A detailed inventory of DNA copy number alterations in four commonly used Hodgkin's lymphoma cell lines

Background and Objectives Classical Hodgkin's lymphoma (cHL) is a common malignant lymphoma characterized by the presence of large, usually multinucleated malignant Hodgkin and Reed Sternberg (HRS) cells which are thought to be derived from germinal center B-cells. In cHL, the HRS cells constitute less than 1% of the tumor volume; consequently the profile of genetic aberrations in cHL is still poorly understood. Design and Methods In this study, we subjected four commonly used cHL cell lines to array comparative genomic hybridization (aCGH) in order to delineate known chromosomal aberrations in more detail and to search for small hitherto undetected genomic imbalances. Results The aCGH profiles of the four cell lines tested confirmed the complex patterns of rearrangements previously demonstrated with multicolor fluorescence in situ hybridization and chromosomal CGH (cCGH). Importantly, aCGH allowed a much more accurate delineation of imbalances as compared to previous studies performed at a chromosomal level of resolution. Furthermore, we detected 35 hitherto undetected aberrations including a homozygous deletion of chromosomal region 15q26.2 in the cell line HDLM2 encompasing RGMA and CHD2 and an amplification of the STAT6 gene in cell line L1236 leading to STAT6 overexpression. Finally, in cell line KM-H2 we found a 2.35 Mb deletion at 16q12.1 putatively defining a small critical region for the recurrent 16q deletion in cHL. This region contains the CYLD gene, a known suppressor gene of the NF-kappa B pathway. Interpretation and Conclusions aCGH was performed on four cHL cell lines leading to the improved delineation of known chromosomal imbalances and the detection of 35 hitherto undetected aberrations. More specifically, our results highlight STAT6 as a potential transcriptional target and identified RGMA, CHD2 and CYLD as candidate tumor suppressors in cHL

Tissue is the issue : when a second biopsy reveals the true diagnosis

We describe the case of a woman with minimal glomerular changes on initial kidney biopsy. On long-term follow-up, the patient developed nephrotic proteinuria and a second kidney biopsy was performed, which revealed focal segmental glomerulosclerosis (FSGS). Findings from electron microscopy (EM) examination suggested a genetic form of FSGS. Next-generation sequencing showed heterozygosity for a mutation in COL4A3. Collagen IV nephropathies can be linked to late-onset FSGS. By establishing a genetic cause of FSGS, immunosuppressive treatment can be avoided. This case emphasizes the importance of re-biopsy in cases of a non-explained rise in proteinuria. EM can be helpful in differentiating between primary and secondary FSGS and informing treatment strategies. In cases of adult-onset FSGS that cannot be categorized by clinical-pathological assessment, genetic testing should be considered

Analysis of chromosomal radiosensitivity of healthy BRCA2 mutation carriers and non-carriers in BRCA families with the G2 micronucleus assay

Breast cancer risk drastically increases in individuals with a heterozygous germline BRCA1 or BRCA2 mutation, while it is estimated to equal the population risk for relatives without the familial mutation (non-carriers). The aim of the present study was to use a G2 phase-specific micronucleus assay to investigate whether lymphocytes of healthy BRCA2 mutation carriers are characterized by increased radiosensitivity compared to controls without a family history of breast/ovarian cancer and how this relates to healthy non-carrier relatives. BRCA2 is active in homologous recombination, a DNA damage repair pathway, specifically active in the late S/G2 phase of the cell cycle. We found a significantly increased radiosensitivity in a cohort of healthy BRCA2 mutation carriers compared to individuals without a familial history of breast cancer (P=0.046; Mann-Whitney U test). At the individual level, 50% of healthy BRCA2 mutation carriers showed a radiosensitive phenotype (radiosensitivity score of 1 or 2), whereas 83% of the controls showed no radiosensitivity (P=0.038; one-tailed Fisher's exact test). An odds ratio of 5 (95% CI, 1.07-23.47) indicated an association between the BRCA2 mutation and radiosensitivity in healthy mutation carriers. These results indicate the need for the gentle use of ionizing radiation for either diagnostic or therapeutic use in BRCA2 mutation carriers. We detected no increased radiosensitivity in the non-carrier relatives

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

BACKGROUND: Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. Given the increased sensitivity, reproducibility and large dynamic range of this methodology, the requirements for a proper internal control gene for normalization have become increasingly stringent. Although housekeeping gene expression has been reported to vary considerably, no systematic survey has properly determined the errors related to the common practice of using only one control gene, nor presented an adequate way of working around this problem. RESULTS: We outline a robust and innovative strategy to identify the most stably expressed control genes in a given set of tissues, and to determine the minimum number of genes required to calculate a reliable normalization factor. We have evaluated ten housekeeping genes from different abundance and functional classes in various human tissues, and demonstrated that the conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested. The geometric mean of multiple carefully selected housekeeping genes was validated as an accurate normalization factor by analyzing publicly available microarray data. CONCLUSIONS: The normalization strategy presented here is a prerequisite for accurate RT-PCR expression profiling, which, among other things, opens up the possibility of studying the biological relevance of small expression differences

Spontaneous Helix Formation in Non-Chiral Bent-Core Liquid Crystals with Fast Linear Electro-Optic Effect

Liquid crystals (LCs) represent one of the foundations of modern communication and photonic technologies. Present display technologies are based mainly on nematic LCs, which suffer from limited response time for use in active colour sequential displays and limited image grey scale. Herein we report the first observation of a spontaneously formed helix in a polar tilted smectic LC phase (SmC phase) of achiral bent-core (BC) molecules with the axis of helix lying parallel to the layer normal and a pitch much shorter than the optical wavelength. This new phase shows fast (∼30 μs) grey-scale switching due to the deformation of the helix by the electric field. Even more importantly, defect-free alignment is easily achieved for the first time for a BC mesogen, thus providing potential use in large-scale devices with fast linear and thresholdless electro-optical response. les

Three birds with one stone: Tidal wetland restoration, carbon sequestration, and enhancing resilience to rising sea levels in the Snohomish River Estuary, Washington

Recent attention has focused on exploring the carbon storage and sequestration values of tidal wetlands to mitigate greenhouse gas emissions. Efforts are now underway to develop the tools and refine the science needed to bring carbon markets to bear on tidal wetland restoration activities. Effective restoration not only maximizes carbon storage in former tidal wetlands but also, through the accumulation of organic and mineral matter, enhances these systems’ resilience to rising sea levels. To this end, this project focuses on the Snohomish River estuary of the Puget Sound, Washington, which offers a continuum of diked and un-diked wetlands including seasonal floodplains, open mudflats, mature and tidal forests, and salt marsh habitats. In addition, there is strong restoration potential in a suite of ongoing and proposed projects. We report here on the carbon storage pools, long-term sediment accretion rates (100 years), and estimated rates of carbon storage, derived from sediment cores collected at representative sites within the Snohomish estuary during the spring and summer of 2013. We found that natural wetlands (open to tidal exchange and riverine inputs) were accreting at rates that equaled or exceeded current rates of eustatic sea level rise, while formerly, or currently diked wetlands (closed to such exchanges and inputs) revealed marked evidence of subsidence. Restored sites showed evidence of both high rates of sediment accretion (1.61 cm/year) and carbon storage (352 g C/m2/year)