Physical Confirmation and Mapping of Overlapping Rat Mammary Carcinoma Susceptibility QTLs, Mcs2 and Mcs6

Only a portion of the estimated heritability of breast cancer susceptibility has been explained by individual loci. Comparative genetic approaches that first use an experimental organism to map susceptibility QTLs are unbiased methods to identify human orthologs to target in human population-based genetic association studies. Here, overlapping rat mammary carcinoma susceptibility (Mcs) predicted QTLs, Mcs6 and Mcs2, were physically confirmed and mapped to identify the human orthologous region. To physically confirm Mcs6 and Mcs2, congenic lines were established using the Wistar-Furth (WF) rat strain, which is susceptible to developing mammary carcinomas, as the recipient (genetic background) and either Wistar-Kyoto (WKy, Mcs6) or Copenhagen (COP, Mcs2), which are resistant, as donor strains. By comparing Mcs phenotypes of WF.WKy congenic lines with distinct segments of WKy chromosome 7 we physically confirmed and mapped Mcs6 to ∼33 Mb between markers D7Rat171 and gUwm64-3. The predicted Mcs2 QTL was also physically confirmed using segments of COP chromosome 7 introgressed into a susceptible WF background. The Mcs6 and Mcs2 overlapping genomic regions contain multiple annotated genes, but none have a clear or well established link to breast cancer susceptibility. Igf1 and Socs2 are two of multiple potential candidate genes in Mcs6. The human genomic region orthologous to rat Mcs6 is on chromosome 12 from base positions 71,270,266 to 105,502,699. This region has not shown a genome-wide significant association to breast cancer risk in pun studies of breast cancer susceptibility

SDSS-IV MaNGA: The Impact of Diffuse Ionized Gas on Emission-line Ratios, Interpretation of Diagnostic Diagrams, and Gas Metallicity Measurements

Diffuse ionized gas (DIG) is prevalent in star-forming galaxies. Using a sample of 365 nearly face-on star-forming galaxies observed by Mapping Nearby Galaxies at APO, we demonstrate how DIG in star-forming galaxies impacts the measurements of emission-line ratios, hence the interpretation of diagnostic diagrams and gas-phase metallicity measurements. At fixed metallicity, DIG-dominated low ΣHα regions display enhanced [S ii]/Hα, [N ii]/Hα, [O ii]/Hβ and [O i]/Hα. The gradients in these line ratios are determined by metallicity gradients and ΣHα. In line ratio diagnostic diagrams, contamination by DIG moves H ii regions towards composite or low-ionization nuclear emission-line region (LI(N)ER)-like regions. A harder ionizing spectrum is needed to explain DIG line ratios. Leaky H ii region models can only shift line ratios slightly relative to H ii region models, and thus fail to explain the composite/LI(N)ER line ratios displayed by DIG. Our result favours ionization by evolved stars as a major ionization source for DIG with LI(N)ER-like emission. DIG can significantly bias the measurement of gas metallicity and metallicity gradients derived using strong-line methods. Metallicities derived using N2O2 are optimal because they exhibit the smallest bias and error. Using O3N2, R23, N2 = [N ii]/Hα and N2S2Hα to derive metallicities introduces bias in the derived metallicity gradients as large as the gradient itself. The strong-line method of Blanc et al. (IZI hereafter) cannot be applied to DIG to get an accurate metallicity because it currently contains only H ii region models that fail to describe the DIG

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE: In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.publishedVersionPeer reviewe