Dataset Information

Porous extraction paddle: a solid-phase extraction technique for studying the urine metabolome.

ABSTRACT: RATIONALE:A method was needed to accomplish solid-phase extraction of a large urine volume in a convenient way where resources are limited, towards a goal of metabolome and xenobiotic exposome analysis at another, distant location. METHODS:A porous extraction paddle (PEP) was set up, comprising a porous nylon bag containing extraction particles that is flattened and immobilized between two stainless steel meshes. Stirring the PEP after attachment to a shaft of a motor mounted on the lid of the jar containing the urine accomplishes extraction. The bag contained a mixture of nonpolar and partly nonpolar particles to extract a diversity of corresponding compounds. RESULTS:Elution of a urine-exposed, water-washed PEP with aqueous methanol containing triethylammonium acetate (conditions intended to give a complete elution), followed by MALDI-TOF/TOF-MS, demonstrated that a diversity of compounds had been extracted ranging from uric acid to peptides. CONCLUSIONS:The PEP allows the user to extract a large liquid sample in a jar simply by turning on a motor. The technique will be helpful in conducting metabolomics and xenobiotic exposome studies of urine, encouraging the extraction of large volumes to set up a convenient repository sample (e.g. 2 g of exposed adsorbent in a cryovial) for shipment and re-analysis in various ways in the future, including scaled-up isolation of unknown chemicals for identification. Copyright © 2016 John Wiley & Sons, Ltd.

SUBMITTER: Shao G

PROVIDER: S-EPMC5350062 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Porous extraction paddle: a solid-phase extraction technique for studying the urine metabolome.

Shao Gang G MacNeil Michael M Yao Yuanyuan Y Giese Roger W RW

Rapid communications in mass spectrometry : RCM 20161201 23

<h4>Rationale</h4>A method was needed to accomplish solid-phase extraction of a large urine volume in a convenient way where resources are limited, towards a goal of metabolome and xenobiotic exposome analysis at another, distant location.<h4>Methods</h4>A porous extraction paddle (PEP) was set up, comprising a porous nylon bag containing extraction particles that is flattened and immobilized between two stainless steel meshes. Stirring the PEP after attachment to a shaft of a motor mounted on t ...[more]

PMID: 27624170

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Project description:Cell-free DNA (cfDNA) is a liquid biopsy marker that can carry signatures (i.e., mutations) associated with certain pathological conditions. Therefore, the extraction of cfDNA from a variety of clinical samples can be an effective and minimally invasive source of markers for disease detection and subsequent management. In the oncological diseases, circulating tumor DNA (ctDNA), a cfDNA sub-class, can carry clinically actionable mutations and coupled with next generation sequencing or other mutation detection methods provide a venue for effective in vitro diagnostics. However, cfDNA mutational analyses require high quality inputs. This necessitates extraction platforms that provide high recovery over the entire ctDNA size range (50 ? 150 bp) with minimal interferences (i.e., co-extraction of genomic DNA), and high reproducibility with a simple workflow. Herein, we present a novel microfluidic solid-phase extraction device (?SPE) consisting of a plastic chip that is activated with UV/O3 to generate surface-confined carboxylic acid functionalities for the ?SPE of cfDNA. The ?SPE uses an immobilization buffer (IB) consisting of polyethylene glycol and salts that induce cfDNA condensation onto the activated plastic microfluidic surface. The ?SPE consists of an array of micropillars to increase extraction bed load (scalable to loads >700 ng of cfDNA) and can be produced at low-cost using replication-based techniques. The entire ?SPE can be fabricated in a single molding step negating the need for adding additional extraction supports to the device simplifying production and keeping device and assay cost low. The ?SPE allowed for recoveries >90% of model cfDNA fragments across a range of sizes (100-700 bp) and even the ability to extract efficiently short cfDNA fragments (50 bp, >70%). In addition, the composition of the IB allowed for reducing the interference of co-extracted genomic DNA. We demonstrated the clinical utility of the ?SPE by quantifying the levels of cfDNA in healthy donors and patients with non-small-cell lung and colorectal cancers. ?SPE extracted cfDNA from plasma samples was also subjected to a ligase detection reaction (LDR) for determining the presence of mutations in the KRAS gene for colorectal and non-small cell lung cancer patients.

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Dataset Information

Porous extraction paddle: a solid-phase extraction technique for studying the urine metabolome.

Publications

Porous extraction paddle: a solid-phase extraction technique for studying the urine metabolome.

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