Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

The overall goal of this procedure is to isolate cells from cell suspension in order to make them available for single cell downstream analysis. This method can help answering key questions in the context of liquid biopsies and cellular heterogeneity. The main advantage of this technique is that it allows antibody-based isolation of single cells and their recovery for subsequent molecular genetic analysis at the single-cell level.

Once cleared for its use in patients, this technique will enable characterization of circulating tumor cells from cancer patients. As this method can provide insight into heterogeneity among single cells, it can be applied to all kinds of cell suspensions containing subpopulations such as blood samples, samples from cell cultures, or disassociated tissues and organs. We first had the idea for this method when we used an in vivo enrichment device not capable for releasing cells for the purpose of downstream analysis.

Visual demonstration of this method is critical as the steps for harvesting single cells using laser microdissection or micromanipulation are difficult to perform successfully because the process of harvesting single cells is prone to cell loss and requires a high level of expertise. In one milliliter of prewarmed cell culture medium, resuspend the HT-29 CFSE-labeled cells and let them regenerate at 37 degrees Celsius for 30 minutes. To harvest the cells, centrifuge at 300 g for three minutes.

Then, resuspend the cell pellet in one milliliter of ready-to-use Hoechst 33342 DNA staining solution at 37 degrees Celsius for 10 minutes. Next, centrifuge the cell suspension at 300 g for three minutes. Then, discard the supernatant and resuspend the cell pellet in four milliliters of 1X phosphate-buffered saline.

Then, count the number of cells using a hemocytometer and check for fluorescence labeling with fluorescence microscope. Next, centrifuge the cells at 300 g for three minutes, discard the supernatant, and resuspend the pellet at approximately 500, 000 cells per milliliter and place the cells on ice. In five milliliters of peripheral blood, add about 500 to 500, 000 cells and then mix by inverting the tube.

After removing the wire from the storage compartment, remove the rubber cap that holds the wire and wash the wire in 1X phosphate-buffered saline and mount it in the cap of the tube. Then, incubate the tube on a tilted roller mixer at five rotations per minute for 30 minutes at room temperature. After incubation, rinse the wire in 1X phosphate-buffered saline thrice.

Then, store the wire in a 15-milliliter tube containing 1X phosphate-buffered saline in the dark. Draw a rectangle area on a glass slide using a grease pen, then add 500 microliters of 1X phosphate-buffered saline onto it. To immerse the functional part of the wire in 1X phosphate-buffered saline, bend the non-functional part of the wire and place it on the glass slide.

To count the number of captured cells, visually inspect both sides of the wire. After inspecting, transfer the wire back in the 15-milliliter tube with 1X phosphate-buffered saline and keep in the dark. In one milliliter of 1X phosphate-buffered saline, dissolve four milligrams of the release buffer component, then filter the solution through 0.2 micrometer sterile filter to obtain the ready-to-use buffer.

Next, warm the release buffer at 37 degrees Celsius for five minutes. Once warmed, transfer 1.6 milliliters of release buffer to completely fill a 1.5-milliliter reaction tube. Next, incubate the functional part of the wire in the release buffer at 37 degrees Celsius in a water bath for 20 minutes.

After the incubation, place the wire on a shaker at 500 rotations per minute for 15 minutes. Then, centrifuge the wire at 300 g for 10 minutes. Once the centrifugation is over, displace the wire from the tube, close the cap, and centrifuge the tube again at 300 g for 10 minutes.

To decrease the volume of cell suspension, discard all but 100 microliters of supernatant for micromanipulation or 300 microliters for subsequent cytocentrifugation and laser microdissection. Then, quickly proceed to single-cell sampling. For micromanipulation, transfer the entire 100 microliters of cell suspension onto a glass slide.

Then, place the glass slide on a microscope equipped with a micromanipulator and allow the cells to settle for five minutes. Then, in 0.2-milliliter PCR tubes, pipette two microliters of cell lysis master mix and transfer on ice. Use the micromanipulator to collect a single cell in one microliter of 1X phosphate-buffered saline.

Then, transfer the cell directly into two microliters of cell lysis master mix. Use a desktop microfuge to quickly spin down the samples at 2, 000 g for three seconds to collect the liquid at the bottom of the tube. Then, transfer the sample on ice and proceed to adapter-linker based whole genome amplification.

Aspirate only one cell using one microliter of buffer at maximum. When transferring the cell into the lysis solution, make sure you see bubbles arising from the solution, indicating that all the aspirated volume has been transferred. For laser microdissection, cytocentrifuge the entire 300 microliters of cell suspension onto a membrane-coated slide at 300 g for five minutes.

Then, place the membrane-coated slide on a microscope capable of laser microdissection. Next, pipette 4.5 microliters of cell lysis master mix into the cap of the 0.2-milliliter PCR tube. Place the cap above the sample and harvest a single cell by laser microdissection.

Directly thereafter, check for isolated cells in the PCR cap, remove the PCR tube from the laser microdissection microscope and close the tube. Collect all the liquid at the bottom of the tube with a short spin. Transfer the sample on ice, and proceed to adapter-linker based whole genome amplification.

Make sure you recover the laser microdissected cell. Therefore, it is important to cover the entire tube cap with the lysis solution. After microdissection, check the tube cap for the presence of the cell.

To show cells that are stained with CFSE and Hoechst 33342, immunofluorescence imaging was done before charging the wire, during the cells being attached to the wire, then detached from the wire, and finally on the slide. The immunofluorescence images of cells before charging show bright nucleic stain in blue, whereas the cytoplasm of the cells show green CFSE stain with heterogeneous inter-cell intensity. Similar staining pattern is also observed for cells that are attached and subsequently detached from the wire.

To check the quality of the whole genome amplification products, a 1%agarose gel was run. The agarose gel shows a DNA smear ranging from 0.2 to greater than 1 kilobase for the PCR products of whole genome amplification. The 4plex quality control PCR products obtained from the single cell yields products of 100, 200, 300, and 400 base pairs.

Products that show fewer than three bands are excluded from further analysis. Once mastered, this technique allows isolation of single cells from cell suspensions in four hours if it is performed properly. While attempting this procedure, it's important to remember to keep the cells submerged in buffer, especially during the time the cells are attached to the wire to avoid harming the cells.

Following this procedure, analysis methods like area-comparative genomic hybridization, next-generation sequencing, and target-specific PCR can be performed in order to characterize single cells based on copy number variations and mutations. After watching this video, you should have a good understanding of how to isolate and recover cells from cell suspensions using a functionalized wire and how to sample single cells for multiple downstream molecular genetic analysis. Don't forget that working with human blood poses the possibility of infection, so wearing gloves and a lab coat are mandatory while performing this procedure.