Genome Wide Methylome Alterations in Lung Cancer.

Aberrant cytosine 5-methylation underlies many deregulated elements of cancer. Among paired non-small cell lung cancers (NSCLC), we sought to profile DNA 5-methyl-cytosine features which may underlie genome-wide deregulation. In one of the more dense interrogations of the methylome, we sampled 1.2 million CpG sites from twenty-four NSCLC tumor (T)-non-tumor (NT) pairs using a methylation-sensitive restriction enzyme- based HELP-microarray assay. We found 225,350 differentially methylated (DM) sites in adenocarcinomas versus adjacent non-tumor tissue that vary in frequency across genomic compartment, particularly notable in gene bodies (GB; p<2.2E-16). Further, when DM was coupled to differential transcriptome (DE) in the same samples, 37,056 differential loci in adenocarcinoma emerged. Approximately 90% of the DM-DE relationships were non-canonical; for example, promoter DM associated with DE in the same direction. Of the canonical changes noted, promoter (PR) DM loci with reciprocal changes in expression in adenocarcinomas included HBEGF, AGER, PTPRM, DPT, CST1, MELK; DM GB loci with concordant changes in expression included FOXM1, FERMT1, SLC7A5, and FAP genes. IPA analyses showed adenocarcinoma-specific promoter DMxDE overlay identified familiar lung cancer nodes [tP53, Akt] as well as less familiar nodes [HBEGF, NQO1, GRK5, VWF, HPGD, CDH5, CTNNAL1, PTPN13, DACH1, SMAD6, LAMA3, AR]. The unique findings from this study include the discovery of numerous candidate The unique findings from this study include the discovery of numerous candidate methylation sites in both PR and GB regions not previously identified in NSCLC, and many non-canonical relationships to gene expression. These DNA methylation features could potentially be developed as risk or diagnostic biomarkers, or as candidate targets for newer methylation locus-targeted preventive or therapeutic agents

The genome compartment represented on the HELP Nimblegen microarray and statistically significant DM loci.

<p>(A) Approximately 91% of the 1.2 million loci represented on the HELP microarray are located in gene body (GB) and intergenic (IG) regions, with a small minority (9%) of the loci located within promoters (PR). (B) Statistical significance (Y-axis) vs. delta (X-axis) (magnitude) of DM. Delta (X-axis) indicates the difference in methylation between tumor (T) vs non-tumor (NT) at a given locus. Loci hypermethylated in T relative to NT have delta < 0. P-value (Y-axis) is calculated based on Benjamini Hochberg adjusted FDR. At FDR p < 0.05, 433,505 loci across all genomic compartments are found to be differentially methylated in T vs NT. Red dots indicate statistically significant DM loci.</p

Magnitude and Direction of differential methylation and its distribution across genomic compartments.

<p>(A) All NSCLC histologies DM was classified as negligible, small or moderate based on the absolute value. (1< abs delta <2 is Moderate/Large; 1< abs delta <0.5 is Small; 0.5< abs delta <0 is Negligible). DM loci with FDR p<0.05 based on paired T-test were considered for this analysis. Majority of hypermethylation in tumors is observed to be of moderate/large magnitude in promoters and gene bodies, while in the intergenic regions, small changes are most frequent. The majority of hypomethylation is observed to be of small magnitude in all the three compartments. A significant fraction of hypomethylation changes are of negligible magnitude yet statistically significant. (B) Direction of DM and the distribution within promoters categorized based on location within CG-islands and CG-shores. Within the category of DM promoter loci, hypermethylation is more frequent in tumors as compared to hypomethylation for those loci within CG-islands and CG-shores. Overall DM differences do vary by PR genomic location (CGI, CGS, other); all NSCLC histologies were ChiSquare p = 2.2E-16; adenocarcinoma-only histology ChiSquare p = 1.9E-4.</p

Methylation vs Expression in Promoter regions.

<p>Analysis of DM loci within promoter regions and their overlap with differential gene expression. (Left panel A) All 21 pairs (all NSCLC histologies), overall differences do vary by PR genomic location (CGI, CGS, other), ChiSquare p = 3.32E-4. <i>(Right panel B)</i> Within the set of adenocarcinomas overall differences do vary by PR genomic location (CGI, CGS, other), ChiSquare p = 1.10E-7. Majority of DM promoter loci are associated with hypermethylation when the DM loci are within CG islands. This effect is more pronounced among adenocarcinomas, where the DM loci in CG islands are mostly associated with downregulation of the gene. KEY: “M” = methylation, “E” = expression. Upward arrow indicates increase and downward arrow indicates decrease.</p

Heat Map of the Top 50 DM Loci within Adenocarcinomas.

<p>(A) Promoter regions; and (B) Gene body regions. Several genes show differential methylation (DM) at more than one locus and appear multiple times in the heatmap. Blue = Non Tumor, Red = Tumor.</p

“Everyone can make games!” : the post-feminist context of women in digital game production

After over a decade of scholarly research and well-documented harassment, sexism, and other forms of exclusion and marginalization, digital games culture is currently the object of heightened attention and discourse related to diversity and inclusion. This paper considers the context of this shift with a particular focus on the relationship between gender-focused inclusivity-based action in the form of women in games incubators, post-feminist discourse, and the neoliberal context of digital games production. As opposed to rife anti-feminism and similar “backlash” sentiments, articulations of post-feminism within the digital game industry provide insights into the tensions inherent in introducing action for change within a conservative culture of production, particularly for women in the industry. At the same time, the contradictions and tensions of the post-feminist ethos allow for actions that function through this logic while subverting it. Through a brief consideration of three exemplary post-feminist articulations by visible female figures in the North American digital games community, this article explores the challenges and opportunities presented by the gaps and contradictions of post-feminism in games culture and production. It concludes with equal measures of caution and optimism, indicating future directions for study and activism