Focused on High Value Cells

Production of Stable Cell Lines to Facilitate the Creation of Therapeutic Recombinant Proteins and Biosimilars

In many cell line development projects, the therapeutic proteins produced will be monoclonal antibodies (mAbs), but some companies also use these stable cell lines to produce enzymes for enzyme replacement therapies in rare diseases.

The New Standard in Cell Line Development Workflow

The Importance of Clonality

In the development of any new stable production cell line it is essential to provide assurance of clonality. Historically, this was assessed based on probability, but more recently, with the development of dedicated imaging, assurance can be provided by a high clarity picture of the single cell in the whole well shortly after seeding.

For any new biological drug, the FDA and EMA both recommend assurance of clonality for the Master Cell Bank (MCB) as part of an IND process.

Additionally, it is crucial to consider the quality and consistency of the protein therapeutic. This is important for batch to batch production, but also in demonstrating equivalence during the production of biosimilars.

Cell Line Development Comes of Age

Cell line development is the key to unlocking so much potential in the  development of new biological medicines and therapies. And yet, for all its promise, CLD can be frustratingly slow, unpredictable and requiring experts. Well, it doesn’t need to be this way, not any more! With the right combination of instrumentation,  reagents and know-how the process can be de-skilled whilst concurrently delivering improvements in workflow timelines, outcomes and assurance.

Leap-In Transposase® for creation of High Producer Clones

Cell line development scientists relying on traditional random integration technology would look for smarter ways to find the rare population of high producers. This involved lengthy IgG secretion assays at the single cell or cloning plate stage.

This whole step can be bypassed by the creation of a population where the majority of the clones are already de facto high producers.

Available from Solentim, developed by our partner ATUM, the Leap-In transposase® platform, is a targeted approach to vector integration giving rise to a transfected population where most clones are high producers. Using the Leap-In technology, the clonal distribution after transfection is shifted such that now over 60% of the clones are in the first quartile for expression level (see figure below). In practical terms, this means that scientists no longer need to try and pre-screen for high producers and far fewer plates of single cell clones are needed per project, saving time and money.

Of commercial importance to customers, use of Leap-In has already received approval in an IND submission to the US FDA.


Typical clonal distribution for Leap-In Transposase (ATUM) mediated stable integration. In this example, 62% of clones are in the first quartile for productivity

Single Cell Cloning and Documentation

From the stable transfection pools, single cells are dispensed into microtiter plate wells, then arrival confirmed, as per requirements.

Ideally, this should be done at high efficiency resulting in the majority of wells containing a single cell which is viable after seeding. These cells will then grow into colonies over the next few days. Cell types used are predominantly CHO suspension cells expressing an antibody or recombinant protein of therapeutic importance.

Current methods for seeding single cells and selecting colonies all have their drawbacks:

  • Limiting Dilutions (inefficient)
  • FACS (difficult to operate and high pressure leads to low outgrowth)
  • ClonePix picking of colonies from semi-solid media (only removes non-producers)
  • Newer single cell printers (need separate whole well imaging) and opto-electronic approaches (expensive to buy and run)
Cell Line Development - Typical seeding efficiency for 96 well plate seeded on VIPS
Typical seeding efficiency for 96 well plate seeded on VIPS. Green = single cells, Red=>1 cell, Grey= no cells. This example shows 88% single cell seeding efficiency

Using our VIPS system provides far greater benefits and results compared with other seeding and colony selection methods. VIPS will generate a resultant plate with high seeding efficiency in around 10 minutes, and due to the gentle nature of the dispensing method combined with our InstiGRO supplement, many of these wells will go on and successfully grow into colonies.

Clone Screening, Assurance and Successful Colony Outgrowth

Regardless of the cell dispensing method used, it is essential to show the successful arrival of the single cell in the well.

From a regulatory perspective, whole well imaging is fundamentally important in providing assurance of clonality. With the advent of high-quality automated imaging in the last 5 years, many customers are now able to perform only one round of cloning, significantly reducing their timelines across the entire cell line development process.

Whole well imaging can be performed on either the VIPS or the Cell Metric. The optimal solution is to have the VIPS and Cell Metric connected via the Sync Server, producing plates with high seeding efficiency and outgrowth, along with the capacity for further outgrowth imaging to be performed as well as further expansion studies of the best clones.

The numbers of plates screened can vary enormously between customers from a handful to several hundred per project. After single cell seeding, cells can settle to the bottom of the well or can be centrifuged.

There are many important considerations for optimising the outgrowth from single cells. One of the key factors is growth supplements which can be added to the growth media. Solentim provide the InstiGRO supplements for both CHO and HEK cells which have been shown to significantly improve the outgrowth and cloning efficiency for the common commercial cells lines such as HD-BIOP3 (Horizon) and CHOZN (Millipore Sigma).

Cells can then be imaged by the Cell Metric for assurance of clonality. The regulator has set out expectations for the imaging and stated that it should be carried out on a whole well basis and completed on Day 0 and then subsequent days of growth and division. The imager should also be used to validate your cloning method (FACS, LD, VIPS etc). This is only feasible if the imager can guarantee focus 100% for every well in the plate. The Cell Metric is uniquely able to do this by adjusting focus in each well for the curvature and distortion of each plate.

Validation methods can be designed for bright field and fluorescence modes. These experiments are essential to generate some statistical support to your cloning methods and the chances of a second cell being in a well which you believe to be clonal. It is generally not recommended or encouraged to use fluorescence labels in the real experiments and some of our customers have shown the Celltracker dyes do reduce outgrowth. Also, given that customers are developing therapeutics for patients, then extraneous fluorescence should be avoided. Imaging is carried out for Day 0 and subsequent days of growth and ultimately colony formation. This can be 10-21 days depending on cell types and protein being expressed.

A library of images is created for each well and it is possible to track back in time from the colony all the way back to Day 0 and confirm if it started from 1 cell or not. It can vary from customer to customer when they do this review of wells. Some customers do it immediately after colony formation and then hit pick the wells which formed a colony and started from a single cell. This could involve picking and re-arraying several hundred clones. Other customers re-array (or cherry-pick) all the wells that grew into fresh 24 DWP which are then shaken in fed-batch mode. Once they have found the best clones based on titre, they will take this smaller subset and review the original well images for assurance of clonal origin. For the clonal wells of choice, the Cell Metric can write a cherry-picking CSV file which can be exported to a third-party liquid handling robot for re-compiling into full 96 well plates of clones.

Finally, a report can be rapidly generated for the well history of the top clones. This documentation package is called the Clonality Report and is importantly something which customers can include as part of their IND submission to the regulator to support their clonality claims.

The Clonality Report - Documentation for the Regulator

In recent years, regulators have indicated that assurance data provided by imagers should meet specific criteria. Solentim has automated this process by creating the Clonality Report, ensuring no errors are made in the collation of this assurance data.

Clonality Report for tracking outgrowth and clonality for each well

Using a barcode system on the plates will eliminate errors in terms of clone history and data tracking. Finally, the Clonality Report generates a tamper-proof reliable report including relevant images for the end-customer, be that a client at a CRO or the regulator for an IND filing. These reports literally only take minutes to annotate and generate, and can be emailed in electronic format. From a user perspective, VIPS and Cell Metric share a common software interface for ease of use. Batch information only needs to be entered once and then is carried through automatically. VIPS data will also be added to the Clonality Report for even more complete tracking and assurance.

These reports, which can form part of the IND submission package, follow the valuable user-selected clonal wells from single cell to colony throughout the growth period with an image series (whole well and single cell image) in order to provide full time-and date-stamped data information for the well from single cell to colony. Annotation is possible of the single cell and any other features e.g. debris. The reports are generated in minutes in PDF or PowerPoint presentation formats which can be exported and shared with interested parties e.g. cell banking groups, or a CMO customer.

Remote data viewer software enables the user to analyse data and generate clonality reports from their office computer.

Growth, Expansion and Earlier Assessment of Critical Quality Attributes

Aside from clonality, many customers also want to get an earlier assessment of Critical Quality Attributes (CQA) for the best clones. For instance, they will look at growth rates and doubling time of clones and will want to measure confluence to normalise with an early protein productivity assessment e.g. from Octet or ELISA. The Cell Metric is the ideal tool for these confluence measurements.

Once this subset of the top clones has been cherry-picked and are in shaking fed-batch culture, then more accurate assessments can be established for protein titre and Qp (Specific Productivity). Many customers carry out this expansion step using 24 DWP in shaking incubators. Solentim now also provide a supplement called InstiSHAKE which will enhance cell growth in shaking culture.

Once a subset of the clones has been cherry-picked and are in shaking fed-batch culture, then more accurate assessments can be established for protein titre and Qp (Specific Productivity). Many customers now do this using 24 DWP in shaking incubators. Again, the Cell Metric has an option for accurate viable cell counting (VCD) using Trypan Blue and these can be used in titre and Qp.

Summary - Setting the New Standard in Cell Line Development Workflow

Solentim has drawn on its many combined years of experience in cell culture to enhance your CLD workflow requirements.
We’ve combined our Cell Metric for whole well imaging, our VIPS for single cell isolation and the Clonality Report for regulatory assurance documentation, along with additional Solentim-verified technologies from our industry-leading partners. These include vector design and transposases, leading commercially available host cell lines, and a range of cell growth and recovery supplements.
And don’t worry if you use alternative gene integration methods or different host cell lines, you can still plug these into our workflow

Customers have already demonstrated that, by using this approach, they have been able to reduce cell line development project timelines from 6 months to <12 weeks (view our case studies to learn more).

Need to know more information about Solentim?

and how we can accelerate your Cell Line Development Projects ....

The Clonality Report

“meets the FDA requirements of whole well image and where single cell feature is located; allows highlighting of other features which can then be described away”

Dr Audrey Jia, Former FDA CMC
Reviewer. IBC Asia, Shanghai, May 2017

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