Pleiotropic and Sex-Specific Effects of Cancer GWAS SNPs on Melanoma Risk in the Population Architecture Using Genomics and Epidemiology (PAGE) Study

Background

Several regions of the genome show pleiotropic associations with multiple cancers. We sought to evaluate whether 181 single-nucleotide polymorphisms previously associated with various cancers in genome-wide association studies were also associated with melanoma risk.

Methods

We evaluated 2,131 melanoma cases and 20,353 controls from three studies in the Population Architecture using Genomics and Epidemiology (PAGE) study (EAGLE-BioVU, MEC, WHI) and two collaborating studies (HPFS, NHS). Overall and sex-stratified analyses were performed across studies.

Results

We observed statistically significant associations with melanoma for two lung cancer SNPs in the TERT-CLPTM1L locus (Bonferroni-corrected p<2.8x10^-4), replicating known pleiotropic effects at this locus. In sex-stratified analyses, we also observed a potential male-specific association between prostate cancer risk variant rs12418451 and melanoma risk (OR=1.22, p=8.0x10^-4). No other variants in our study were associated with melanoma after multiple comparisons adjustment (p>2.8e^-4).

Conclusions

We provide confirmatory evidence of pleiotropic associations with melanoma for two SNPs previously associated with lung cancer, and provide suggestive evidence for a male-specific association with melanoma for prostate cancer variant rs12418451. This SNP is located near TPCN2, an ion transport gene containing SNPs which have been previously associated with hair pigmentation but not melanoma risk. Previous evidence provides biological plausibility for this association, and suggests a complex interplay between ion transport, pigmentation, and melanoma risk that may vary by sex. If confirmed, these pleiotropic relationships may help elucidate shared molecular pathways between cancers and related phenotypes.     

Neurobiology of the scallop. II. structure of the parietovisceral ganglion lateral lobes in relation to afferent projections from the mantle eyes

The lateral lobes of the scallop parietovisceral ganglion have been examined morphologically with respect to their functional role as optic lobes. The gross morphology of the lateral lobe and projections of optic nerve fibers within it were investigated by 1) supravital methylene blue staining, and 2) autoradiography using tritiated proline injected intraocularly for incorporation and transport by the optic fibers. Ultrastruc‐turally, the lateral lobe was examined using standard electron microscopic techniques. The lateral lobe is composed of a cortical rind of cells, 8–15 μm in diameter at the ventral surface and 15–20 μm in diameter at the ventral surface, surrounding a central neuropil. The neuropil contains three distinct regions: 1) the glomerular neuropil, a series of densely staining spherical subunits associated with the eyes and pallial nerves, 2) the subcellular neuropil, a synaptic region adjacent to the ventral cell layer also having a visual function, and 3) the subglomerular neuropil, the remaining, rather unspecialized neuropil of the lateral lobe. Synaptic profiles with symmetrical membrane thickenings, a 32 nm synaptic cleft, and three types of vesicles are seen throughout the neuropil, although the density of synapses is greater in the glomerular region. Clear, dense core and neurosecretory vesicles are seen individually or as mixed populations in the presynaptic terminals. Autoradiographic experiments have revealed that optic fibers enter the lateral lobe and project directly to the subcellular neuropil where they synapse with cells located on the ventral surface of the lateral lobe cells. These cells in turn form the dense glomerular structures previously identified as visual association centers and send efferent fibers into the pallial nerves. The projection of optic fibers to the ventral surface of the lobe is consistent with previous electrophysiological recordings of visual activity at this site.     

Towards the characterization of the hidden world of small proteins in Staphylococcus aureus,a proteogenomics approach

Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.     

Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei)

Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.     

On the Origin of Large Flexibility of P-glycoprotein in the Inward-facing State

P-glycoprotein (Pgp) is one of the most biomedically relevant transporters in the ATP binding cassette (ABC) superfamily due to its involvement in developing multidrug resistance in cancer cells. Employing molecular dynamics simulations and double electron-electron resonance spectroscopy, we have investigated the structural dynamics of membrane-bound Pgp in the inward-facing state and found that Pgp adopts an unexpectedly wide range of conformations, highlighted by the degree of separation between the two nucleotide-binding domains (NBDs). The distance between the two NBDs in the equilibrium simulations covers a range of at least 20 Å, including, both, more open and more closed NBD configurations than the crystal structure. The double electron-electron resonance measurements on spin-labeled Pgp mutants also show wide distributions covering both longer and shorter distances than those observed in the crystal structure. Based on structural and sequence analyses, we propose that the transmembrane domains of Pgp might be more flexible than other structurally known ABC exporters. The structural flexibility of Pgp demonstrated here is not only in close agreement with, but also helps rationalize, the reported high NBD fluctuations in several ABC exporters and possibly represents a fundamental difference in the transport mechanism between ABC exporters and ABC importers. In addition, during the simulations we have captured partial entrance of a lipid molecule from the bilayer into the lumen of Pgp, reaching the putative drug binding site. The location of the protruding lipid suggests a putative pathway for direct drug recruitment from the membrane.     

A method for detecting the temporal sequence of muscle activation during cycling using MRI

Surface electromyography (EMG) can assess muscle recruitment patterns during cycling, but has limited applicability to studies of deep muscle recruitment and electrically stimulated contractions. We determined whether muscle recruitment timing could be inferred from MRI-measured transverse relaxation time constant (T(2)) changes and a cycle ergometer modified to vary power as a function of pedal angle. Six subjects performed 6 min of single-leg cycling under two conditions (E0°-230° and E90°-230°), which increased the power from 0°-230° and 90-230° of the pedal cycle, respectively. The difference condition produced a virtual power output from 0-180° (V0°-180°). Recruitment was assessed by integrating EMG over the pedal cycle (IEMG) and as the (post-pre) exercise T(2) change (ΔT(2)). For E0°-230°, the mean IEMG for vastus medialis and lateralis (VM/VL; 49.3 ± 3.9 mV·s; mean ± SE) was greater (P < 0.05) than that for E90°-230° (17.9 ± 1.9 mV·s); the corresponding ΔT(2) values were 8.7 ± 1.0 and 1.4 ± 0.5 ms (P < 0.05). For E0°-230° and E90°-230°, the IEMG values for biceps femoris/long head (BF(L)) were 37.7 ± 5.4 and 27.1 ± 5.6 mV·s (P > 0.05); the corresponding ΔT(2) values were 0.9 ± 0.9 and 1.5 ± 0.9 ms (P > 0.05). MRI data indicated activation of the semitendinosus and BF/short head for E0°-230° and E90°-230°. For V0°-180°, ΔT(2) was 7.2 ± 0.9 ms for VM/VL and -0.6 ± 0.6 ms for BF(L); IEMG was 31.5 ± 3.7 mV·s for VM/VL and 10.6 ± 7.0 mV·s for BF(L). MRI and EMG data indicate VM/VL activity from 0 to 180° and selected hamstring activity from 90 to 230°. Combining ΔT(2) measurements with variable loading allows the spatial and temporal patterns of recruitment during cycling to be inferred from MRI data.