Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk.

Genome-wide association studies (GWASs) have characterized 13 loci associated with melanoma, which only account for a small part of melanoma risk. To identify new genes with too small an effect to be detected individually but which collectively influence melanoma risk and/or show interactive effects, we used a two-step analysis strategy including pathway analysis of genome-wide SNP data, in a first step, and epistasis analysis within significant pathways, in a second step. Pathway analysis, using the gene-set enrichment analysis (GSEA) approach and the gene ontology (GO) database, was applied to the outcomes of MELARISK (3,976 subjects) and MDACC (2,827 subjects) GWASs. Cross-gene SNP-SNP interaction analysis within melanoma-associated GOs was performed using the INTERSNP software. Five GO categories were significantly enriched in genes associated with melanoma (false discovery rate ≤ 5% in both studies): response to light stimulus, regulation of mitotic cell cycle, induction of programmed cell death, cytokine activity and oxidative phosphorylation. Epistasis analysis, within each of the five significant GOs, showed significant evidence for interaction for one SNP pair at TERF1 and AFAP1L2 loci (pmeta-int  = 2.0 × 10(-7) , which met both the pathway and overall multiple-testing corrected thresholds that are equal to 9.8 × 10(-7) and 2.0 × 10(-7) , respectively) and suggestive evidence for another pair involving correlated SNPs at the same loci (pmeta-int  = 3.6 × 10(-6) ). This interaction has important biological relevance given the key role of TERF1 in telomere biology and the reported physical interaction between TERF1 and AFAP1L2 proteins. This finding brings a novel piece of evidence for the emerging role of telomere dysfunction into melanoma development.

Large-area nanopatterning of self-assembled monolayers of alkanethiolates by interferometric lithography.

We demonstrate that interferometric lithography provides a fast, simple approach to the production of patterns in self-assembled monolayers (SAMs) with high resolution over square centimeter areas. As a proof of principle, two-beam interference patterns, formed using light from a frequency-doubled argon ion laser (244 nm), were used to pattern methyl-terminated SAMs on gold, facilitating the introduction of hydroxyl-terminated adsorbates and yielding patterns of surface free energy with a pitch of ca. 200 nm. The photopatterning of SAMs on Pd has been demonstrated for the first time, with interferometric exposure yielding patterns of surface free energy with similar features sizes to those obtained on gold. Gold nanostructures were formed by exposing SAMs to UV interference patterns and then immersing the samples in an ethanolic solution of mercaptoethylamine, which etched the metal substrate in exposed areas while unoxidized thiols acted as a resist and protected the metal from dissolution. Macroscopically extended gold nanowires were fabricated using single exposures and arrays of 66 nm gold dots at 180 nm centers were formed using orthogonal exposures in a fast, simple process. Exposure of oligo(ethylene glycol)-terminated SAMs to UV light caused photodegradation of the protein-resistant tail groups in a substrate-independent process. In contrast to many protein patterning methods, which utilize multiple steps to control surface binding, this single step process introduced aldehyde functional groups to the SAM surface at exposures as low as 0.3 J cm(-2), significantly less than the exposure required for oxidation of the thiol headgroup. Although interferometric methods rely upon a continuous gradient of exposure, it was possible to fabricate well-defined protein nanostructures by the introduction of aldehyde groups and removal of protein resistance in nanoscopic regions. Macroscopically extended, nanostructured assemblies of streptavidin were formed. Retention of functionality in the patterned materials was demonstrated by binding of biotinylated proteins.

A versatile diffractive maskless lithography for single-shot and serial microfabrication.

We demonstrate a diffractive maskless lithographic system that is capable of rapidly performing both serial and single-shot micropatterning. Utilizing the diffractive properties of phase holograms displayed on a spatial light modulator, arbitrary intensity distributions were produced to form two and three dimensional micropatterns/structures in a variety of substrates. A straightforward graphical user interface was implemented to allow users to load templates and change patterning modes within the span of a few minutes. A minimum resolution of approximately 700 nm is demonstrated for both patterning modes, which compares favorably to the 232 nm resolution limit predicted by the Rayleigh criterion. The presented method is rapid and adaptable, allowing for the parallel fabrication of microstructures in photoresist as well as the fabrication of protein microstructures that retain functional activity.