Measurement of BK-polyomavirus Non-Coding Control Region Driven Transcriptional Activity Via Flow Cytometry

This protocol follows the guidelines of human research as approved by the ethic committee of the medical faculty of the University of Duisburg-Essen (14-6028-BO).

1. Collection of blood or urine samples and isolation of polyomavirus DNA

1.  Collect at least 3 mL of blood in EDTA tubes or urine in acquisition tubes.
2. Centrifuge the sample at 2,500 x g for 15 min. If needed, pipette plasma into a new tube and store the plasma samples at 4 °C for several days or freeze at -20 °C for longer storage.
3. Prepare 40 µL of proteinase K into a 1.5 mL microcentrifuge tube and add 400 µL of plasma by pipetting.
4. Lyse the sample by adding 400 µL of lysis buffer, vortex for 15 s, and incubate for 10 min at 56 °C.
5. Isolate the DNA using a DNA blood extraction kit as described in the manufacturer's instructions. Briefly, add alcohol and load the lysates onto a spin column containing a DNA binding silica-based membrane. Wash the columns several times to yield pure DNA.
6. Elute the yielded DNA in 30-50 µL of TE buffer.

2. Amplification of the non-coding control region (NCCR)

1. Perform the following procedure in physically separated rooms. Use an isolated room to prepare the reagents and distribute the mix to the PCR tubes.
2. Prepare the Master Mix for the pre-PCR using primer pair A (Table 1) in a total volume of 50 µL and use the previously isolated DNA from step 1.6. The pipetting scheme for preparing the master mix for the pre and nested PCR is printed in Table 2.
3. Distribute 45 µL of the master mix into the PCR tubes.
4. Add 5 µL of the isolated DNA into the PCR tubes.
   NOTE: Use another room than the one for the master mix preparation to avoid contamination.
5. Run the PCR with the reaction conditions as illustrated in Table 3. Repeat denaturation, annealing, and extension in 35 cycles.
6. For the nested amplification use primer pair B harboring the restriction sites for AgeI and SpeI (Table 1).
7. Run the nested PCR with the reaction conditions as described in steps 2.2 to 2.5 using 5 µL of the pre-PCR.
8. Mix 10 µL of the PCR product with 2 µL of 6x gel loading dye. Load 10 µL of the mix on a 1.5% agarose gel, and run the gel for 30 min at 60 mA.
9. Visualize the gel using an appropriate UV documentation system.
   NOTE: The size of the amplicon is expected to be between 300-500 bp depending on whether rearrangements (deletions, insertions, or duplications) occurred (Figure 2C).
10. Purify the PCR amplicons using a PCR purification kit according to the manufacturer's instructions. Elute the PCR amplicons in 30 µL of elution buffer.
11. Send the amplicons for Sanger sequencing using primer pair B.

3. Cloning of the NCCR into the dual fluorescence reporter

1. Digest the purified amplicons (step 2.10) with AgeI and SpeI for 2 h at 37 °C as described in Table 4.
2. Repeat step 2.10 and purify the digested amplicons.
3. In parallel, also digest the plasmid backbone (1.5 µg) with AgeI and SpeI for 2 h at 37 °C as described in Table 5. This step only needs to be performed once. For subsequent reactions, freeze the digestion at -20 °C.
4. Analyze the digested plasmid backbone on a 0.8% low melt agarose gel.
   NOTE: Do not run the gel with a current higher than 40 mA. The expected insert of the spacer region originally derived from the plasmid pEX-K4 2-LTR CD3¹³ is 128 bp (Figure 2C).
5. Visualize DNA fragments using long-wave UV light (320 nm) and cut out the backbone band using a clean scalpel. Transfer the low melt gel fragment into a new 1.5 mL microcentrifuge tube. Avoid long UV exposure times to prevent DNA damage.
   NOTE: Since low melt agarose is used, it is not necessary to purify the DNA before ligation.
6. Heat the backbone containing the low melt agarose piece for 10 min at 65 °C in order to melt the gel piece and mix every 2 min by gentle vortexing. The melted gel can be directly used for ligation.
7. Ligate the backbone and the digested amplicon using T4 DNA ligase over night at 16 °C using the scheme shown in Table 6.
8. Perform transformation in E. coli using the heat shock method, plate bacteria on LB-amp plates, and culture at 37 °C over night.
9. On the next day, select three positive clones and prepare overnight E. coli cultures (5 mL of LB-Amp) and culture at 37 °C.
10. Isolate the plasmid-DNA using standard protocols as described elsewhere¹⁴, perform AgeI and SpeI digestion to check for positive clones and visualize cut out fragments on a 1% agarose gel. The spacer band (128 bp) will be replaced by the larger NCCR-sequence (300-500 bp, see above).
11. Send the plasmid for Sanger sequencing using primer EGFP-N or primer pair B (Table 1).
12. Since mutations might spontaneously occur, compare the sequencing results with the sequencing results obtained with the amplicon. Only use the clones containing identical sequences compared to the amplicon.
13. Use a molecular workbench software (e.g., freeware GENtle 1.9.4 or other sequence editing programs) to align and edit the obtained sequences (Figure 3).
14. Start GENtle 1.9.4 and import the DNA sequences by clicking on the Import button (green down arrow).
15. Next click on Tool and select Alignment from the menu (Use Ctrl+G as a shortcut) and choose the DNA sequences for alignment.
16. Add a sequence to the alignment by clicking on Add or remove a sequence by clicking on Remove. Include an archetypical NCCR consensus sequence like JN192438¹⁵, do not use the NCCR-sequence from the commonly used Dunlop-strain¹⁶, since it harbors rearrangements and duplications others than the archetypical BKPyV strains.
    NOTE: The NCCR already contains the translational start codon (Figure 3).
17. Choose a method for the alignment by clicking on Algorithm in the toolbar and choose clustal W. Set the alignment parameters to match 2; gap extension penalty -1; gap penalty -2 and click on OK to run the alignment.

4. Transient transfection of HEK293T cells with the reporter plasmid and treatment with potential antiviral agents

1. To prepare sufficient amounts of plasmid DNA for subsequent transfection experiments prepare a 150 mL overnight culture. Isolate the plasmid DNA using a plasmid isolation kit. Alternatively, other plasmid purification kits may be used.
2. Seed 1 x 10⁵ HEK293T cells in DMEM containing 10% FCS, penicillin and streptomycin (1x) per well of a 12-well plate 24 h prior to transfection and incubate overnight at 37 °C and 5% CO₂ to maintain active proliferation during transfection.
   NOTE: Cells should be approximately 80% confluent at transfection.
3. Place 250 µL of reduced serum media in a sterile tube and add 1 µg of each reporter plasmid DNA and mix gently by pipetting.
4. Add 3 µL of the transfection reagent to the DNA mixture, mix gently by pipetting and incubate for 15 min. Pre warm the transfection reagent to the ambient temperature of 22 °C and vortex gently before use.
5. Add the mixture drop-wise to the wells and gently distribute to the well.
6. After 4 h, replace the supernatant with fresh medium containing the testing agents and solvent control. Incubate at 37 °C until analysis. In this example, the mTOR inhibitors INK128 (100 ng/mL) and rapamycin (100 ng/mL) were used.

5. Fluorescence microscopy and flow cytometry

1. Check cells for the red and green fluorescence under the fluorescence microscope (Figure 4).
   NOTE: Red and green fluorescence correspond to the early and late BKPyV gene expression, respectively.
2. After 72 h post transfection, aspirate the supernatant and wash the cells twice with 1 mL of cold PBS.
3. Gently add 500 µL of trypsin and turn the plate slightly to avoid premature detachment of the cells. This step is important to avoid cell doublets.
4. After addition, remove the trypsin directly with the same pipette tip.
5. Incubate the cells for at least 5 min at 37 °C.
6. Resuspend trypsinized cells with 1 mL of PBS containing 3% FCS and transfer the suspension in pre-labeled FACS tubes.
7. Add DAPI (1 µg/mL) prior to the FACS analysis.
8. Analyze the cells using a flow cytometer. For each sample, measure at least 10,000 living cells, which are negative for DAPI staining.

6. Data analysis

1. Import the data to the flow cytometry analysis software and add samples by Click and Drag into the workspace.
2. Double click on the imported file and create a graph plot. Choose FSC-A versus SSC-A by clicking on the x- and y-axis. Gate the main cell population by clicking on Polygon at the toolbar and framing the cell population (Figure 5). Name the chosen cell population as required (for example "single cells"). The "single cells" will appear as a new workspace.
3. Proceed with gating "single cells" for DAPI negative (i.e., "living cells"). To identify living cells compare the cell population with and without DAPI staining. In both plots choose FSC-A versus pacific-blue-A.
4. Click on the rectangle and choose the DAPI negative cell population, name the chosen cell population "living cells", and create a new dot-plot showing FITC (eGFP) versus PE (tdTomato) as described before.
5. Add quadrants in "living cells" by choosing Quad from the toolbar. Gate the population by dragging the center of the quadrant to the edge of each population. The quadrants represent 1) eGFP-tdTOM-, 2) eGFP-tdTOM+, 3) eGFP+tdTOM-, 4) eGFP+tdTOM+.
   NOTE: Due to the spectral overlay of emission spectra between FITC and PE, initial compensation is essential to distinguish between red and green signals and to achieve accurate results.
6. Determine mean fluorescence intensities (MFIs) by right clicking on the quadrant and choosing Add Statistics. Choose Mean and click OK. The mean MFI is now displayed below the population in the section "statistics". Quadrants 2 and 4 correspond to early expression, while quadrants 3 and 4 represent late expression.
7. Add additional replicates in the same manner for statistical power.
8. For data interpretation plot MFI values of early and late into a bar plot:
9. To compare NCCR activities obtained from different donors or virus strains, add an archetypical control or the Dunlop strain¹⁶ and set its relative MFIs to 100%, and calculate the relative MFI values. Repeat with each replicate and determine mean and standard deviation.
10. To evaluate an effect of potential compounds on the transcriptional activity, set the solvent-control to 100% and plot the MFI of the treated cells.