A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

<p>Abstract</p> <p>Background</p> <p>Marfan syndrome (MFS) is a heritable connective tissue disorder caused by mutations in the fibrillin-1 gene. This syndrome constitutes a significant identifiable subtype of aortic aneurysmal disease, accounting for over 5% of ascending and thoracic aortic aneurysms.</p> <p>Results</p> <p>We used spotted membrane DNA macroarrays to identify genes whose altered expression levels may contribute to the phenotype of the disease. Our analysis of 4132 genes identified a subset with significant expression differences between skin fibroblast cultures from unaffected controls versus cultures from affected individuals with known fibrillin-1 mutations. Subsequently, 10 genes were chosen for validation by quantitative RT-PCR.</p> <p>Conclusion</p> <p>Differential expression of many of the validated genes was associated with MFS samples when an additional group of unaffected and MFS affected subjects were analyzed (p-value < 3 × 10^-6under the null hypothesis that expression levels in cultured fibroblasts are unaffected by MFS status). An unexpected observation was the range of individual gene expression. In unaffected control subjects, expression ranges exceeding 10 fold were seen in many of the genes selected for qRT-PCR validation. The variation in expression in the MFS affected subjects was even greater.</p

Environmental and Molecular Mutagenesis Meeting Report Assessing Human Germ-Cell Mutagenesis in the Post-Genome Era: A Celebration of the Legacy of William Lawson (Bill) Russell

ABSTRACT Although numerous germ-cell mutagens have been identified in animal model systems, to date, no human germ-cell mutagens have been confirmed. Because the genomic integrity of our germ cells is essential for the continuation of the human species, a resolution of this enduring conundrum is needed. To facilitate such a resolution, we organized a workshop at The Jackson Laboratory in Bar Harbor, Maine on September [28][29][30] 2004. This interactive workshop brought together scientists from a wide range of disciplines to assess the applicability of emerging molecular methods for genomic analysis to the field of human germ-cell mutagenesis. Participants recommended that focused, coordinated human germ-cell mutation studies be conducted in relation to important societal exposures. Because cancer survivors represent a unique cohort with well-defined exposures, there was a consensus that studies should be designed to assess the mutational impact on children born to parents who had received certain types of mutagenic cancer chemotherapy prior to conceiving their children. Within this high-risk cohort, parents and children could be evaluated for inherited changes in (a) gene sequences and chromosomal structure, (b) repeat sequences and minisatellite regions, and (c) global gene expression and chromatin. Participants also recommended studies to examine trans-generational effects in humans involving mechanisms such as changes in imprinting and methylation patterns, expansion of nucleotide repeats, or induction of mitochondrial DNA mutations. Workshop participants advocated establishment of a bio-bank of human tissue samples that could be used to conduct a multiple-endpoint, comprehensive, and collaborative effort to detect exposure-induced heritable alterations in the human genome. Appropriate animal models of human germ-cell mutagenesis should be used in parallel with human studies to provide insights into the mechanisms of mammalian germ-cell mutagenesis. Finally, participants recommended that 4 scientific specialty groups be convened to address specific questions regarding the potential germ-cell mutagenicity of environmental, occupational, and lifestyle exposures. Strong support from relevant funding agencies and engagement of scientists outside the fields of genomics and germ-cell mutagenesis will be required to launch a full-scale assault on some of the most pressing and enduring questions in environmental mutagenesis: Do human germ-cell mutagens exist, what risk do they pose to future generations, and are some parents at higher risk than others for acquiring and transmitting germ-cell mutations?

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts-0

<p><b>Copyright information:</b></p><p>Taken from "A Marfan syndrome gene expression phenotype in cultured skin fibroblasts"</p><p>http://www.biomedcentral.com/1471-2164/8/319</p><p>BMC Genomics 2007;8():319-319.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2174953.</p><p></p>qRT-PCR. Above each gene name are two "box-and-whisker" plots of expression levels for that gene across 32 unaffected control (UC) samples (left plot of each pair, blue, up-triangles) and 42 MFS affected samples (right, red, down-triangles). Vertical axis is logratio of expression level to the median UC level. Each "box" shows the inter-quartile range (IQR), i.e., the range between the 25and 75percentiles of the log ratios; the horizontal line in each box is the 50th percentile (median). (Median log ratio for UC is always zero, by definition.) "Whiskers" (vertical lines) extend from each box to the most extreme values within 1.5 times the IQR from the box; in normally distributed data this would on average encompass 99% of the values. Triangles mark more extreme points. The lower curve shows log(p-value) for a Wilcoxon rank sum test of the null hypothesis that the UC and MFS distribution are identical; horizontal line marks the p = 0.05 significance level. 6 of 10 genes have p-values < 0.05 by this test. Most genes exhibit noticeably greater variability across the MFS samples than across UC samples, although the Wilcoxon test is not sensitive to this. To highlight one example, for Elastin (), the middle 50% of the UC sample log ratios fall between -0.23 and +0.14 (i.e., the 25and 75percentiles of the values fall 1.70-fold below and 1.38-fold above the median, respectively), and all but 4 fall between -0.58 and +0.34 (4-fold below and 2.2-fold above median). In contrast, median Elastin level is 26 fold lower in MFS samples, only four MFS samples are above the UC median, and the null hypothesis has a p-value of 1.6 × 10

Whole-exome sequencing reveals a C-terminal germline variant in CEBPA-associated acute myeloid leukemia: 45-year follow-up of a large family.

Familial acute myeloid leukemia is rare and linked to germline mutations in RUNX1, GATA2 or CCAAT/enhancer binding protein-α (CEBPA). We re-evaluated a large family with acute myeloid leukemia originally seen at NIH in 1969. We utilized whole-exome sequencing to study this family, and conducted in silico bioinformatics analysis, protein structural modeling and laboratory experiments to assess the impact of the identified CEBPA Q311P mutation. Unlike most previously identified germline mutations in CEBPA, which were N-terminal frameshift mutations, we identified a novel Q311P variant that was located in the C-terminal bZip domain of C/EBPα. Protein structural modeling suggested that the Q311P mutation alters the ability of the CEBPA dimer to bind DNA. Electrophoretic mobility shift assays showed that the Q311P mutant had attenuated binding to DNA, as predicted by the protein modeling. Consistent with these findings, we found that the Q311P mutation has reduced transactivation, consistent with a loss-of-function mutation. From 45 years of follow-up, we observed incomplete penetrance (46%) of CEBPA Q311P. This study of a large multi-generational pedigree reveals that a germline mutation in the C-terminal bZip domain can alter the ability of C/EBP-α to bind DNA and reduces transactivation, leading to acute myeloid leukemia