Performance of Spectrophotometric and Fluorometric DNA Quantification Methods

Accurate DNA quantification is a highly important method within molecular biology. Methods widely used to quantify DNA are UV spectrometry and fluorometry. In this research, seven different DNA samples and one blank (MilliQ ultrapure water) were quantified by three analysts using one spectrophotometric (i.e., a NanoDrop instrument) and three fluorometric (i.e., the AccuGreen High Sensitivity kit, the AccuClear Ultra High Sensitivity kit, and the Qubit dsDNA HS Assay kit) methods. An analysis of variance (ANOVA) scheme was used to determine the influence of the analyst, the method, and the combination of analyst and method, on DNA quantification. For most samples, the measured DNA concentration was close to or slightly above the concentration of 10 ng/μL as specified by the supplier. Results obtained by the three analysts were equal. However, it was found that, compared to the fluorometric kits, the used spectrophotometric instrument in the case of fish DNA samples tends to overestimate the DNA concentration. Therefore, if sufficient sample volume is available, a combination of a spectrophotometric and a fluorometric method is recommended for obtaining data on the purity and the dsDNA concentration of a sample

Microsieves for the detection of circulating tumor cells in leukapheresis product in non-small cell lung cancer patients

Background: Circulating tumor cells (CTC) in non-small cell lung cancer (NSCLC) patients are a prognostic and possible therapeutic marker, but have a low frequency of appearance. Diagnostic leukapheresis (DLA) concentrates CTC and mononuclear cells from the blood. We evaluated a protocol using two VyCAP microsieves to filter DLA product of NSCLC patients and enumerate CTC, compared with CellSearch as a gold standard. Methods: DLA was performed in NSCLC patients before starting treatment. DLA product equaling 2×108 leukocytes was diluted to 9 mL with CellSearch dilution buffer in a Transfix CTC tube. Within 72 hours the sample was filtered with a 7 μm pore microsieve and subsequently over a 5μm pore microsieve. CTC were defined as nucleated cells which stained for cytokeratin, but lacked CD45 and CD16. CellSearch detected CTC in the same volume of DLA. Results: Of 29 patients a median of 1.4 mL DLA product (range, 0.5-4.1) was filtered (2% of total product) successfully in 93% and 45% of patients using 7 and 5 μm pores, respectively. Two DLA products were unevaluable for CTC detection. Clogging of the 5 μm but not 7 μm microsieves was positively correlated with fixation time (ρ=0.51, P<0.01). VyCAP detected CTC in 44% (12/27) of DLA products. Median CTC count per mL DLA was 0 [interquartile range (IQR): 0-1]. CellSearch detected CTC in 63% of DLA products (median =0.9 CTC per mL DLA, IQR: 0-2.1). CTC counts detected by CellSearch were significantly higher compared with VyCAP (P=0.05). Conclusions: VyCAP microsieves can identify CTC in DLA product, but workflows need to be optimized

Collection of cells for single-cell RNA sequencing using high-resolution fluorescence microscopy

FACS sorting followed by single-cell RNA-sequencing (SORT-Seq) is a popular procedure to select cells of interest for single-cell transcriptomics. However, FACS is not suitable for measurement of subcellular distribution of fluorescence or for small samples (<1,000 cells). The VYCAP puncher system overcomes these limitations. Here, we describe a workflow to capture, image, and collect fluorescent human retina pigment epithelium cells for SORT-Seq using this system. The workflow can be used for any cell type with a diameter of ∼5-50 μm. For complete details on the use and execution of this protocol, please refer to Segeren et al. (2020)

In Vivo Detection of Circulating Cancer-Associated Fibroblasts in Breast Tumor Mouse Xenograft: Impact of Tumor Stroma and Chemotherapy

Cancer-associated fibroblasts (CAFs) are important drivers in the tumor microenvironment and facilitate the growth and survival of tumor cells, as well as metastasis formation. They may travel together with tumor cells to support their survival and aid in the formation of a metastatic niche. In this study, we aimed to study circulating CAFs (cCAFs) and circulating tumor cells (CTCs) in a preclinical breast tumor model in mice in order to understand the effect of chemotherapy on cCAFs and CTC formation. Tumors with MDA-MB-231 human breast tumor cells with/without primary human mammary fibroblasts (representing CAFs) were coinjected in SCID mice to develop tumors. We found that the tumors with CAFs grew faster than tumors without CAFs. To study the effect of the stroma on CTCs and cCAFs, we isolated cells using microsieve filtration technology and established ITGA5 as a new cCAF biomarker, which showed good agreement with the CAF markers FAP and α-SMA. We found that ITGA5+ cCAFs shed in the blood of mice bearing stroma-rich coinjection-based tumors, while there was no difference in CTC formation. Although treatment with liposomal doxorubicin reduced tumor growth, it increased the numbers of both cCAFs and CTCs in blood. Moreover, cCAFs and CTCs were found to form clusters in the chemotherapy-treated mice. Altogether, these findings indicate that the tumor stroma supports tumor growth and the formation of cCAFs. Furthermore, chemotherapy may exacerbate the formation of cCAFs and CTCs, which may eventually support the formation of a metastasis niche in breast cancer

Collection of cells for single-cell RNA sequencing using high-resolution fluorescence microscopy

FACS sorting followed by single-cell RNA-sequencing (SORT-Seq) is a popular procedure to select cells of interest for single-cell transcriptomics. However, FACS is not suitable for measurement of subcellular distribution of fluorescence or for small samples (<1,000 cells). The VYCAP puncher system overcomes these limitations. Here, we describe a workflow to capture, image, and collect fluorescent human retina pigment epithelium cells for SORT-Seq using this system. The workflow can be used for any cell type with a diameter of ∼5-50 μm. For complete details on the use and execution of this protocol, please refer to Segeren et al. (2020)

Performance of Spectrophotometric and Fluorometric DNA Quantification Methods

Accurate DNA quantification is a highly important method within molecular biology. Methods widely used to quantify DNA are UV spectrometry and fluorometry. In this research, seven different DNA samples and one blank (MilliQ ultrapure water) were quantified by three analysts using one spectrophotometric (i.e., a NanoDrop instrument) and three fluorometric (i.e., the AccuGreen High Sensitivity kit, the AccuClear Ultra High Sensitivity kit, and the Qubit dsDNA HS Assay kit) methods. An analysis of variance (ANOVA) scheme was used to determine the influence of the analyst, the method, and the combination of analyst and method, on DNA quantification. For most samples, the measured DNA concentration was close to or slightly above the concentration of 10 ng/μL as specified by the supplier. Results obtained by the three analysts were equal. However, it was found that, compared to the fluorometric kits, the used spectrophotometric instrument in the case of fish DNA samples tends to overestimate the DNA concentration. Therefore, if sufficient sample volume is available, a combination of a spectrophotometric and a fluorometric method is recommended for obtaining data on the purity and the dsDNA concentration of a sampl

VyCAP's puncher technology for single cell identification, isolation, and analysis

Here we present the Puncher technology for the isolation of single cells. This technology combines a silicon chip with microwells, fluorescence imaging, and a punching method to isolate and transfer the single cells to standard reaction tubes. The technology is compatible with commercially available downstream workflows and instrumentation. Here we focus on the isolation of CTC but the Puncher technology can be applied to isolate single cells from liquid biopsies and more general from cell suspensions. It is especially suited for cell suspensions that contain: * Cells of interest at a frequency of 1 per 10,000 or less * A low total number of cells ranging from 1 to 100,000, that are present in a volume of 0.01 to 50 mL. The frequency of appearance of CTC in blood is in the order of the 1 per 106 leukocytes. To be able to isolate the single CTC with the Puncher technology, enrichment of the CTC by a 3 logs reduction of the leukocytes is required. Here we describe the use of Rosettesep and Parsortix as examples of pre‐enrichment methods that are compatible with the Puncher technology and further downstream applications. © 2018 International Society for Advancement of Cytometry Over the last couple of decades, multiple technologies have been developed for the enrichment and isolation of rare cells, including circulating tumor cell (CTC). Compatibility between these technologies, is however mostly not present 1-3. Enriched sample volumes are too large or the number of unwanted cells in the enriched samples is too high to identify and isolate the cells of interest. This leads to low recovery rates when isolating single CTC from the enriched samples. The Puncher technology for single cell isolation overcomes most of these issues

Self-Seeding Microwells to Isolate and Assess the Viability of Single Circulating Tumor Cells

The availability of viable tumor cells could significantly improve the disease management of cancer patients. Here we developed and evaluated a method using self-seeding microwells to obtain single circulating tumor cells (CTC) and assess their potential to expand. Conditions were optimized using cells from the breast cancer cell line MCF-7 and blood from healthy volunteers collected in EDTA blood collection tubes. 43% of the MCF-7 cells (nucleus+, Ethidium homodimer-1-, Calcein AM+, &#945;-EpCAM+, &#945;-CD45-) spiked into 7.5 mL of blood could be recovered with 67% viability and these could be further expanded. The same procedure tested in metastatic breast and prostate cancer patients resulted in a CTC recovery of only 0&#8315;5% as compared with CTC counts obtained with the CellSearch&#174; system. Viability of the detected CTC ranged from 0&#8315;36%. Cell losses could be mainly contributed to the smaller size and greater flexibility of CTC as compared to cultured cells from cell lines and loss during leukocyte depletion prior to cell seeding. Although CTC losses can be reduced by fixation, to obtain viable CTC no fixatives can be used and pore size in the bottom of microwells will need to be reduced, filtration conditions adapted and pre-enrichment improved to reduce CTC losses