Identification of the Genomic Insertion Site of the Thyroid Peroxidase Promoter–Cre Recombinase Transgene Using a Novel, Efficient, Next-Generation DNA Sequencing Method

Background: It can be useful to know the transgene insertion site in transgenic mice for a variety of reasons, but determining the insertion site generally is a time consuming, expensive, and laborious task. Methods: A simple method is presented to determine transgene insertion sites that combines the enrichment of a sequencing library by polymerase chain reaction (PCR) for sequences containing the transgene, followed by next-generation sequencing of the enriched library. This method was applied to determine the site of integration of the thyroid peroxidase promoter?Cre recombinase mouse transgene that is commonly used to create thyroid-specific gene deletions. Results: The insertion site was found to be between bp 12,372,316 and 12,372,324 on mouse chromosome 9, with the nearest characterized genes being Cntn5 and Jrkl, ?1.5 and 0.9?Mbp from the transgene, respectively. One advantage of knowing a transgene insertion site is that it facilitates distinguishing hemizygous from homozygous transgenic mice. Although this can be accomplished by real-time quantitative PCR, the expected Ct difference is only one cycle, which is challenging to assess accurately. Therefore, the transgene insertion site information was used to develop a 3-primer qualitative PCR assay that readily distinguishes wild type, hemizygous, and homozygous TPO-Cre mice based upon size differences of the wild type and transgenic allele PCR products. Conclusions: Identification of the genomic insertion site of the thyroid peroxidase promoter?Cre mouse transgene should facilitate the use of these mice in studies of thyroid biology.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140267/1/thy.2015.0215.pd

Weight loss for obese prostate cancer patients on androgen deprivation therapy

PURPOSE: Excess fat mass (FM) contributes to poor prostate cancer (PCa) prognosis and comorbidity. However, FM gain is a common side effect of androgen deprivation therapy (ADT). We examined the efficacy of a 12-wk weight loss intervention to reduce FM and maintain lean mass (LM) in ADT-treated obese PCa patients. METHODS: Fourteen ADT-treated obese PCa patients (72 ± 9 yr, 39.7% ± 5.4% body fat) were recruited for a self-controlled prospective study, with 11 completing the 6-wk control period, followed by a 12-wk intervention comprising 300 min·wk-1 of exercise including supervised resistance training and home-based aerobic exercise, and dietitian consultations advising a daily energy deficit (2100-4200 kJ) and protein supplementation. Body composition was assessed by dual x-ray absorptiometry. Secondary outcomes included muscle strength (one-repetition maximum), cardiorespiratory fitness (maximal oxygen consumption), and blood biomarkers. RESULTS: There were no significant changes during the control period. Patients attended 89% of supervised exercise sessions and 100% of dietitian consultations. No changes in physical activity or energy intake were observed. During the intervention, patients experienced significant reductions in weight (-2.8 ± 3.2 kg, P = 0.016), FM (-2.8 ± 2.6 kg, P \u3c 0.001), and trunk FM (-1.8 ± 1.4 kg, P \u3c 0.001), with LM preserved (-0.05 ± 1.6 kg, P = 0.805). Muscle strength (4.6%-24.7%, P \u3c 0.010) and maximal oxygen consumption (3.5 ± 4.7 mL·min-1·kg-1, P = 0.041) significantly improved. Leptin significantly decreased (-2.2 (-2.7 to 0.5) ng·mL-1, P = 0.016) with no other changes in blood biomarkers such as testosterone and lipids (P = 0.051-0.765); however, C-reactive protein (rs = -0.670, P = 0.024) and triglycerides (r = -0.667, P = 0.025) were associated with individual changes in LM. CONCLUSIONS: This study shows preliminary efficacy for an exercise and nutrition weight loss intervention to reduce FM, maintain LM, and improve muscle strength and cardiorespiratory fitness in ADT-treated obese PCa patients. The change in body composition may affect blood biomarkers associated with obesity and PCa progression; however, further research is required

The effects of mitoquinone pretreatment on doxorubicin-induced acute cardiac dysfunction

Introduction: Doxorubicin (DOX) is a widely used anti-cancer drug notorious for its irreversible cardiac toxicity. Currently, Dexrazoxane is the only FDA-approved treatment for this toxicity. However, Dexrazoxane still bears some serious adverse events, and developing new strategies to mitigate DOX-induced heart damage is critical. Our lab has shown that pretreatment of the H9c2 myoblast cells with mitoquinone (MitoQ), a mitochondrial-targeted antioxidant, and significantly improved cells’ resiliency to DOX. This study aimed to determine if MitoQ pretreatment can preserve cardiac function against DOX-induced damage in isolated rat hearts. Objectives: The effects of DOX and MitoQ on cardiac function were evaluated in isolated rat hearts. Moreover, the benefits of MitoQ pretreatment on DOX-induced cardiac dysfunction were also assessed. Methods: Langendorff heart preparation was performed after anesthesia of male SD rats (275-325 g). Hearts were isolated and retrograde perfused with Krebs’ buffer at a constant pressure of 80 mmHg with 37 ⁰C and pH of 7.35-7.45. Cardiac parameters, including left ventricle end-systolic pressure (LVESP), left ventricle end-diastolic pressure (LVEDP), left ventricular developed pressure (LVDP=LVESP-LVEDP), maximal rate of rise of LVP (dP/dt(max)), and heart rate (HR), were measured by a pressure transducer placed in the left ventricle of the rat heart. After obtaining a stable initial cardiac function, DOX (20 µM or 25 µM) or MitoQ (0.1-0.5 or 1-2.5 µM) were infused into the heart for 60 min. to determine the individual drug\u27s effects on the cardiac function. Moreover, another set of hearts was pretreated with MitoQ (0.25-0.5 or 1-2.5 µM) for 10-15 min before giving DOX (25 µM) to evaluate if MitoQ pretreatment would mitigate DOX-induced cardiac dysfunction. Cardiac functions were recorded every 5 min. throughout the experiments. The ratio between the final and initial recordings was calculated and compared among experimental groups. Results: Acute infusion of DOX into the isolated hearts dose-dependently reduced some cardiac parameters. Higher dose DOX (25 μM, n=5) induced a higher reduction in the ratios of LVESP, LVDP, and dP/dt(max) to 0.39±0.05, 0.35±0.06, and 0.26±0.05 than those of lower dose DOX infusion (20 μM, n=2; 0.77±0.01, 0.75±0.01, and 0.57±0.01), respectively. DOX had no effects on LVEDP and HR. Moreover, lower doses of MitoQ (0.1-0.5 μM, n=6) only slightly reduced HR to 0.77±0.01 without affecting other parameters. By contrast, higher doses of MitoQ (1-5 μM, n=4) reduced the ratios of LVESP, LVDP, dP/dt(max), and HR to 0.72±0.12, 0.51±0.18, and 0.45±0.17 0.65±0.07, respectively. Interestingly, MitoQ pretreatment before DOX (25 µM) exhibited better cardiac function accompanied by reduced HR than DOX alone. Higher MitoQ (1-2.5 µM) pretreatment improved the ratios of cardiac LVESP, LVDP, and dP/dt(max) to 0.67±0.14, 0.65±0.16, and 0.40±0.09, which were higher than those of lower dose MitoQ (0.25-0.5 μM, n=3; 0.49±0.11, 0.44±0.11, and 0.36±0.08), respectively. Conclusion: The preliminary data suggest that infusion of DOX into the heart acutely attenuated cardiac systolic function. Higher doses of MitoQ, not lower doses, also suppressed cardiac function. MitoQ pretreatment mitigated DOX-induced heart dysfunction. Acknowledgement: The project is funded by CCDA at PCOM

Maintaining weight loss in obese men with prostate cancer following a supervised exercise and nutrition program—A pilot study

Supervised exercise and nutrition programs can mitigate or reverse androgen deprivation therapy (ADT) induced fat mass (FM) gain, lean mass (LM) loss, and impaired physical function. It is unclear whether these benefits are retained following transition to self-management. This study examined the effect of a home-based weight maintenance program on body composition and physical function in obese men with prostate cancer (PCa) on ADT following a 12-week supervised weight loss intervention. Eleven obese PCa patients (74 ± 5 years, 40.0 ± 4.9% body fat) on ADT ( \u3e 6 months) com-pleted a 12-week self-managed home-based weight maintenance program consisting of 150 min/week of aerobic and resistance training while maintaining a healthy balanced diet. Body composition (DXA), muscle strength (1RM), and cardiorespiratory fitness (400 m walk) were assessed. Significant reductions in weight (−2.8 ± 3.2 kg) and FM (−2.8 ± 2.6 kg), preservation of LM (−0.05 ± 1.6 kg), and improvements in muscle strength and VO2max were achieved across the supervised intervention. Across the home-based program, no significant changes were observed in weight (−0.6 ± 2.8 kg, p = 0.508), FM (0.2 ± 1.4 kg, p = 0.619), LM (−0.8 ± 1.6 kg, p = 0.146), muscle strength (−0.2 to 4.1%, p = 0.086–0.745), or estimated VO2max (0.3 ± 2.1 mL/min/kg, p = 0.649). Self-managed, home-based exercise and nutrition programs are a viable strategy to promote maintenance of body composition and physical function following a supervised intervention in obese PCa patients on ADT

The effects of Mitoquinone on simulated ischemia/reperfusion injuries in H9c2 cells

Introduction: Reperfusion to an ischemic myocardium could result in damage termed myocardial ischemia/reperfusion (I/R) injury. Mitochondrial dysfunction is a major factor in I/R injury, producing less ATP and generating more reactive oxygen species (ROS). Mitoquinone (MitoQ) is an antioxidant that highly accumulates in the mitochondria. However, the dose-response effects and underlying mechanisms of MitoQ on simulated I/R injury have not been well established. Objectives: We hypothesized that H9c2 myoblast cells would be damaged by simulated I/R. Moreover, MitoQ would attenuate myocardial injury, characterized by increased cell viability, compared to non-treated control. Methods: The H9c2 myoblast cells (less than 20 passages) were treated with or without various concentrations of MitoQ (0.005, 0.05, 0.1, 0.5, 1, 2, 5 μM) under 3 different mediums: normal (containing 4.5 g glucose and pyruvate), low glucose (containing 1 g glucose and pyruvate), and no glucose/pyruvate medium. Three different experiments were conducted on the cells. The first experiment aimed to determine if MitoQ alone exerts different effects under different medium conditions by treating the cells with MitoQ for 24 hrs in a normal incubator. The second experiment aimed to determine if MitoQ increased cell viability under simulated ischemia conditions after MitoQ pretreatment. The third experiment aimed to determine if MitoQ increased cell viability under simulated I/R conditions after MitoQ pretreatment. Cell viability was measured by absorbance at 450 nm after adding a cell counting agent. The change in cell viability was expressed as ratios relative to the untreated controls. Results: Low concentrations of MitoQ alone slightly increased cell viability in all three mediums. The maximum increased cell viability was 1.25 ± 0.07 (n=9) at 0.005 μM MitoQ in the normal medium, 1.35 ± 0.23 (n=5, p MitoQ pretreatment exerts protection to cells in simulated ischemia conditions at certain MitoQ concentrations. The maximum increased cell viability was 1.37 ± 0.3 (n=4) at 0.01 μM MitoQ in normal medium, 1.20 ± 0.13 (n=4) at 1.0 μM MitoQ in low glucose medium, and 1.45 ± 0.24 (n=3) at 0.1 μM MitoQ in no glucose medium compared to the untreated control. MitoQ effects on simulated I/R injury will be reported in the future. Discussion: Preliminary data shows the effects of MitoQ alone and MitoQ pretreatment in ischemic conditions on cell viability is influenced by different mediums and concentrations of MitoQ

Comparison of the inhibition of an OCT3 transporter inhibitor, Nilotinib, on Doxorubicin’s effects on cardiac and cancer cell lines

Introduction Doxorubicin (DOX)-induced cardiotoxicity remains a significant barrier limiting its clinical application due to a lack of effective resolution. Targeting how DOX enters cardiac and cancer cells is a promising new strategy. Research suggests that an OCT3 transporter significantly contributes to DOX entry into the heart tissue. By contrast, it expresses much lower on breast cancer cell lines. Moreover, Nilotinib (NIB) can suppress OCT3 transporter function by 80%. Therefore, exploring the impact of NIB on the DOX’s effects on cardiac and cancer cell lines by altering DOX intracellular accumulation is intriguing. Objective First, we would establish a dose-response curve of DOX and NIB alone to assess their individual effects on cell viability. Secondly, we would record the impact of NIB on DOX entry within cardiac myoblasts (H9C2) and breast cancer cells (MCF7) through OCT3 transporter antagonism to assess if NIB can exert cardioprotective effects while maintaining DOX’s anticancer effect. Methods H9C2 myoblast and MCF7 breast cancer cells were seeded in 96-well black plates. Cells were treated with only DOX or NIB to establish a dose-response curve. Moreover, NIB was combined with DOX as a cotreatment or pretreatment regimen to evaluate the impacts of NIB on DOX’s effect. Titrated combinations of NIB (10 nM, 50 nM, 100 nM, 500 nM, 1 µM, 2 µM, 5 µM) and DOX (10 µM and 40µM) were used. Bioassays were conducted after cells were treated for 24 hours. Intracellular DOX fluorescence intensity was measured at 488/590 nm by fluoroskan. Subsequently, cell viability was detected by measuring absorbance at 450 nm after adding a cell counting reagent. The data were expressed as a ratio relative to untreated or the DOX control. Results DOX dose-dependently reduced viability of H9c2 and MCF7 cells. H9c2 cell showed significantly lower cell viability at 1 µM (0.86±0.04, n=10, p\u3c0.05) and 40 µM (0.40±0.02, n=10, p\u3c0.05) when compared to those of MCF7 cells (1.07±0.05 and 0.68±0.08 for 1 µM and 40 µM, respectively, n=7). By contrast, NIB (10 nM-2 µM) only slightly increased cell viability to 1.13±0.05 (n=11) in H9c2 cells and to 1.16±0.13 (n=7) in MCF7 cells, respectively, when compared to untreated control. The highest tested dose of NIB (5 µM) showed a similar reduction of cell viability to 0.83±0.07 in H9c2 cells and to 0.81±0.10 in MCF7 cells. Furthermore, NIB cotreatment mitigated DOX-induced damages in H9c2 by increasing cell viability to 1.28±0.07 (n=5) and 1.26±0.11 (n=7) when compared to the DOX controls (10 µM and 40µM), respectively. Interestingly, NIB cotreatment enhanced DOX’s anti-cancer effects in by decreasing MCF7 cell viability to 0.66±0.10 (n=7) and 0.70±0.09 (n=6) when compared to the DOX controls (10 µM and 40µM), respectively. The intracellular DOX fluorescence data and NIB pretreatment results are still being gathered. Conclusion DOX, not NIB, dose-dependently induced H9c2 and MCF7 cell death. Moreover, DOX-induced damage was more potent in H9c2 cells than in MCF7 cells. NIB cotreatment mildly protected H9c2 cells against DOX, whereas it increased DOX’s anti-cancer effects in MCF7 cells

Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA

This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain conditions, much less RNA is available for library construction. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several commercial RNA amplification kits are available for amplification prior to library construction for next-generation sequencing, but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-seq for picogram amounts of RNA. To address this, 4 types of amplification kits were tested with 3 different concentrations, from 5 ng to 50 pg, of a commercially available RNA. Kits were tested at multiple sites to assess reproducibility and ease of use. The human total reference RNA used was spiked with a control pool of RNA molecules in order to further evaluate quantitative recovery of input material. Additional control data sets were generated from libraries constructed following polyA selection or ribosomal depletion using established kits and protocols. cDNA was collected from the different sites, and libraries were synthesized at a single site using established protocols. Sequencing runs were carried out on the Illumina platform. Numerous metrics were compared among the kits and dilutions used. Overall, no single kit appeared to meet all the challenges of small input material. However, it is encouraging that excellent data can be recovered with even the 50 pg input total RNA

A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples

<p>Abstract</p> <p>Background</p> <p>Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor sample CN to normal reference sample CN. While advances in microarray technology have improved detection of copy number alterations, the increase in the number of measured signals, noise from array probes, variations in signal-to-noise ratio across batches and disparity across laboratories leads to significant limitations for the accurate identification of CNA regions when comparing tumor and normal samples.</p> <p>Methods</p> <p>To address these limitations, we designed a novel "Virtual Normal" algorithm (VN), which allowed for construction of an unbiased reference signal directly from test samples within an experiment using any publicly available normal reference set as a baseline thus eliminating the need for an in-lab normal reference set.</p> <p>Results</p> <p>The algorithm was tested using an optimal, paired tumor/normal data set as well as previously uncharacterized pediatric malignant gliomas for which a normal reference set was not available. Using Affymetrix 250K Sty microarrays, we demonstrated improved signal-to-noise ratio and detected significant copy number alterations using the VN algorithm that were validated by independent PCR analysis of the target CNA regions.</p> <p>Conclusions</p> <p>We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation.</p