Contribution of Chromosome 14 to Exercise Capacity and Training Responses in Mice.

Quantitative trait loci for exercise capacity and training-induced changes in exercise capacity were identified previously on mouse Chromosome 14. The aim of this study was to further investigate the role of Chromosome 14 in exercise capacity and responses to training in mice. Exercise phenotypes were measured in chromosome substitution strain mice carrying Chromosome 14 from the PWD/PhJ donor strain on the genetic background of a host C57BL/6J (B6) strain (B6.PWD14). Eight week old female and male mice from both strains completed a graded exercise test to exhaustion to assess intrinsic or baseline exercise capacity. A separate group of 12-week old female and male mice, randomly assigned to sedentary control (SED) or exercise training (EX) groups, completed a graded exercise test before and after a 4-week exercise training period. EX mice completed a 4-week training program consisting of treadmill running 5 days/week, 60 min/day at a final intensity of approximately 65% of maximum. For intrinsic exercise capacity, exercise time and work were significantly greater in female and male B6.PWD14 than sex-matched B6 mice. In the training study, female B6.PWD14 mice had higher pre-training exercise capacity than B6 mice. In contrast, there were no significant differences for pre-training exercise capacity between male B6 and B6.PWD14 mice. There were no significant strain differences for responses to training. These data demonstrate that PWD/PhJ alleles on Chromosome 14 significantly affect intrinsic exercise capacity. Furthermore, these results support continued efforts to identify candidate genes on Chromosome 14 underlying variation in exercise capacity.

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods.

RNA sequencing (RNA-seq) is revolutionizing the study of cancer by providing a highly sensitive and robust tool to interrogate the transcriptome. It leverages the power of deep sequencing technology and provides global and multidimensional views of transcriptional landscapes in healthy and tumor tissues. Such information is contributing innovative insights to our understanding of the genetic basis of cancer and the progression of the disease. RNA-seq is a superior technology to DNA microarrays in that it provides digital rather than analog information on transcripts and their isoforms. The front end (sequencing library preparation and validation) is technically complex and time intensive. The primary objective in preparing a sequencing library is to eliminate or minimize bias, so that the library is reflective of the input RNA sample in terms of both sequence content and transcript abundance. This chapter describes the RNA-seq approach, and reviews methods and good practices for library preparation and sequencing.

Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol.

Nonylphenol (NP) arises from the environmental degradation of nonylphenol ethoxylates. It is a ubiquitous environmental contaminant and has been detected at levels up to 167 nM in rivers in the United States. NP is an endocrine disruptor (ED) that can act as an agonist for estrogen receptors. The Adverse Outcome Pathway (AOP) framework defines an adverse outcome as the causal result of a series of molecular initiating events (MIEs) and key events (KEs) that lead to altered phenotypes. This study examined the liver transcriptome after a 21 day exposure to NP and 17ß-estradiol (E2) by exploiting the zebrafish (Danio rerio) as a systems toxicology model. The goal of this study was to tease out non-estrogenic genomic signatures associated with NP exposure using DNA microarray and RNA sequencing. Our experimental design included E2 as a positive and potent estrogenic control in order to effectively compare and contrast the 2 compounds. This approach allowed us to identify hepatic transcriptomic perturbations that could serve as MIEs for adverse health outcomes in response to NP. Our results revealed that exposure to NP was associated with differential expression (DE) of genes associated with the development of steatosis, disruption of metabolism, altered immune response, and metabolism of reactive oxygen species, further highlighting NP as a chemical of emerging concern (CEC).

MAPK Reliance via Acquired CDK4/6 Inhibitor Resistance in Cancer.

Purpose: Loss of cell-cycle control is a hallmark of cancer, which can be targeted with agents, including cyclin-dependent kinase-4/6 (CDK4/6) kinase inhibitors that impinge upon the G1-S cell-cycle checkpoint via maintaining activity of the retinoblastoma tumor suppressor (RB). This class of drugs is under clinical investigation for various solid tumor types and has recently been FDA-approved for treatment of breast cancer. However, development of therapeutic resistance is not uncommon.Experimental Design: In this study, palbociclib (a CDK4/6 inhibitor) resistance was established in models of early stage, RB-positive cancer.Results: This study demonstrates that acquired palbociclib resistance renders cancer cells broadly resistant to CDK4/6 inhibitors. Acquired resistance was associated with aggressive in vitro and in vivo phenotypes, including proliferation, migration, and invasion. Integration of RNA sequencing analysis and phosphoproteomics profiling revealed rewiring of the kinome, with a strong enrichment for enhanced MAPK signaling across all resistance models, which resulted in aggressive in vitro and in vivo phenotypes and prometastatic signaling. However, CDK4/6 inhibitor-resistant models were sensitized to MEK inhibitors, revealing reliance on active MAPK signaling to promote tumor cell growth and invasion.Conclusions: In sum, these studies identify MAPK reliance in acquired CDK4/6 inhibitor resistance that promotes aggressive disease, while nominating MEK inhibition as putative novel therapeutic strategy to treat or prevent CDK4/6 inhibitor resistance in cancer. Clin Cancer Res; 24(17); 4201-14. ©2018 AACR.

Genomics pipelines and data integration: challenges and opportunities in the research setting.

INTRODUCTION: The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine. Areas covered: The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools. The main obstacles revolve around analysis provenance, data management of massive datasets, ease of use of software, interpretability and reproducibility of results. Expert commentary: The authors review the challenges associated with implementing bioinformatics best practices in a large-scale setting, and highlight the opportunity for establishing bioinformatics pipelines that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings.

Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine.

Monitoring disease activity in a complex, heterogeneous disease such as lupus is difficult. Both over- and undertreatment lead to damage. Current standard of care serologies are unreliable. Better measures of disease activity are necessary as we move into the era of precision medicine. We show here the use of a data-driven, modular approach to genomic biomarker development within lupus-specifically lupus nephritis.

Systems analysis of the prostate transcriptome in African-American men compared with European-American men.

AIM: African-Americans (AA) have increased prostate cancer risk and a greater mortality rate than European-Americans (EA). AA exhibit a high prevalence of vitamin D deficiency. We examined the global prostate transcriptome in AA and EA, and the effect of vitamin D3 supplementation. PATIENTS & METHODS: Twenty-seven male subjects (ten AA and 17 EA), slated to undergo prostatectomy were enrolled in the study. Fourteen subjects received vitamin D3 (4000 IU daily) and 13 subjects received placebo for 2 months prior to surgery. RESULTS: AA show higher expression of genes associated with immune response and inflammation. CONCLUSION: Systems level analyses support the concept that Inflammatory processes may contribute to disease progression in AA. These transcripts can be modulated by a short course of vitamin D3 supplementation.

Time- and Oil-Dependent Transcriptomic and Physiological Responses to Deepwater Horizon Oil in Mahi-Mahi (Coryphaena hippurus) Embryos and Larvae.

The Deepwater Horizon (DWH) oil spill contaminated the spawning habitats for numerous commercially and ecologically important fishes. Exposure to the water accommodated fraction (WAF) of oil from the spill has been shown to cause cardiac toxicity during early developmental stages across fishes. To better understand the molecular events and explore new pathways responsible for toxicity, RNA sequencing was performed in conjunction with physiological and morphological assessments to analyze the time-course (24, 48, and 96 h post fertilization (hpf)) of transcriptional and developmental responses in embryos/larvae of mahi-mahi exposed to WAF of weathered (slick) and source DWH oils. Slick oil exposure induced more pronounced changes in gene expression over time than source oil exposure. Predominant transcriptomic responses included alteration of EIF2 signaling, steroid biosynthesis, ribosome biogenesis and activation of the cytochrome P450 pathway. At 96 hpf, slick oil exposure resulted in significant perturbations in eye development and peripheral nervous system, suggesting novel targets in addition to the heart may be involved in the developmental toxicity of DHW oil. Comparisons of changes of cardiac genes with phenotypic responses were consistent with reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil.

Effect of chromosome substitution on intrinsic exercise capacity in mice.

Previous research identified a locus on Chromosome 14 as an important regulator of endurance exercise capacity in mice. The aim of this study was to investigate the effect of chromosome substitution on intrinsic exercise capacity and identify quantitative trait loci (QTL) associated with exercise capacity in mice. Mice from a chromosome substitution strain (CSS) derived from A/J and C57Bl/6J (B6), denoted as B6.A14, were used to assess the contribution of Chromosome 14 to intrinsic exercise capacity. All mice performed a graded exercise test to exhaustion to determine exercise capacity expressed as time (min) or work (kg·m). Exercise time and work were significantly greater in B6 mice than B6.A14 and A/J mice, indicating the presence of a QTL on Chromosome 14 for exercise capacity. To localize exercise-related QTL, 155 B6.A14 x B6 F 2 mice were generated for linkage analysis. Suggestive QTL for exercise time (57 cM, 1.75 LOD) and work (57 cM, 2.08 LOD) were identified in the entire B6.A14 x B6 F 2 cohort. To identify putative sex-specific QTL, male and female F 2 cohorts were analyzed separately.  In males, a significant QTL for exercise time (55 cM, 2.28 LOD) and a suggestive QTL for work (55 cM, 2.19 LOD) were identified.  In the female cohort, no QTL was identified for time, but a suggestive QTL for work was located at 16 cM (1.8 LOD). These data suggest that one or more QTL on Chromosome 14 regulate exercise capacity. The putative sex-specific QTL further suggest that the genetic architecture underlying exercise capacity is different in males and females.  Overall, the results of this study support the use of CSS as a model for the genetic analysis of exercise capacity. Future studies should incorporate the full panel of CSS using male and female mice to dissect the genetic basis for differences in exercise capacity.

Identification of exercise capacity QTL using association mapping in inbred mice.

There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.