Abstract P1-02-01: Genomic analysis of single cells isolated by a pulse laser retrieval system

Background: Isolating tumor cells of interest and harvesting histologically pure samples is important for genomic studies. Laser capture microdissection (LCM) is an established method to obtain such purified cell populations for various applications including DNA, gene expression, and single cell analyses. However, LCM possesses problems such as limited optical resolution, cell fragmentation from dissection, and adherence of adjacent tissue to the cells which interrupts with single cell isolation from tissue sections. To overcome these obstacles, we developed a high-throughput pulse laser retrieval system which uses a wavelength that minimizes damage to the cellular content and is processed with a sacrificial layer that provides applicable optical resolution. The aim of this study was to evaluate the performance of the pulse laser retrieval system to provide appropriate samples for genomic analysis using breast cancer tissue.

Methods: An indium tin oxide (ITO) coated glass slide was prepared using fresh frozen breast cancer tissue sections of 4㎛ thickness and stained by hematoxylin and eosin. The slide was mounted on the cell isolation machine and imaging was performed with a charge-coupled device camera using a 20× lens. Following identification of the target cells by a pathologist, nano-second pulsed laser (wavelength= 1064nm) was irradiated on the target. Isolated cells were collected in a polymerase chain reaction tube and whole genome amplification (WGA) was carried out using Illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Amplified genomic DNA was fragmented and Illumina sequencing libraries were constructed. Sequencing was carried out to generate data with 0.1∼0.2× depth throughout the whole genome for each sample. Copy number variation (CNV) was analyzed by the Variable binning algorithm.

Results: Whole genome amplification was performed using bulk tissue and 10 captured single cells from the same specimen. No difference in amplification coverage was observed between the two samples. A CNV analysis of captured single cells revealed similar CNV profiles with those in a matched bulk tumor. Whole exome sequencing (WES) of captured single cells yielded a variant frequency of 15% at a read depth of 15× and 50M base coverage, compared to 0% at 100× and 50M for WES using bulk tumor and 0.5% at 1200× and 100K for targeted sequencing using bulk tumor. Laser capture was performed for DCIS and stromal cells from the same slide. CNV analysis of the two samples showed minimal CNV in normal stromal cells in contrast to DCIS where multiple CNVs were observed.

Conclusions: Newly developed pulse laser retrieval system is suitable for capturing single cells for genomic analysis of breast cancer. WGA, WES, and CNV analysis was successfully carried out using the captured single cells and showed no difference in profile compared to those performed with bulk tissue. This method may have the potential to replace LCM for certain applications such as single cell analyses.

Citation Format: Lee H-B, Kim S, Lee K-M, Jung Y, Lee AC, Kim J, Bae S, Ryu HS, Yoo T-K, Moon H-G, Noh D-Y, Kwon S, Han W. Genomic analysis of single cells isolated by a pulse laser retrieval system. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-02-01.

The Effects of Diverse Warm-up Exercises on Balance

[Purpose] To examine how stretching, plyometric, and treadmill exercises influence the dynamic balance necessary for sports activities. [Subjects and Methods] Twenty-two healthy subjects participated in this study. The subjects conducted stretching, plyometric exercises, and treadmill walking for set times over a period of three days. The subjects’ dynamic balance was then measured. The measurements were taken prior to the intervention, immediately after the intervention, and 20 minutes after the intervention. All the intervention times were set at 16 minutes, excluding resting times. The data were analyzed with using the two-way ANOVA. [Results] There was no interaction between exercises and time. There were no statistical differences among the exercises and no statistical differences in changes over time. [Conclusion] This study found that warm-up exercises such as plyometric exercises, stretching, and treadmill walking have no effect on the dynamic of balance in healthy subjects.

Anti-TNF-α therapy for patients with sepsis: a systematic meta-analysis

OBJECTIVE

In humans, the role of anti-tumour necrosis factor (TNF)-α therapy in severe sepsis and septic shock is debatable. The aim of this meta-analysis was to determine the efficacy of anti-TNF-α therapies against placebo in patients with severe sepsis or septic shock.

METHODS

A structured literature search was undertaken to identify randomised controlled trials (RCTs) conducted in patients with severe sepsis or septic shock receiving anti-TNF-α therapy or placebo. A meta-analysis on relative risk (OR) with a 95% confidence interval (95% CI) was performed.

RESULTS

Seventeen studies with a total of 8971 patients were included. When all forms of anti-TNF-α therapy were pooled together, there was a significant reduction of 28-day all-cause mortality with respect to placebo (OR = 0.91, 95% CI: 0.83-0.99; p = 0.04). Subgroup analysis showed that anti-TNF-α antibodies (monoclonal and polyclonal) reduced mortality (OR = 0.90, 95% CI: 0.81-0.99; p = 0.04). Monoclonal antibodies enhanced survival (OR = 0.91, 95% CI: 0.82-1.00; p = 0.05), while polyclonal antibodies or receptor blockers did not enhance survival (OR = 0.71, 95% CI: 0.39-1.28, p = 0.25; OR = 0.95, 95% CI: 0.78-1.17, p = 0.65). There was a trend towards better survival in patients with high levels of IL-6 (> 1000 pg/ml) and patients with shock if they were treated with anti-TNF-α therapy (OR = 0.85, 95% CI: 0.72-1.00; OR = 0.80, 95% CI: 0.62-1.04). Publication bias and statistical heterogeneity (I(2)  < 50% and p > 0.1) were absent. Sensitivity analysis suggests that these results are highly stable.

CONCLUSIONS

This meta-analysis suggests that in patients with severe sepsis (before shock), immunotherapy with anti-TNF-α monoclonal antibodies reduces overall mortality. In patients with shock or high levels of IL-6 (> 1000 pg/ml), anti-TNF-α therapy may improve survival.

Frequency of electrocardiogram testing among HIV-infected patients at risk for medication-induced QTc prolongation

OBJECTIVES

HIV-infected patients are commonly prescribed several medications and are thus at risk for drug interactions that may result in QTc prolongation. We sought (1) to identify the frequency of electrocardiogram (ECG) monitoring (2), to determine the prevalence of drug interactions involving QTc-prolonging medications, and (3) to quantify the prevalence of QTc prolongation.

METHODS

A cross-sectional study was conducted among HIV-infected adults. Demographics, medications, drug interactions and comorbidities were abstracted from patients' medical records. Abnormal QTc interval was defined per the UK Committee for Proprietary Medicinal Products. Clinical characteristics were compared among ECG recipients and nonrecipients. Among ECG recipients, the prevalence and predictors of QTc prolongation were assessed.

RESULTS

Among the 454 patients included in the study, 80.8% were prescribed a medication associated with QTc prolongation and 39% had drug interactions expected to increase QTc prolongation risk. There were 138 patients (30.3%) who received ECG testing. Receipt of ECG monitoring was associated with increasing age, diabetes, increasing total number of medications and gastroesophageal reflux disease. Among ECG recipients, the prevalence of abnormal QTc interval was 27.5%. Chronic kidney disease [prevalence ratio (PR) 3.47; 95% confidence interval (CI) 1.37-8.83; P = 0.009], hepatitis C virus coinfection (PR 2.26; 95% CI 0.97-5.27; P = 0.06) and hypertension (PR 2.11; 95% CI 0.93-4.81; P = 0.07) were independently associated with an abnormal QTc interval.

CONCLUSIONS

A low frequency of ECG testing was observed, despite a high use of medications associated with QTc prolongation. The risk of abnormal QTc interval was highest among patients with chronic kidney disease, hypertension and hepatitis C virus coinfection.