Advancing the automation of plant nucleic acid extraction for rapid diagnosis of plant diseases in space

Human space exploration missions will continue the development of sustainable plant cultivation in what are obviously novel habitat settings. Effective pathology mitigation strategies are needed to cope with plant disease outbreaks in any space-based plant growth system. However, few technologies currently exist for space-based diagnosis of plant pathogens. Therefore, we developed a method of extracting plant nucleic acid that will facilitate the rapid diagnosis of plant diseases for future spaceflight applications. The microHomogenizer^™ from Claremont BioSolutions, originally designed for bacterial and animal tissue samples, was evaluated for plant-microbial nucleic acid extractions. The microHomogenizer^™ is an appealing device in that it provides automation and containment capabilities that would be required in spaceflight applications. Three different plant pathosystems were used to assess the versatility of the extraction process. Tomato, lettuce, and pepper plants were respectively inoculated with a fungal plant pathogen, an oomycete pathogen, and a plant viral pathogen. The microHomogenizer^™, along with the developed protocols, proved to be an effective mechanism for producing DNA from all three pathosystems, in that PCR and sequencing of the resulting samples demonstrated clear DNA-based diagnoses. Thus, this investigation advances the efforts to automate nucleic acid extraction for future plant disease diagnosis in space.

Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection

Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 10⁴ cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.

Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station

The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct) values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g) controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for molecular biology and demonstrates the feasibility of more complex wet bench experiments in the ISS National Lab environment.

Abstract LB-263: Analysis of microenvironment effects on pancreatic cancer biomarker expression using a novel method for FFPE RNA extraction

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths. There are virtually no biomarkers to aid in early detection or predicting therapy response, newly diagnosed patients have less than a 7% 5-year survival rate and the median survival from the time of diagnosis is less than 12 months. Next-Generation Sequencing (NGS) together with in vitro/in vivo functional studies is likely to identify and validate new biomarkers of PDAC onset, progression and therapy resistance. Importantly, the substantial archives of formalin-fixed, paraffin-embedded (FFPE) samples from PDAC patients are likely to be a rich resource for linking molecular signatures to relevant clinical data. However, NGS methods on FFPE samples are severely hindered because extracting high-quality nucleic acid material from these samples is time-consuming and inefficient. We have sought to develop novel methods for improving the extraction of high-quality RNA from FFPE samples within the context of commercially-available FFPE RNA kits and protocols. Together with researchers and clinicians at Claremont BioSolutions, AntiCancer Inc. and UCSD our laboratory has developed a novel nucleic acid extraction method that significantly increases RNA yield and integrity from PDAC cell line and Patient-Derived Xenograft FFPE samples. By briefly (<5 minutes) integrating the newly designed Claremont BioSolutions’ microhomogenizer (mH) tool within the commercially available Qiagen FFPE RNA extraction protocol, RNA recovery from these samples is increased by approximately 3-fold while maintaining standard 260/280 ratios (2.03 +/- 0.02 w/ mH step) and high RNA Quality Index (RQI) values (7.3 +/- 0.6 w/ mH step). Bioanalyzer testing further demonstrated that the mH-purified FFPE RNA was longer. Previous studies have revealed that PDAC cell gene expression signatures vary significantly when cells are propagated in vitro versus in vivo as subcutaneous or orthotopic xenografts. Notably, we found that the previously published expression patterns for KRas dependency genes within these three microenvironments were most accurately reproduced when extracting PDAC FFPE RNA with our mH-based method. Finally, we used our mH-based method to test the effects of the in vivo tumor microenvironment (TME) on the expression trends of a panel of novel PDAC biomarkers. In this regard, we demonstrate that PEAK1 and MST1R expression levels are decreased and increased, respectively, by over 100 fold in the orthotopic microenvironment relative to the subcutaneous microenvironment. These results reveal the critical nature of the tumor microenvironment when evaluating the clinical relevance of new biomarkers in cell lines or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to positively impact the FFPE-RNA-NGS workflow for cancer biomarker identification/validation.

Citation Format: Malachia Hoover, Yvess Adamian, Mark Brown, Ali A. Maawy, Robert Hoffman, Michael Bouvet, Robert Doebler, Jonathan A. Kelber. Analysis of microenvironment effects on pancreatic cancer biomarker expression using a novel method for FFPE RNA extraction. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-263.

Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis

Nucleic acid amplification testing (NAAT) enables rapid and sensitive diagnosis of tuberculosis (TB), which facilitates treatment and mitigates transmission. Nucleic acid extraction from sputum constitutes the greatest technical challenge in TB NAAT for near-patient settings. This report presents preliminary data for a semi-automated sample processing method, wherein sputum is disinfected and liquefied, followed by PureLyse^® mechanical lysis and solid-phase nucleic acid extraction in a miniaturized, battery-operated bead blender. Sputum liquefaction and disinfection enabled a >10⁴ fold reduction in viable load of cultured Mycobacterium tuberculosis (M.tb) spiked into human sputum, which mitigates biohazard concerns. Sample preparation via the PureLyse^® method and a clinically validated manual method enabled positive PCR-based detection for sputum spiked with 10⁴ and 10⁵ colony forming units (cfu)/mL M.tb. At 10³ cfu/mL sputum, four of six and two of six samples amplified using the comparator and PureLyse^® method, respectively. For clinical specimens from TB cases and controls, the two methods provided 100% concordant results for samples with 1 mL input volume (N = 41). The semi-automated PureLyse^® method therefore performed similarly to a validated manual comparator method, but is faster, minimally instrumented, and can be integrated into TB molecular diagnostic platforms designed for near-patient low-resource settings.

Effect of protein aggregation in the aqueous phase on the binding of membrane proteins to membranes

Analysis of the binding of hydrophobic peptides or proteins to membranes generally assumes that the solute is monomeric in both the aqueous phase and the membrane. Simulations were performed to examine the effect of solute self-association in the aqueous phase on the binding of monomeric solute to lipid vesicles. Aggregation lowered the initial concentration of monomeric solute, which was then maintained at a relatively constant value at the expense of the aggregated solute, as the lipid concentration was increased. The resultant binding isotherm has a more linear initial portion rather than the classic hyperbolic shape. Although this shape is diagnostic of solute self-association in the aqueous phase, various combinations of values for the membrane partition coefficient and the solute self-association constant will generate similar isotherms. Data for cytochrome b5 were analyzed and, when the self-association constant was estimated by gel filtration, a unique value for the membrane partition coefficient was obtained. Thus, to obtain a true partition coefficient the state of the solute in the aqueous phase must be known. If the concentration of the monomeric solute species in the aqueous phase can be independently determined, then, even with heterogeneous aggregates, the true partition coefficient can be obtained.