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.

Leachate water quality of soils amended with different swine manure-based amendments

In the face of the rising level of manure production from concentrated animal feeding operations (CAFOs), management options are being sought that can provide nutrient recycling for plant growth and improved soil conditions with minimal environmental impacts. Alternatives to direct manure application are composting and thermochemical conversion which can destroy pathogens and improve handling and storage. The effect of four forms of swine manure-based soil amendments (raw, compost, hydrochar, and pyrochar) on soil fertility and leachate water quality characteristics of a sandy soil were investigated in soil incubation experiments. All four amendments significantly increased soil carbon, cation exchange capacity and available nutrient contents of the soil. However, hydrochar amended soil leached lower amounts of N, P, and K compared to the other amendments including the control. On the other hand, pyrochar amended soil leached higher concentrations of P and K. Subsequent tests on the hydrochar for K and N adsorption isotherms and surface analysis via XPS suggested that these nutrients were not sorbed directly to the hydrochar surface. Although it is still not clear how these nutrients were retained in the soil amended with hydrochar, it suggests a great potential for hydrochar as an alternative manure management option as the hydrochar can be soil applied while minimizing potential environmental issues from the leaching of high nutrient concentrations to water bodies.

Impact of Cognitive Frailty on Daily Activities in Older Persons

OBJECTIVES

To identify the relationships between physical and/or cognitive frailty and instrumental activities of daily living (IADL) functioning in community living older persons.

DESIGN

Cross sectional observation study.

SETTING

Data extracted from the 2011-2013 of the National Center for Geriatrics and Gerontology-Study of Geriatric Syndromes (NCGG-SGS) database.

PARTICIPANTS

A total of 8,864 older adults aged ≥ 65 years who were enrolled in the NCGG-SGS.

MEASUREMENTS

We characterized physical frailty as limitations in three or more of the following five domains: slow walking speed, muscle weakness, exhaustion, low activity and weight loss. To screen for cognitive impairment, we used the National Center for Geriatrics and Gerontology-Functional Assessment Tool (NCGG-FAT) which included tests of word list memory, attention and executive function (tablet version of the Trail Making Test, part A and B), and processing speed (tablet version of the Digit Symbol Substitution Test). Two or more cognitive impairments indicated by an age-adjusted score of at least 1.5 standard deviations below the reference threshold was characterized as cognitive impairment. Each participant reported on their IADL status (use of public transportation, shopping, management of finances, and housekeeping) and several potential confounders such as demographic characteristics.

RESULTS

The overall prevalence of physical frailty, cognitive impairment, and cognitive frailty, i.e. co-occurrence of frailty and cognitive impairment, was 7.2%, 5.2%, and 1.2%, respectively. We found significant relationships between IADL limitations and physical frailty (Odds Ratio (OR) 1.24, 95% confidence interval (95% CI) 1.01 to 1.52), cognitive impairment (OR 1.71, 95% CI 1.39 to 2.11), and cognitive frailty (OR 2.63, 95% CI 1.74 to 3.97).

CONCLUSION

Using the NCGG-SGS frailty criteria, we found more participants with physical frailty than with cognitive frailty. The individuals with cognitive frailty had the highest risks of IADL limitations. Future investigation is necessary to determine whether this population is at increased risk for incidence of disability or mortality.

INCREASED RISK OF CHILDHOOD BRAIN TUMORS AMONG CHILDREN WHOSE PARENTS HAD FARM-RELATED PESTICIDE EXPOSURES DURING PREGNANCY

Malignant brain tumors rank second in both incidence and mortality by cancer in children, and they are the leading cause of cancer death in children. Relatively little is known about the etiology of childhood brain tumor (CBT). While there are several studies which link pesticide exposure to increased risk of CBT, findings have been inconsistent. We performed a meta-analysis on 15 published epidemiological studies to test that in utero exposure to pesticides may be involved in the development of brain cancer in children. Meta-analysis was performed using the general variance-based method and homogeneity was tested by means of the Q statistic. Summary relative risk (RR) estimates were calculated for childhood brain cancer from (1) paternal exposure to pesticides prior to conception, (2) both maternal and paternal exposure to pesticides during pregnancy, (3) maternal exposure during pregnancy to: (a) agricultural and (b) non-agricultural activities, and (4) childhood exposure to: (a) agricultural and (b) nonagricultural activities up to date of diagnosis with CBT. The comparative toxicogenomics database (CTD) was used to identify gene-pesticide-CBT interactions. Findings of meta-analyses revealed a significantly increased risk of CBT among children whose mothers had farm-related exposures during pregnancy (RR=1.48, 95% CI=1.18-1.84). A dose response was recognized when this risk estimate was compared to those for risk of CBT from maternal exposure to non-agricultural pesticides (e.g., home extermination, pest strips) during pregnancy (RR=1.36, 1.10-1.68), and risk of CBT among children exposed to agricultural activities (RR=1.32, 1.04-1.67). Three studies combined for the paternal exposure to pesticides during preconception produced a calculated summary risk estimate of odds ratio (OR) = 2.29 (95% CI: 1.39-3.78). Meta-analysis of five studies of paternal exposure to pesticides during pregnancy produced a final calculated summary risk estimate of OR = 1.63 (95% CI: 1.16-2.31). The search of the CTD databases revealed association between herbicide and astrocytoma and more than 300 genes are altered by exposure to herbicide, fungicide, insecticide or pesticides. In summary, comparing results from our categories of exposure, preconception and pregnancy exposure estimates were slightly higher than childhood exposure estimates, paternal exposures produced slightly higher risk estimates compared to maternal exposures, agricultural exposures produced slightly higher risk estimates compared to non-agricultural exposures and CTD search revealed potential genes-pesticides-astrocytoma interactions. Based on the collective results of these meta-analyses, it appears that pesticide exposure may increase risk of CBT, with preconception and prenatal exposures being especially important factors in increasing risk of its development. Interestingly, paternal exposure may be as important, if not more important than maternal exposures, particularly during the preconception period. Whether this is a result of paternal exposures being more prevalent than maternal exposures or the consequence of a biological process, is a question that deserves further attention in future investigations of CBT etiology.

Normal range of bleeding scores for the ISTH-BAT: adult and pediatric data from the merging project

Bleeding Assessment Tools (BATs) have been developed to aid in the standardized evaluation of bleeding symptoms. The Vicenza Bleeding Questionnaire (BQ), published in 2005, established a common framework and scoring key that has undergone subsequent modification over the years, culminating in the publication of the ISTH-BAT in 2010. Understanding the normal range of bleeding scores is critical when assessing the utility of a BAT. Within the context of The Merging Project, a bioinformatics system was created to facilitate the merging of legacy data derived from four different (but all Vicenza-based) BATs; the MCMDM1-VWD BQ, the Condensed MCMDM-1VWD BQ, the Pediatric Bleeding Questionnaire and the ISTH-BAT. Data from 1040 normal adults and 328 children were included in the final analysis, which showed that the normal range is 0-3 for adult males, 0-5 for adult females and 0-2 in children for both males and females. Therefore, the cut-off for a positive or abnormal BS is ≥4 in adult males, ≥6 in adult females and ≥3 in children. This information can now be used to objectively assess bleeding symptoms as normal or abnormal in future studies.

Developing a national database for metastatic colorectal cancer management: perspectives and challenges

BACKGROUND

The changing treatment landscape for metastatic colorectal cancer creates multiple potential treatment strategies. An Australian-centric database capturing comprehensive information across a range of treatment locations would create a valuable resource enabling multiple important research questions to be addressed.

AIMS

To establish a collection of a consensus dataset capturing treatment and outcomes at multiple public and private hospitals across Australia.

METHODS

An electronic database was developed by a panel of clinicians, to capture an agreed dataset for patients with newly diagnosed metastatic colorectal cancer. Of particular interest were clinician decision-making, the impact of comorbidities and the frequency of major adverse events.

RESULTS

Since July 2009, data collection has been established at six public and eight private hospitals across three Australian states and territories. Successful linkage and analysis, with support from BioGrid Australia, of selected data on the initial 864 patients demonstrates that data can be captured from diverse sites, including public and private practice, that multiple factors impact on treatment delivered and outcomes achieved and that comprehensive data on rare but important adverse events can be captured. As a clinical research tool, the project has been highly successful, generating multiple presentations at national and international conferences related to a diverse range of research questions.

CONCLUSIONS

Multistate, project-specific data collection involving large numbers of patients is achievable. Providing invaluable insight into the routine clinical management of metastatic colorectal cancer in the era of targeted therapies, this also creates a significant resource for research, including many questions not being addressed by clinical trials.

A New Robust Method for Nonlinear Regression

BACKGROUND

When outliers are present, the least squares method of nonlinear regression performs poorly. The main purpose of this paper is to provide a robust alternative technique to the Ordinary Least Squares nonlinear regression method. This new robust nonlinear regression method can provide accurate parameter estimates when outliers and/or influential observations are present.

METHOD

Real and simulated data for drug concentration and tumor size-metastasis are used to assess the performance of this new estimator. Monte Carlo simulations are performed to evaluate the robustness of our new method in comparison with the Ordinary Least Squares method.

RESULTS

In simulated data with outliers, this new estimator of regression parameters seems to outperform the Ordinary Least Squares with respect to bias, mean squared errors, and mean estimated parameters. Two algorithms have been proposed. Additionally and for the sake of computational ease and illustration, a Mathematica program has been provided in the Appendix.

CONCLUSION

The accuracy of our robust technique is superior to that of the Ordinary Least Squares. The robustness and simplicity of computations make this new technique more appropriate and useful tool for the analysis of nonlinear regressions.

Robust Logistic and Probit Methods for Binary and Multinomial Regression

In this paper we introduce new robust estimators for the logistic and probit regressions for binary, multinomial, nominal and ordinal data and apply these models to estimate the parameters when outliers or inluential observations are present. Maximum likelihood estimates don't behave well when outliers or inluential observations are present. One remedy is to remove inluential observations from the data and then apply the maximum likelihood technique on the deleted data. Another approach is to employ a robust technique that can handle outliers and inluential observations without removing any observations from the data sets. The robustness of the method is tested using real and simulated data sets.

The presence of a cytopathologist increases the diagnostic accuracy of endoscopic ultrasound-guided fine needle aspiration cytology for pancreatic adenocarcinoma: a meta-analysis

OBJECTIVE

A meta-analysis has not been previously performed to evaluate critically the diagnostic accuracy of endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) of solely pancreatic ductal adenocarcinoma and address factors that have an impact on variability of accuracy. The aim of this study was to determine whether the presence of a cytopathologist, variability of the reference standard and other sources of heterogeneity significantly impacts diagnostic accuracy.

METHODS

We conducted a comprehensive search to identify studies, in which the pooled sensitivity, specificity, likelihood ratios for a positive or negative test (LR+, LR-) and summary receiver-operating curves (SROC) could be determined for EUS-FNA of the pancreas for ductal adenocarcinoma using clinical follow-up, and/or surgical biopsy or excision as the reference standard.

RESULTS

We included 34 distinct studies (3644 patients) in which EUS-FNA for a solid pancreatic mass was evaluated. The pooled sensitivity and specificity for EUS-FNA for pancreatic ductal adenocarcinoma was 88.6% [95% confidence interval (CI): 87.2-89.9] and 99.3% (95% CI: 98.7-99.7), respectively. The LR+ and LR- were 33.46 (95% CI: 20.76-53.91) and 0.11 (95% CI: 0.08-0.16), respectively. The meta-regression model showed rapid on-site evaluation (ROSE) (P = 0.001) remained a significant determinant of EUS-FNA accuracy after correcting for study population number and reference standard.

CONCLUSION

EUS-FNA is an effective modality for diagnosing pancreatic ductal adencarcinoma in solid pancreatic lesions, with an increased diagnostic accuracy when using on-site cytopathology evaluation.

Graphene mode-locked femtosecond Cr:ZnSe laser at 2500 nm

We report, for the first time to our knowledge, femtosecond pulse generation from a graphene mode-locked Cr:ZnSe laser at 2500 nm. To minimize the insertion losses at the lasing wavelength, high-quality monolayer graphene transferred on a CaF(2) substrate was used in the experiments. Once mode-locking was initiated, the laser generated a stable train of 226 fs pulses with a time-bandwidth product of 0.39. The mode-locked laser operated at a pulse repetition rate of 77 MHz and produced 80 mW output power with an incident pump power of 1.6 W. To our knowledge, this is the longest laser wavelength at which graphene-based passive mode-locking has been demonstrated to date.

An initial watch and wait approach is a valid strategy for selected patients with newly diagnosed metastatic colorectal cancer

BACKGROUND

A range of treatments are available for patients with metastatic colorectal cancer (mCRC). An initial period without active treatment, a 'watch and wait approach', is variably employed in routine practice; however, there is no data to support this approach.

PATIENTS AND METHODS

We prospectively collected data regarding clinician treatment recommendations for patients with newly diagnosed mCRC in addition to subsequent treatment and outcomes. Follow-up and management was according to standard protocols.

RESULTS

Seven hundred and thirty-six patients (59.1% male, 40.9% female) with mCRC (January 2003-December 2010) were analysed; the median age was 67.9 years (range 26.2-95.5). Three hundred and seventy-seven patients (51.2%) received immediate chemotherapy. For 133 (18.1%), treatment was considered inappropriate. 34 patients (4.6%) declined therapy. For 192 (26.1%), a watch and wait policy was adopted and 168 (87.5%) of these received treatment, at a median of 3.7 months (range 2-35 months) from diagnosis. Compared with patients immediately treated, the number receiving all active chemotherapy agents (30.4 versus 39.3%) was similar and median survival (27 versus 17 months, P = 0.0008) was superior.

CONCLUSIONS

Our study demonstrates that a substantial minority of patients underwent an initial watch and wait approach. Ultimately, they received a similar treatment exposure to patients treated immediately and the survival outcomes were not compromised.

Quantification of genes and gene transcripts for microbial perchlorate reduction in fixed-bed bioreactors

AIMS

Optimization of full-scale, biological perchlorate treatment processes for drinking water would benefit from knowledge of the location and quantity of perchlorate-reducing bacteria (PRB) and expression of perchlorate-related genes in bioreactors. The aim of this study was to quantify perchlorate removal and perchlorate-related genes (pcrA and cld) and their transcripts in bioreactors and to determine whether these genes or transcripts could serve as useful biomarkers for perchlorate treatment processes.

METHODS AND RESULTS

Quantitative PCR (qPCR) assays targeting pcrA and cld were applied to two pilot-scale, fixed-bed bioreactors treating perchlorate-contaminated groundwater. pcrA and cld genes per microgram of DNA were two- to threefold higher and three- to fourfold higher, respectively, in the bioreactor showing superior perchlorate-removal performance. In a laboratory-scale bioreactor, quantities of pcrA and cld genes and transcripts were compared under two distinct performance conditions (c.60 and 20% perchlorate removal) for a 5-min empty bed contact time. cld genes per microgram of DNA were approximately threefold higher and cld transcripts per microgram of RNA were approximately sixfold higher under the higher perchlorate-removal condition. No differences in pcrA genes or transcripts per microgram of DNA or RNA, respectively, were detected between the c.60 and 20% perchlorate-removal conditions, possibly because these assays did not accurately quantify pcrA genes and transcripts in the mixed culture present.

CONCLUSIONS

Quantities of cld genes and transcripts per microgram of DNA and RNA, respectively, were found to be higher when perchlorate removal was higher. However, quantities of pcrA and cld genes or transcripts were not found to directly correlate with perchlorate-removal rates.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this study represents the first application of qPCR assays to quantify perchlorate-related genes and transcripts in continuous-flow bioreactors. The results indicate that cld gene and transcript quantities can provide insights regarding the quantity, location and gene expression of PRB in bioreactors.

First Report of Rice stripe virus of Proso Millet in Korea

Rice stripe virus (RSV; genus Tenuivirus) is a serious threat to rice production in Korea (2). In 1965, a disease outbreak was observed on rice in South Korea, with plants showing yellow stripe symptoms (2). Reoccurrence of RSV in rice was observed again in 1980 in Gyeonggi and Chungcheong. In 2001, RSV was estimated to be infecting approximately 4,663 ha of rice in the provinces of Gyeonggi and Gangwha and approximately 5,000 ha of riceland in the provinces of Buan and, Seocheon (3). Proso millet (Panicum miliaceum L.) is grown as a cereal grain crop and used mainly for human food in South Korea (1). In June 2009, proso millet plants that displayed yellow stripe symptoms were collected at Sinjeon-Myeon, Gangjin-Gun, and Jeollanam-do provinces, where an outbreak of RSV in rice was reported. Diseased plants tested positive to RSV with an ELISA Kit (KisanBio, Seoul, Korea). Total RNA was extracted from leaf tissue with an RNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). RSV coat protein specific-primers were produced (5' TGTGGAACATAGTCCCACAGTAAGT 3'(upstream), 5' CTAAGCCGCAACCATTCCTCCAGT 3'(downstream). Reverse transcription-PCR confirmed the presence of a 494-bp product as predicted for the presence of RSV. The coat protein of RSV isolates collected from proso millet, rice, and foxtail millet in the same area was also sequenced. Results confirmed that phylogenetic relationships were of high homology: 98.9% between RSV isolates from rice and foxtail millet, 99.2% between isolates from rice (GenBank Accession No. JN245626) and proso millet (GenBank Accession No. JN245627); 99.6% between rice and foxtail millet (GenBank Accession No. JN245628); and 99.6% between foxtail millet and proso millet. In addition, sequence comparisons showed 96 to 99% identity with known RSV sequences available in GenBank (Accession No. X53563) (4). To our knowledge, this is the first report of RSV of proso millet in South Korea. The finding of this disease confirms further spread of the virus within the northern part of South Korea and the need for research to develop more effective management options to reduce the impact of RSV in proso millet. References: (1) Y. Y. Choi et al. Biosci. Biotechnol. Biochem. 69:31, 2005. (2) B. C. Lee et al. Res. Plant Dis. 10:30, 2004. (3) B. C. Lee et al. Res. Plant Dis. 14:210, 2008. (4) Y. Zhu. J. Gen. Virol. 72:763, 1991.