Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion.

Microwave-assisted acid hydrolysis for whole-bone proteomics and paleoproteomics.

RATIONALE: Whole-bone proteomic analyses rely on lengthy sample preparation including demineralization and digestion to break bone down into peptides to recover using mass spectrometry. However, microwave-assisted acid hydrolysis, a technique used in proteomic analyses of other soft tissues and cells, will combine both demineralization and digestion and only take minutes. METHODS: To test microwave-assisted hydrolysis on whole moose bone, we microwaved five concentrations of acetic and formic acids (15%, 12.5%, 10%, 7.5% and 5%) for three times (10, 20 and 30 min) at 140°C using an ETHOS UP high performance microwave digestion system. Peptides were injected and separated using Thermo BioBasic C18 columns and detected with an LTQ Orbitrap Velos mass spectrometer. We searched the raw data on PEAKS 8.5 against the white-tailed deer database. RESULTS: Formic acid hydrolysis led to the most complete digestion, and therefore the highest number of peptide spectrum matches, more protein groups and better sequence coverage for collagenous proteins. However, for the formic acid samples there is a tradeoff with digestion completeness and a higher incidence of in vitro modifications (i.e. formylation) that are not induced using acetic acid. Acetic acid has greater cleavage specificity and higher sequence coverage for non-collagenous proteins. CONCLUSIONS: Depending on the goals of analysis, there are benefits and drawbacks to using both acetic acid and formic acid. Overall, microwave-assisted acid hydrolysis was successful in demineralizing and digesting bone fragments to considerably speed up the preparation for bottom-up proteomics analysis.

Characterization of Zinc Carboxylates in an Oil Paint Test Panel.

Zinc (carboxylate) soaps, formed by reactions between zinc oxide (ZnO) and fatty acids in a drying oil, are known to cause deterioration in the paint layers of modern and contemporary oil paintings. This study investigates zinc carboxylates that developed in an oil painting test panel designed to mimic the aging and degradation encountered in actual works of art. Following accelerated and natural aging, protrusions were noted on the surface of the test panel. A large protrusion with erupted gel features was extracted from the test panel, mounted in top view, and then cut to reveal the sample's cross section. The gel features, which resulted from the unreacted oil binder's separation from the paint matrix, facilitated zinc carboxylate formation. Using reflectance µ-FTIR and SEM-EDX analysis, the morphologies and spatial distributions of zinc carboxylates within the gel regions of the protrusion were studied. A concentration gradient of zinc within the gel material was observed in the cross-sectional view, indicating patterns of zinc carboxylate formation and migration.

Related strains of African swine fever virus with different virulence: genome comparison and analysis.

Two strains of African swine fever virus (ASFV), the high-virulence Lisboa60 (L60) and the low-virulence NH/P68 (NHV), which have previously been used in effective immunization/protection studies, were sequenced. Both were isolated in Portugal during the 11-year period after the introduction of ASFV to the European Continent in 1957. The predicted proteins coded by both strains were compared, and where differences were found these were also compared to other strains of known virulence. This highlighted several genes with significant alterations in low-virulence strains of ASFV that may constitute virulence factors, several of which are still uncharacterized regarding their function. Phylogenetic analysis grouped L60 and NHV closest to other P72 genotype I ASFV strains from Europe and West Africa, consistent with the assumed West African origin of all European strains. Interestingly, a relatively lower genomic identity exists between L60 and NHV, both isolated in a similar geographical location 8 years apart, than with other European and west African strains isolated subsequently and in more distant locations. This may reflect the intensive passage in tissue culture, during the early 1960s, of a Portuguese isolate to obtain an attenuated vaccine, which may have led to NHV. This study contributes to a better understanding of the evolution of ASFV, and defines additional potential virulence genes for future studies of pathogenesis towards the development of effective vaccines.

The genome of Yoka poxvirus.

Yoka poxvirus was isolated almost four decades ago from a mosquito pool in the Central African Republic. Its classification as a poxvirus is based solely upon the morphology of virions visualized by electron microscopy. Here we describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most closely related to viruses in the Orthopoxvirus genus, but it is clearly distinct from previously described poxviruses. Collectively, the phylogenetic and genomic sequence analyses suggest that Yoka poxvirus is the prototype member of a new genus in the family Poxviridae.

Evaluation of serum magnesium differences in hypertensive crises and control patients: A randomly matched case-control study.

Although the role of magnesium in blood pressure has been well studied among hypertensive patients, no study has explored the role of magnesium in hypertensive crises. The primary objective of this study is to evaluate the differences in serum magnesium levels between hypertensive crises patients and matched controls (age-, sex-, race-, and diabetes-matched) in a 1:1 random match. This study is a single-center, retrospective, chart review, case-control study of patients with hypertensive crises (case group) and patients without hypertensive crises (control group). Patients were included in the case group if they were 18 years of age or older with hypertensive crises and have a documented magnesium level. The control group patients were required to be 18 years of age or older, have no diagnosis of hypertensive crises, and have a documented magnesium level. The primary outcome of the study was to compare the mean serum magnesium in patients with hypertensive crises versus patients without hypertensive crises. Three hundred and fifty-eight patients were included in the study: 179 patients in both the case group and control group. The primary outcome results showed that serum magnesium concentration was not significantly different between the case group (1.89 ± 0.29 mg/dl) and control group (1.90 ± 0.31 mg/dl) (p = .787). This study found no significant difference in serum magnesium levels in patients with hypertensive crises compared to a random matched control group. Larger observational or experimental studies may be useful to evaluate the effect of magnesium on blood pressure in hypertensive crises.

A library-based screening method identifies neoantigen-reactive T cells in peripheral blood prior to relapse of ovarian cancer.

Mutated cancer antigens, or neoantigens, represent compelling immunological targets and appear to underlie the success of several forms of immunotherapy. While there are anecdotal reports of neoantigen-specific T cells being present in the peripheral blood and/or tumors of cancer patients, effective adoptive cell therapy (ACT) against neoantigens will require reliable methods to isolate and expand rare, neoantigen-specific T cells from clinically available biospecimens, ideally prior to clinical relapse. Here, we addressed this need using "mini-lines", large libraries of parallel T cell cultures, each originating from only 2,000 T cells. Using small quantities of peripheral blood from multiple time points in an ovarian cancer patient, we screened over 3.3 × 106 CD8+ T cells by ELISPOT for recognition of peptides corresponding to the full complement of somatic mutations (n = 37) from the patient's tumor. We identified ten T cell lines which collectively recognized peptides encoding five distinct mutations. Six of the ten T cell lines recognized a previously described neoantigen from this patient (HSDL1L25V), whereas the remaining four lines recognized peptides corresponding to four other mutations. Only the HSDL1L25V-specific T cell lines recognized autologous tumor. HSDL1L25V-specific T cells comprised at least three distinct clonotypes and could be identified and expanded from peripheral blood 3-9 months prior to the first tumor recurrence. These T cells became undetectable at later time points, underscoring the dynamic nature of the response. Thus, neoantigen-specific T cells can be expanded from small volumes of blood during tumor remission, making pre-emptive ACT a plausible clinical strategy.

Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157.

BACKGROUND: Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is approximately 190 kb and contains a large number of unique genes in addition to the set of conserved Chordopoxvirus genes found in all such viruses. Upon sequencing the viral genome, others noted that this virus was also unusual because of the lack of a series of common immuno-suppressive genes. However, the genome contains multiple genes of unknown function that are likely to function in reducing the anti-viral response of the host. RESULTS: By using sensitive database searches for similarity, we observed that gene 157 of CRV-strain Zimbabwe (CRV-ZWE) encodes a protein with a domain that is predicted to bind dsRNA. Domain characterization supported this prediction, therefore, we tested the ability of the Robetta protein structure prediction server to model the amino acid sequence of this protein on a well-characterized RNA binding domain. The model generated by Robetta suggests that CRV-ZWE-157 does indeed contain an RNA binding domain; the model could be overlaid on the template protein structure with high confidence. CONCLUSION: We hypothesize that CRV-ZWE-157 encodes a novel poxvirus RNA binding protein and suggest that as a non-core gene it may play a role in host-range determination or function to dampen host anti-viral responses. Potential targets for this CRV protein include the host interferon response and miRNA pathways.

Loudness perception in the domestic cat: reaction time estimates of equal loudness contours and recruitment effects.

The domestic cat is the primary physiological model of loudness coding and recruitment. At present, there are no published descriptions of loudness perception in this species. This study used a reaction time task to characterize loudness perception in six behaviorally trained cats. The psychophysical approach was based on the assumption that sounds of equal loudness elicit responses of equal latency. The resulting equal latency contours reproduced well-known features of human equal loudness contours. At the completion of normal baseline measures, the cats were exposed to intense sound to investigate the behavioral correlates of loudness recruitment, the abnormally rapid growth of loudness that is commonly associated with hearing loss. Observed recruitment effects were similar in magnitude to those that have been reported in hearing-impaired humans. Linear hearing aid amplification is known to improve speech intelligibility but also exacerbate recruitment in impaired listeners. The effects of speech spectra and amplification on recruitment were explored by measuring the growth of loudness for natural and amplified vowels before and after sound exposure. Vowels produced more recruitment than tones, and the effect was exacerbated by the selective amplification of formant structure. These findings support the adequacy of the domestic cat as a model system for future investigations of the auditory processes that underlie loudness perception, recruitment, and hearing aid design.