GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction.

High-throughput DNA and RNA sequencing are revolutionizing precision oncology, enabling personalized therapies such as cancer vaccines designed to target tumor-specific neoepitopes generated by somatic mutations expressed in cancer cells. Identification of these neoepitopes from next-generation sequencing data of clinical samples remains challenging and requires the use of complex bioinformatics pipelines. In this paper, we present GeNeo, a bioinformatics toolbox for genomics-guided neoepitope prediction. GeNeo includes a comprehensive set of tools for somatic variant calling and filtering, variant validation, and neoepitope prediction and filtering. For ease of use, GeNeo tools can be accessed via web-based interfaces deployed on a Galaxy portal publicly accessible at https://neo.engr.uconn.edu/. A virtual machine image for running GeNeo locally is also available to academic users upon request.

Endometrial decidualization: a rare cause of acute appendicitis during pregnancy.

Appendicular endometriosis is a rare and poorly understood pathology that affects women in their reproductive years. In the gravid woman, ectopic endometrial tissue undergoes decidualization. This physiological process can result in acute appendicitis in exceptional cases. Here we describe a patient in her second trimester of pregnancy who presented with right iliac fossa pain and clinical, laboratory and imaging findings consistent with acute appendicitis. A laparoscopic appendectomy was performed with intraoperative findings suspicious for malignancy. Histological analysis made the surprising diagnosis of decidualized endometriosis causing luminal constriction resulting in acute appendicitis. We also detail the challenging diagnostic and management issues faced by clinicians in such cases.

Novel role of NADPH oxidase in ischemic myocardium: a study with Nox2 knockout mice.

Several potential sources of reactive oxygen species (ROS) in cells exist. One source is NADPH oxidase, which is especially important for superoxide radical production. Nox2 is a primary regulatory subunit of NADPH oxidase. In the present study, we examined the role of ROS and NADPH oxidase in ischemic preconditioning (IP)-mediated cardioprotection by using Nox2(-/-) mice. Both wild-type (WT) and Nox2(-/-) mice were subjected to either 30 min of ischemia followed by 2 h of reperfusion (IR) or IP prior to 30 min ischemia and 2 h of reperfusion. Reduction in left ventricular developed pressure (60.1 versus 63 mmHg), dp/dt (max) (893 versus 1,027 mmHg/s), and aortic flow (0.9 versus 1.8 ml/min) was observed in Nox2(-/-)IPIR compared to WTIPIR along with increased infarct size (33% versus 22%) and apoptosis after 120 min of reperfusion. Differentially regulated genes were demonstrated by comparing gene expression in WTIPIR versus Nox2(-/-) IPIR hearts. Selected differentially regulated genes such as ß-catenin, SRPK3, ERDR1, ACIN1, Syntaxin-8, and STC1 were validated by real-time PCR. Taken together, this is the first report identifying important, differentially expressed genes during ischemic preconditioning in Nox2(-/-) mice by using microarray analysis.

CD13 is dispensable for normal hematopoiesis and myeloid cell functions in the mouse.

The robust and consistent expression of the CD13 cell surface marker on very early as well as differentiated myeloid hematopoietic cells has prompted numerous investigations seeking to define roles for CD13 in myeloid cells. To address the function of myeloid CD13 directly, we created a CD13 null mouse and assessed the responses of purified primary macrophages or DCs from WT and CD13 null animals in cell assays and inflammatory disease models, where CD13 has been implicated previously. We find that mice lacking CD13 develop normally with normal hematopoietic profiles except for an increase in thymic but not peripheral T cell numbers. Moreover, in in vitro assays, CD13 appears to be largely dispensable for the aspects of phagocytosis, proliferation, and antigen presentation that we tested, although we observed a slight decrease in actin-independent erythrocyte uptake. However, in agreement with our published studies, we show that lack of monocytic CD13 completely ablates anti-CD13-dependent monocyte adhesion to WT endothelial cells. In vivo assessment of four inflammatory disease models showed that lack of CD13 has little effect on disease onset or progression. Nominal alterations in gene expression levels between CD13 WT and null macrophages argue against compensatory mechanisms. Therefore, although CD13 is highly expressed on myeloid cells and is a reliable marker of the myeloid lineage of normal and leukemic cells, it is not a critical regulator of hematopoietic development, hemostasis, or myeloid cell function.

Miscarriage risk for asymptomatic women after a normal first-trimester prenatal visit.

OBJECTIVE: To estimate the risk of miscarriage among asymptomatic women after a prenatal visit between 6 and 11 weeks of gestation where proof of fetal viability of a singleton was obtained by office ultrasonography at the same visit. METHODS: This was a prospective cohort study performed over 2 years (March 2004-2006) at an antenatal clinic at a large tertiary hospital in Victoria, Australia. Those recruited were 697 asymptomatic women who attended their first antenatal visit between 6 (+2 days) and 11(+6 days) weeks of gestation, where evidence of fetal cardiac activity of a singleton was obtained by office ultrasonography. The main outcome measure was rates of miscarriage, stratified by gestation at presentation. RESULTS: One case was lost to follow-up. The risk of miscarriage among the entire cohort was 11 of 696 (1.6%). The risk fell rapidly with advancing gestation; 9.4% at 6 (completed) weeks of gestation, 4.2% at 7 weeks, 1.5% at 8 weeks, 0.5% at 9 weeks and 0.7% at 10 weeks (chi(2); test for trend P=.001). Most who miscarried received their ultrasound diagnoses many weeks after their visit; five (45%) were diagnosed in the second trimester, and all but one received their ultrasound diagnoses after 10 weeks of gestation. CONCLUSION: For women without symptoms, the risk of miscarriage after attending a first antenatal visit between 6 and 11 weeks is low (1.6% or less), especially if they present at 8 weeks of gestation and beyond. Our data could be used to reassure such women that the probability of progressing to later than 20 weeks of gestation is very good.

Wnt pathway anomalies in developing amygdalae of Turner syndrome-like mice.

Certain neurobehavioral deficiencies associated with Turner Syndrome have been attributed to brain volumetric abnormalities, particularly of the amygdala. Haplo-insufficiency of a non-dosage compensated gene or genes on the X chromosome has been hypothesized to be the cause of the neuroanatomical defect. We examined gene expression levels of 6,628 genes in developing amygdalae of late-stage embryos of a mouse model for Turner Syndrome. In total, 161 genes show significant differences in expression level between TS and normal female amygdala. In silico pathway analysis of both X-linked and autosomal mis-regulated genes suggests that modulation of Wnt signaling is a critical factor in the normal growth and development of the amygdala.

Genome-wide reprogramming in hybrids of somatic cells and embryonic stem cells.

Recent experiments demonstrate that somatic nuclei can be reprogrammed to a pluripotent state when fused to ESCs. The resulting hybrids are pluripotent as judged by developmental assays, but detailed analyses of the underlying molecular-genetic control of reprogrammed transcription in such hybrids are required to better understand fusion-mediated reprogramming. We produced hybrids of mouse ESCs and fibroblasts that, although nearly tetraploid, exhibit characteristics of normal ESCs, including apparent immortality in culture, ESC-like colony morphology, and pluripotency. Comprehensive analysis of the mouse embryonic fibroblast/ESC hybrid transcriptome revealed global patterns of gene expression reminiscent of ESCs. However, combined analysis of variance and hierarchical clustering analyses revealed at least seven distinct classes of differentially regulated genes in comparisons of hybrids, ESCs, and somatic cells. The largest class includes somatic genes that are silenced in hybrids and ESCs, but a smaller class includes genes that are expressed at nearly equivalent levels in hybrids and ESCs that contain many genes implicated in pluripotency and chromatin function. Reprogrammed genes are distributed throughout the genome. Reprogramming events include both transcriptional silencing and activation of genes residing on chromosomes of somatic origin. Somatic/ESC hybrid cell lines resemble their pre-fusion ESC partners in terms of behavior in culture and pluripotency. However, they contain unique expression profiles that are similar but not identical to normal ESCs. ESC fusion-mediated reprogramming provides a tractable system for the investigation of mechanisms of reprogramming. Disclosure of potential conflicts of interest is found at the end of this article.

The cytochromes P450 (CYP) response to allergic inflammation of the lung.

The expression of the mouse Cyp family and key inflammatory mediators were examined in a model of ovalbumin (OVA)-induced allergic airway disease. The expression of IL-4, IL-13 and Ccl11 increased during the acute phase of allergic inflammation and decreased with its resolution. Interestingly, the expression of Ccl20 was increased during the resolution phase. The response of the Cyp gene family to the development of allergic inflammation was differential and correlated with the evolution of the inflammatory response. During the acute inflammatory phase the mRNA levels of Cyp2e1, Cyp2f2, Cyp2j6, Cyp4b1, Cyp8a1 and Cypor were decreased while the mRNA levels of Cyp4f18, Cyp5a1 and Cyp7b1 were elevated. With resolution of the inflammation the expression patterns returned to normal. These changes suggest that the Cyp family may play a role in the allergic inflammation by modulating the metabolism of xenobiotics and endogenous compounds such as LTB4, TXA1, PGI2 and native anti-glucocorticoids.

Experimental design for three-color and four-color gene expression microarrays.

MOTIVATION: Three-color microarrays, compared with two-color microarrays, can increase design efficiency and power to detect differential expression without additional samples and arrays. Furthermore, three-color microarray technology is currently available at a reasonable cost. Despite the potential advantages, clear guidelines for designing and analyzing three-color experiments do not exist. RESULTS: We propose a three- and a four-color cyclic design (loop) and a complementary graphical representation to help design experiments that are balanced, efficient and robust to hybridization failures. In theory, three-color loop designs are more efficient than two-color loop designs. Experiments using both two- and three-color platforms were performed in parallel and their outputs were analyzed using linear mixed model analysis in R/MAANOVA. These results demonstrate that three-color experiments using the same number of samples (and fewer arrays) will perform as efficiently as two-color experiments. The improved efficiency of the design is somewhat offset by a reduced dynamic range and increased variability in the three-color experimental system. This result suggests that, with minor technological improvements, three-color microarrays using loop designs could detect differential expression more efficiently than two-color loop designs. AVAILABILITY: http://www.jax.org/staff/churchill/labsite/software SUPPLEMENTARY INFORMATION: Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at http://www.jax.org/staff/churchill/labsite/pubs/yong.

Prevalence of Veraguth's eyelid folds during depression in different ethnic groups.

A common physical sign associated with depression, Veraguth's eyelid folds, was found considerably more often in white than in African American patients with depressive illness. Moreover, the folds are more strongly correlated with severity of depression in patients of European descent when they occur. The reported high rate of misdiagnosis of depressive illness in Americans of African descent may thus be related in part to differences in the facial expression of affect. The implications of this finding are discussed in regard to the importance of careful gathering of history for diagnostic purposes.