CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

The functional roles of SNPs within the 8q24 gene desert in the cancer phenotype are not yet well understood. Here, we report that CCAT2, a novel long noncoding RNA transcript (lncRNA) encompassing the rs6983267 SNP, is highly overexpressed in microsatellite-stable colorectal cancer and promotes tumor growth, metastasis, and chromosomal instability. We demonstrate that MYC, miR-17-5p, and miR-20a are up-regulated by CCAT2 through TCF7L2-mediated transcriptional regulation. We further identify the physical interaction between CCAT2 and TCF7L2 resulting in an enhancement of WNT signaling activity. We show that CCAT2 is itself a WNT downstream target, which suggests the existence of a feedback loop. Finally, we demonstrate that the SNP status affects CCAT2 expression and the risk allele G produces more CCAT2 transcript. Our results support a new mechanism of MYC and WNT regulation by the novel lncRNA CCAT2 in colorectal cancer pathogenesis, and provide an alternative explanation of the SNP-conferred cancer risk

Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula

Oesophageal atresia (OA) with or without tracheoesophageal fistula (TOF) are rare anatomical congenital malformations whose cause is unknown in over 90% of patients. A genetic background is suggested, and among the reported genetic defects are copy number variations (CNVs). We hypothesized that CNVs contribute to OA/TOF development. Quantifying their prevalence could aid in genetic diagnosis and clinical care strategies. Therefore, we profiled 375 patients in a combined Dutch, American and German cohort via genomic microarray and compared the CNV profiles with their unaffected parents and published control cohorts. We identified 167 rare CNVs containing genes (frequency<0.0005 in our in-house cohort). Eight rare CNVs - in six patients - were de novo, including one CNV previously associated with oesophageal disease. (hg19 chr7:g.(143820444-143839360)-(159119486-159138663)del) 1.55% of isolated OA/TOF patients and 1.62% of patients with additional congenital anomalies had de novo CNVs. Furthermore, three (15q13.3, 16p13.3 and 22q11.2) susceptibility loci were identified based on their overlap with known OA/TOF-associated CNV syndromes and overlap with loci in published CNV association case-control studies in developmental delay. Our study suggests that CNVs contribute to OA/TOF development. In addition to the identified likely deleterious de novo CNVs, we detected 167 rare CNVs. Although not directly disease-causing, these CNVs might be of interest, as they can act as a modifier in a multiple hit model, or as the second hit in a recessive condition

T(6;9)(p22;q34)/DEK-NUP214-rearranged pediatric myeloid leukemia: An international study of 62 patients

Acute myeloid leukemia with t(6;9)(p22;q34) is listed as a distinct entity in the 2008 World Health Organization classification, but little is known about the clinical implications of t(6;9)-positive myeloid leukemia in children. This international multicenter study presents the clinical and genetic characteristics of 62 pediatric patients with t(6;9)/DEK-NUP214-rearranged myeloid leukemia; 54 diagnosed as having acute myeloid leukemia, representing <1% of all childhood acute myeloid leukemia, and eight as having myelodysplastic syndrome. The t(6;9)/DEK-NUP214 was associated with relatively late onset (median age 10.4 years), male predominance (sex ratio 1.7), French-American-British M2 classification (54%), myelodysplasia (100%), and FLT3-ITD (42%). Outcome was substantially better than previously reported with a 5-year event-free survival of 32%, 5-year overall survival of 53%, and a 5-year cumulative incidence of relapse of 57%. Hematopoietic stem cell transplantation in first complete remission improved the 5-year event-free survival compared with chemotherapy alone (68% versus 18%; P<0.01) but not the overall survival (68% versus 54%; P=0.48). The presence of FLT3-ITD had a non-significant negative effect on 5-year overall survival compared with non-mutated cases (22% versus 62%; P=0.13). Gene expression profiling showed a unique signature characterized by significantly higher expression of EYA3, SESN1, PRDM2/RIZ, and HIST2H4 genes. In conclusion, t(6;9)/DEK-NUP214 represents a unique subtype of acute myeloid leukemia with a high risk of relapse, high frequency of FLT3-ITD, and a specific gene expression signature

Lanthanide-based time-resolved luminescence immunoassays

The sensitive and specific detection of analytes such as proteins in biological samples is critical for a variety of applications, for example disease diagnosis. In immunoassays a signal in response to the concentration of analyte present is generated by use of antibodies labeled with radioisotopes, luminophores, or enzymes. All immunoassays suffer to some extent from the problem of the background signal observed in the absence of analyte, which limits the sensitivity and dynamic range that can be achieved. This is especially the case for homogeneous immunoassays and surface measurements on tissue sections and membranes, which typically have a high background because of sample autofluorescence. One way of minimizing background in immunoassays involves the use of lanthanide chelate labels. Luminescent lanthanide complexes have exceedingly long-lived luminescence in comparison with conventional fluorophores, enabling the short-lived background interferences to be removed via time-gated acquisition and delivering greater assay sensitivity and a broader dynamic range. This review highlights the potential of using lanthanide luminescence to design sensitive and specific immunoassays. Techniques for labeling biomolecules with lanthanide chelate tags are discussed, with aspects of chelate design. Microtitre plate-based heterogeneous and homogeneous assays are reviewed and compared in terms of sensitivity, dynamic range, and convenience. The great potential of surface-based time-resolved imaging techniques for biomolecules on gels, membranes, and tissue sections using lanthanide tracers in proteomics applications is also emphasized

Translocation t (6; 9)(p22; q34)/DEK-NUP214 rearranged Pediatric AML:: A Retrospective international Study

The cytogenetic subgroup t(6;9)(p22;q34), previously often reported as a breakpoint in 6p23, is defined as a distinct entity in the 2008 WHO classification of acute myeloid leukemia (AML). The translocation results in a chimeric fusion between DEK at 6p22.3 and NUP214 at 9q34.13 generating the DEK-NUP214 fusion gene. In adults, t(6;9) is associated with young age, very poor outcome, and a higher prevalence of FLT3-ITD than in any other type of AML. To date, the clinical impact of t(6;9) has not been independently described in a pediatric cohort. In this retrospective study, we aimed to characterize the clinical, genetic and morphological features of t(6;9) in childhood AML and to evaluate outcome. Children aged 0\u201318 years and diagnosed with t(6;9)-positive AML or MDS within the period January 1, 1993 to December 31, 2011 were included. The presence of the translocation was determined by conventional karyotyping, FISH, or RT-PCR. Patients with Down syndrome and therapy-related AML were excluded. All major pediatric AML study groups were invited to submit clinical data. In addition, diagnostic smears and biopsies were requested for central reviewing and viable cells or RNA for gene expression profiling (GEP). All karyotypes were centrally reviewed and described according to the International System for Human Cytogenetic Nomenclature. GEP was performed on available frozen diagnostic samples from 297 pediatric AML patients including 6 patients with t(6;9). Based on p-value, log-fold change and biological relevance, the following 4 genes were selected for validation by quantitative real-time PCR (RT-qPCR); eyes absent homolog 3 at 1p35.3 (EYA3), sestrin 1 at 6q21(SESN1), PR domain containing 2, with ZNF domain at 1p36.21 (PRDM2, also known as RIZ1), and histone cluster 2, H4a at 1q21.2 (HIST2H4). Validation was performed on 48 patient samples: t(6;9) (n=17), other pediatric AML (n=31) and 14 cell lines including one with t(6;9)(p22;q34). A total of 58 pediatric patients with a DEK-NUP214 t(6;9) myeloid malignancy from 24 study groups were included in the study: 50 were diagnosed as de novo AML (0.5% of all AML during the study period) and 8 as MDS. Patients with t(6;9) were characterized by a late onset as well as male preponderance; median age was 11 years (range 3\u201318 years) and the male:female ratio 39:19 (p<0.01). The median white blood cell count (WBC) was 15.6x109/L (range 0.2\u2013191). Bilinear dysplasia with pseudo-Pelger-Hu\uebt cells was commonly seen (92% of reviewed evaluable material), and Auer rods were reported in 10 patients, whereas basophilia, in contrast to adults, was absent in this pediatric cohort. FAB-M2 dominated (45%), followed by M4 in 24%. The t(6;9) was the sole cytogenetic abnormality in 81%. Trisomies 8 and 13 constituted 40% of the additional aberrations, either alone or together. FLT3-ITD was present in 44% (n=11) of the cohort with known FLT3 status. The 5-year OS for AML and MDS was 55% and 86%, 5-year EFS was 33% and 56%, respectively. Presence of FLT3-ITD had a non-significant negative effect on OS: 32% for FLT3-ITD-positive cases vs. 67% for FLT3-ITD-negative cases, (p=0.15). The 5-year OS for patients treated with stem cell transplant (SCT) in 1st complete remission (CR) or with refractory disease (RD) was 82% (n=20) vs. 56% with chemotherapy (n=30), (p=0.10). Children who died within 3 months from diagnosis were excluded from the analysis of SCT vs. chemotherapy. The GEP performed on 6 pediatric t(6;9) positive patients showed a unique signature with 180 significantly differentially expressed genes. High expression of EYA3, SESN1, PRDM2/RIZ1 and HIST2H4, was confirmed by RT q-PCR. The levels of expression were significantly elevated for all 4 genes in the t(6;9)-positive cases compared with other AML subtypes. In conclusion, we present a large international series of 58 children with DEK-NUP214/ t(6;9)(p22;q34)-positive myeloid leukemia, representing 0.5% of all childhood AML. The cases were characterized by late onset, male predominance, myelodysplasia, and a unique gene expression signature. The 5-year OS was intermediate and substantially better than reported in adults. SCT in 1st CR or in RD did non-significantly improve the OS compared with conventional chemotherapy alone

Deletions at chromosome regions 7q11.23 and 7q36 in a patient with Williams syndrome

We report on a patient with Williams syndrome and a complex de novo chromosome rearrangement, including microdeletions at 7q11.23 and 7q36 and additional chromosomal material at 7q36. The nature of this additional material was elucidated by spectral karyotyping and first assigned to chromosome 22. Subsequent fluorescence in situ hybridization (FISH) experiments showed that it consisted of satellite material only. Refinement of the 7q36 breakpoint was performed with several FISH probes, showing a deletion distal to the triphalangeal thumb (TPT) region. The phenotype of the patient principally results from the microdeletion of the 7q11.23; the small deletion at 7qter and the extra satellite material may not be of clinical significanc