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Process improvement delivered by a high efficiency, automated single cell cloning system
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Presented by Andrea Gough, Solentim at CCE XVI in Tampa, FL (May 2018)
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Process improvement delivered by a high efficiency, automated single cell cloning system
1.
Process improvement delivered
by a high efficiency, automated single cell cloning system Andrea Gough*, Erika Parkinson, Ian Taylor, Solentim Limited, UK. Andrea.Gough@solentim.com *First author Abstract Single cell cloning (SCC) and associated cloning efficiency (colony outgrowth) is currently regarded as an important and discrete step in stable cell line development and cell engineering. Even with improved targeted gene editing like CRISPR/Cas9, many hundreds of single cell clones still need to be created and analyzed. For many laboratories, flow cytometry (FACS) or limiting dilution (LD) is the current method of choice for single cell deposition, however, each method has its drawbacks. When using FACS, very high seeding efficiency results can be achieved but often at the expense of cell survival and growth due to the harsh treatment of the cells during processing.WhenusingLD,thereverseisthecase;whereby good cell survival can be achieved but at low seeding efficiencies. These intrinsic inefficiencies often result in a combination of the two processes being implemented and used on a case by case basis; FACS for robust cell lines and LD for sensitive cell lines. In addition to these drawbacks, neither of these processes offer independent confirmation of the single cell deposition. In this poster, we introduce a new dedicated SCC platform called Verified In-Situ Plate Seeding (or VIPS™), which combines gentle single cell deposition with concurrent in-situ image verification of the single cell in a well. VIPS uses a proprietary process of SMART™ LD whereby the cell droplet is imaged immediately on dispensing in the well to confirm presence or absence of a single cell (see figure 2). Introduction Previous technology developed by Solentim successfully addressed the issue of verifying clonality and colony outgrowth monitoring in cell line development. However, there remains a bottleneck upstream of this - the efficient dispensing of single cells. The VIPS represents a unique approach to single cell dispensing: • Simple to use • Gentle (low pressure) on cells therefore applicable to a wide range of cell lines • Uses statistically accepted distribution models • Less labour intensive • Improves seeding efficiencies • Enhanced clonality report and evidence gathering • Fluorescence option for validation The VIPS™ system is a small bench top instrument that is placed within a standard biological safety cabinet (class II) for sterility (see figure 1) with all tubing and components that come into contact with cells easily sterilised or replaced. This avoids reliance on expensive proprietary consumable supplies. The system dispenses a single droplet into an empty well followed by immediate imaging of the droplet. If a cell was deposited, the well will be filled with media. If a cell was not detected, the system will deposit another drop to the side and image the position again (see figure 3). The system uses a stack of images to assess the presence of a cell and this will take place a maximum of 16 times to effectively ‘re-use’ any empty wells and increase the frequency of single cell wells. Figure 2: Flow diagram representation of the VIPS workflow. Solentim Ltd VIPS and SMART LD are a trademarks of Solentim. Other brands or product names are trademarks of their respective holders. © Copyright 2018 Solentim Ltd. All rights reserved. Results are reported in real time so that the user can see which wells have been populated, and this achieves the entire dispensing of a 96 well plate in approximately 10 minutes (dependent upon the cell density being used). All together the VIPS efficiently improves the process of clonal cell line development by combining droplet imaging, single cell verification, outgrowth assessment and seeding validation using FL capabilities. Methods and materials Five cell lines were tested for seeding and cloning efficiency using the VIPS: • 2x CHOZN® pools (supplied by Millipore Sigma, St Louis, USA) • DLD-1 (adherent colon adenocarcinoma) • HCT116 (adherent colorectal carcinoma) • THP-1 (suspension monocyte-like cell line) Cell lines were grown as per manufacturers instructions. The CHOZN pools were grown in AC free conditions. Cells were diluted to 18,000 cells/ml and seeded to 96well plates using the VIPS. Plates were then imaged by the CellMetric (brightfield) on days 0, 2, 7 and 10 to assess outgrowth. HCT116, DLD-1 and THP-1 were also cloned by limiting dilution for comparison. Results and discussion CHOZN pool seeding and outgrowth data Seeding efficiencies for both pools resulted in an average of 52% of wells containing a single cell (see figure 4). Clonal outgrowth for the two pools was an average of 75% and 62% (see figure 5) compared to 30-50% and 60- 70% respectively using their normal limiting dilutions approach (results not shown). Figure 6 displays a specific example from a plate seeded withaCHOZNpool. 85%ofwellswereconfirmedtohavea single cell at the time of seeding (green wells). Outgrowth monitoring revealed 65% of these cells divided and formed colonies with a large range in colony size after 13 days (see figure 7). All data is available to the user and can be used to track and monitor cell growth from the moment the cell is dispensed into a well. SystemValidation In addition to the brightfield ca- pabilities to monitor colony out- growth, the VIPS has fluorescent imaging capability. Utilising fluo- rescent cells the VIPS data can be validated using the QC application on day 0 using the whole well im- age. In this case outgrowth is not necessary for results saving the user time and money. Presented at: CCE – XVI Conference, Tampa, May 2018 DISPENSE Small cell droplet deposited into empty well Under low pressure Continual cell agitation 96 well plate DETECT Image droplet BF standard imaging Fluorescence imaging for qualification CONFIRM Image feedback loop No cell = Repeat cell droplet Cell present = Media fill Figure 1: VIPS System location in biological safety cabinet (class II). Figure 3: Three images captured of a well being processed by the VIPS during a seeding run. A) An empty well before dispensing. B) The same well with a single drop deposited – highlighted by an arrow in the image. C) The same well after cell detection; the well is filled with the media. 2. AFTER DISPENSING 3. MEDIA FILLING 1. BEFORE DISPENSING Figure 4: Average seeding results obtained by dispensing two CHOZN pools using the VIPS system into 7 x 96 well plates per pool. Pool 1 Pool 2 0 20 40 60 Percentage% Average Seeding Efficiency P1 P2 P3 P4 P5 P6 P7 0 10 20 30 40 50 60 70 80 90 Percentage(%) Cloning Efficiency Average Cloning Efficiency P1 P2 P3 P4 P5 P6 P7 Cloning efficiency A) CHOZN pool 1 B) CHOZN pool 2 Figure 5: Outgrowth results obtained by dispensing two CHOZN pools using the VIPS system into 7 x 96 well plates per pool. The orange line indicates the average cloning efficiency obtained across the seven plates for each pool. Figure 7: Left image – well B8. Right image - well D10. Growth Rate graph displaying the growth rate as determined using whole well confluence %. The whole well image and the confluence readings highlight the difference in clonal growth between single seeded cells. Hour 2 Day 2 Day7 Day 9 Day 13 0.00 5.00 10.00 15.00 20.00 Confluence% B8 D10 Figure 9: Well output verifying the presence on of a single cell, a well containing multiple cells and a well containing no cells using the fluorescence imaging capabilities of the VIPS. Figure 8: Graphical representation of the improvement achieved when using the VIPS to seed HCT116, DLD1 and THP1 cell lines compared to standard limiting dilution. Data is shown as number of clonal colonies produced with VIPS and limiting dilution for each cell line and the resulting percentage increase using VIPS over limiting dilution. HCT116 DLD1 THP1 0 5 10 15 20 25 30 35 LD- Average # Clonal Growth VIPS - Average # Clonal Growth Averagenumberofclonalcolonies per96wellplate increase in the production of clonally derived colonies using VIPS vs limiting dilution for alternative cell lines Figure 6: Software output from VIPS seeding results (left image) and whole well imaging (right image) of a 96 well plate at point of seeding and at 13 days post seeding to show colony growth. The images captured of well D8 are also displayed at each time point to show the tracking of a single cell into a colony and how the software can report this data. Figure 10: Enhanced clonality report displaying the VIPS drop image containing evidence of the single cell combined with a whole well image, taken at day 8, containing the growing clone a single or multiple whole well images at selected time points can be included in the report. Figure 11: A) Cell reservoir. B) Media tubing. Both made from materials suitable for sterilisation and provided as consumables if required. HCT116, DLD-1 andTHP-1 cell line data Cell line development and the requirement to dispense a single cell is required for many applications. To demonstrate the versatility and sensitivity of the VIPS, three additional cell lines were seeded using the VIPS and outgrowth monitored. For all the cell lines dispensed we saw a marked increase in the number of clonal colonies achieved per plate with VIPS seeding vs standard limiting dilution (see figure 8). Enhanced Clonality Report The VIPS system generates an enhanced clonality report that will include the drop image containing the single cell andsubsequentwholewellimagesofthecolonyoutgrowth (see figure 10). This report is time and date stamped and can be produced as a PDF or PowerPoint. Consumables TheVIPSsystemoffersuserstheoptiontoeliminatetheneed for expensive proprietary consumables (see figure 11), the only parts that come into contact with the cell culture and media are the cell reservoir and media tubing. Both can be sterilised and re-used if required and Solentim can provide thesepartsasconsumables.AlternativelyCellReservoirsand tubing can be provide as“Project Kits”and treated as single- use disposables The data presented here show that the VIPS improves the cloning and outgrowth efficiency of cell lines not just for therapeutics but potentially across many other applications, when compared to FACS and limiting dilution. Integrating this system into a cell line development laboratory will provide increased output of clonesforassessment,clonalityassuranceandsupporting documentation.
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