Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.

Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.

Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine.

Improving the utilization of tumor tissue from diagnostic biopsies is an unmet medical need. This is especially relevant today in the rapidly evolving precision oncology field where tumor genotyping is often essential for the indication of many advanced and targeted therapies. National Comprehensive Cancer Network (NCCN) guidelines now mandate molecular testing for clinically actionable targets in certain malignancies. Utilizing advanced stage lung cancer as an example, an improved genotyping approach for solid tumors is possible. The strategy involves optimization of the microdissection process and analysis of a large number of identical target cells from formalin-fixed paraffin-embedded (FFPE) specimens sharing similar characteristics, in other words, single-cell subtype analysis. The shared characteristics can include immunostaining status, cell phenotype, and/or spatial location within a histological section. Synergy between microdissection and droplet digital PCR (ddPCR) enhances the molecular analysis. We demonstrate here a methodology that illustrates genotyping of a solid tumor from a small tissue biopsy sample in a time- and cost-efficient manner, using immunostain targeting as an example.

Purification and In Situ Ligand Exchange of Metal-Carboxylate-Treated Fluorescent InP Quantum Dots via Gel Permeation Chromatography.

Recently the addition of M2+ Lewis acids (M = Cd, Zn) to InP quantum dots (QDs) has been shown to enhance the photoluminescence quantum yield (PL QY). Here we investigate the stability of this Lewis acid layer to postsynthetic processing such as purification and ligand exchange. We utilize gel permeation chromatography to purify the quantum-dot samples as well as to aid in the ligand-exchange reactions. The Lewis-acid-capped particles are stable to purification and maintain the enhanced luminescence properties. We demonstrate successful ligand exchange on the quantum dots by switching the native carboxylate ligands to phosphonate ligands. Changes in the optical spectra after exposure to ambient environment indicate that both carboxylate- and phosphonate-capped QDs remain air-sensitive.

Gel permeation chromatography as a multifunctional processor for nanocrystal purification and on-column ligand exchange chemistry.

This article illustrates the use of gel permeation chromatography (GPC, organic-phase size exclusion chromatography) to separate nanocrystals from weakly-bound small molecules, including solvent, on the basis of size. A variety of colloidal inorganic nanocrystals of different size, shape, composition, and surface termination are shown to yield purified samples with greatly reduced impurity concentrations. Additionally, the method is shown to be useful in achieving a change of solvent without requiring precipitation of the nanocrystals. By taking advantage of the different rates at which small molecules and nanoparticles travel through the column, we show that it is furthermore possible to use the GPC column as a multi-functional flow reactor that can accomplish in sequence the steps of initial purification, ligand exchange with controlled reactant concentration and interaction time, and subsequent cleanup without requiring a change of phase. This example of process intensification via GPC is shown to yield nearly complete displacement of the initial surface ligand population upon reaction with small molecule and macromolecular reactants to form ligand-exchanged nanocrystal products.