bacterial infections, the development of an EBV-induced lymphoma, and immune dysregulation reflected by severe autoimmune cytopenia. Impaired generation of immune diversity under conditions of limited LigIV activity can cause a human SCID variant with a characteristic immunological phenotype.

We performed genome-wide analysis of copy-number changes and loss of heterozygosity (LOH) in Barrett's esophageal adenocarcinoma by single nucleotide polymorphism (SNP) microarrays to identify associated genomic alterations. DNA from 27 esophageal adenocarcinomas and 14 matching normal tissues was subjected to SNP microarrays. The data were analyzed using dChipSNP software. Copy-number changes occurring in at least 25% of the cases and LOH occurring in at least 19% were regarded as relevant changes. As a validation, fluorescence in situ hybridization (FISH) of 8q24.21 (CMYC) and 8p23.1 (SOX7) was performed. Previously described genomic alterations in esophageal adenocarcinomas could be confirmed by SNP microarrays, such as amplification on 8q (CMYC, confirmed by FISH) and 20q13 or deletion/LOH on 3p (FHIT) and 9p (CDKN2A). Moreover, frequent gains were detected on 2p23.3, 7q11.22, 13q31.1, 14q32.31, 17q23.2 and 20q13.2 harboring several novel candidate genes. The highest copy numbers were seen on 8p23.1, the location of SOX7, which could be demonstrated to be involved in amplification by FISH. A nuclear overexpression of the transcription factor SOX7 could be detected by immunohistochemistry in two amplified tumors. Copy-number losses were seen on 18q21.32 and 20p11.21, harboring interesting candidate genes, such as CDH20 and CST4. Finally, a novel LOH region could be identified on 6p in at least 19% of the cases. In conclusion, SNP microarrays are a valuable tool to detect DNA copynumber changes and LOH at a high resolution. Using this technique, we identified several novel genes and DNA regions associated with esophageal adenocarcinoma. KEYWORDS: Barrett's adenocarcinoma; copy-number changes; esophageal carcinoma; LOH; mapping array; SNP array Genomic alterations, such as amplification, deletion, translocation and loss of heterozygosity (LOH) play an important role in the pathogenesis and progression of cancer due to the activation of oncogenes or inactivation of tumor suppressor genes. Apart from numeric aberrations, such as gene amplification or deletion, which are frequently detected in carcinomas, other genomic changes in carcinogenesis, such as LOH, do not necessarily lead to DNA copy-number gain or loss. Several causes of LOH have been described, including deletion, non-disjunction and reduplication, mitotic recombination and gene conversion. 1 The two-hit model describes a tumor suppressor gene inactivation due to a loss of one allele and mutation of the other allele, resulting in an LOH. 2 Besides detailed investigation of known oncogenes and tumor suppressor genes, screening for novel genomic alterations in different cancers and precursor lesions provides information of molecular mechanisms in carcinogenesis.The incidence of esophageal (Barrett's) adenocarcinoma, mostly arising within the precancerous Barrett's esophagus, with the normal esophageal squamous epithelium changed into intestinal metaplasia, has risen in the past decades in western countries. 3 Screening for chromosomal alterations has bee...

Approximately 10% of gastric carcinomas (GC) worldwide are associated with Epstein-Barr virus (EBV). GC is one of the most frequent human malignancies associated with EBV. The latent expression of the EBV-oncogene BARF1 is restricted to epithelial malignancies. To investigate the underlying BARF1-related mechanisms of oncogenic epithelial transformation, we analyzed gene expression profiles of a BARF1-transfected epithelial (HaCaT+) and the corresponding BARF1-negative (HaCaT-) cell line by cDNA microarray analysis. Real-time PCR was performed to confirm the cDNA microarray results. In addition, immunohistochemistry and fluorescence in situ hybridization were performed on a tissue microarray of 181 GC including 11 EBV-associated GC. Among other genes cyclin D1 expression was significantly upregulated in HaCaT+ on the transcriptional and protein level. Cyclin D1 protein expression in GC revealed a significant overexpression of cyclin D1 in EBV-associated GC (p<0.012) but not in EBV-negative GC. Cyclin D1 FISH showed that cyclin D1 overexpression was not due to gene amplification in EBV-associated GC. Cyclin D1 is induced in HaCaT+ by BARF1 and is overexpressed in EBV-associated GC indicating an interaction of viral BARF1 and cyclin D1.

No abstract

We report a case of an invasive ductal breast carcinoma with significant heterogeneity: a HER-2+ tumor component was densely infiltrated by T-cells, whereas the HER2- tumor component, including two axillary lymph node metastases, showed much fewer tumor infiltrating lymphocytes. Array comparative genomic hybridization of dissected tumor cells from both components revealed many shared chromosomal aberrations but also unique alterations of the HER2+ tumor cell population besides HER2 amplification. We found a clonally dominated T-cell receptor rearrangement of the tumor infiltrating lymphocytes in the HER2+, but not in the HER2- tumor component. Thus, in this case HER2 overexpression is associated with a marked infiltration by T-cells suggesting a specific T-cell response against the HER2+ tumor cell population.