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https://doi.org/10.1038/s41551- 021- 00699- 9
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Chapter 4
Advancements intheManufacture ofMonoclonal Antibodies andOther Large Molecule Protein Therapeutics: Recent Innovations inCell Culture Technology Enabling Process Intensication
GregoryW.Hiller
Abstract This chapter on recent advances in upstream process development will
discuss the limitations of fed-batch processes, the recent resurgence of interest in traditional “classical steady-state” perfusion in which viable cell density is held nearly constant, and the development of non-conventional “dynamic” perfusion processes in which viable cell density is allowed to peak and decline. Many variants and hybrid processes that combine elements of both perfusion and fed-batch, or even link bioreactors together for a unique, isolated control of the growth phase and the more quiescent production phase will be explored. Other process intensication methodologies such as N-1 perfusion for high-density production reactor inocula­tion will also be examined.
A section on the pragmatic control of mammalian cell metabolism will explain recent advances designed to precisely control lactic acid formation and limit ammo­nium ion accumulation. Genetic engineering approaches such as enzyme knock outs and catabolic pathway reconstitution to limit the formation of previously unknown growth-inhibitory by-products of metabolism will also be delineated.
Keywords Perfusion · Glucose limitation · N-1 perfusion · Batch · Fed-batch · Linked bioreactors · High-intensity low-volume perfusion
G. W. Hiller (*) Bioprocess Research and Development, Biotherapeutics Pharmaceutical Sciences, Pzer Inc., Andover, MA, USA e-mail: greg@greghiller.com
K. Gadamasetti, S. A. Kolodziej (eds.), Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry,
https://doi.org/10.1007/978-3-031-62007-2_4
73© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024
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4.1 Introduction

The market for monoclonal antibodies (mAbs) and large molecule protein therapeu­tics continues to grow at a vigorous pace partly because such medicines are now more affordable as the economic prosperity of enormous populations around the world has increased over the past several decades [1]. The incredible specicity, and lack of off-target effects and therefore adverse therapeutic events, continues to make protein therapeutics an essential tool to treat an enormous array of human diseases. When using animal cell culture as the production methodology, the vast majority of large molecule protein therapeutics are produced as secreted, extracellular products. The same cell culture principles that will be discussed in this chapter also apply to a great extent to the newly developing elds of autologous or allogenic cell therapy and the production of recombinant adeno-associated virus (rAAV) for gene therapy (though rAAV production is intracellular).
In recent years, some have questioned the need for increased productivity at the large scale [2] as the number of blockbuster monoclonal antibodies may be decreas­ing as we move into an age of more personalized medicine, with genetic variant testing of individual forms of disease determining a highly specic and potentially more efcacious treatment plan. This potentially logical argument for less interest in high-capacity processes, however, did not envision the massive and sudden global need for effective antibody therapeutics to treat coronavirus disease 2019 (COVID-19) in the face of the rst global pandemic to strike the world for more than a century in 2020.
4.2 Modes ofBioreactor Operation
4.2.1 Batch
The simplest mode of bioreactor operation is batch. If repeated multiple times in succession, these processes are known as repeated batch or batch re-feed operations [3]. Repeated batch operations are still performed today in some commercial pro­cesses for labile molecules or proteins that are primarily produced only during the growth phase (growth-associated). Due to the limited solubility of many media components, those that are quickly consumed may be depleted from a batch culture and limit growth or productivity. Additionally, high concentrations of even benign nutrients such as certain amino acids and even glucose can inhibit initial cell growth, particularly when inoculation densities are low. Furthermore, as each component is added to the media at ever higher concentrations, the increasing osmolality of the medium also becomes a constraining factor since mammalian cells will only grow in a narrow range of osmotic strength [4] and will produce proteins only in a slightly wider range of osmotic strength than they will grow [5].
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Innovative cell culture scientists realized decades ago that while cells consume certain nutrients, and these must be provided to continue growth and protein expres­sion, components such as salts and other ions in many cases are not appreciably depleted during the course of growth, even when reaching very high cell densities. As mammalian cells are limited in their tolerance of osmotic strength, the ability to further fortify media is also limited. It was realized that much of the excess salts could be removed from the “classical” cell culture media that were designed for low density cell culture back in the 1960s and 1970s. Somewhat surprisingly, some mammalian cells seem to be able to adapt to ion concentrations of sodium and potassium well outside of the physiological concentration range observed within the body of any mammal in existence, despite what one might have learned in a course on cellular physiology!
The removal of these salts supplied signicant osmotic “space” for the supple­mentation of amino acids and additional glucose. Provided such parameters as pH and dissolved oxygen (DO) were controlled, adding these nutrients “up front” in the cell culture medium allowed cell cultures to reach much higher cell densities with­out any feeds being required. Of course, cell culture scientists were never satised with those cell densities either and after optimizing cell culture processes with high nutrient content basal media the scientists also began again to include concentrated nutrient feeds in their processes.
4.2.2 Fed-Batch
Fed-batch cell culture processes add the key components that cells need to continue to grow and produce protein, principally glucose and amino acids. It is sometimes useful to think of a mammalian cell in culture as a polymerization catalyst. In essence, the only important purpose that all mammalian cells serve in an industrial protein production process is to string together amino acids (the monomers) into long chains that fold into proteins (the polymer). Of course, N- and O-linked glyco­sylation also occurs, but as a fraction of the mass of a therapeutic polypeptide, these are minor reactions by comparison for most proteins. For an efcient fed-batch process with discrete occasional bolus feeds and little waste products being formed, it is quite possible over the course of only 5–10 hours to detect a signicant decline of osmotic strength. This can easily be observed by running frequent samples on a freezing-point osmometer. The phenomenon occurs because the monomer amino acids are being added to large polypeptides with such high molecular weights that their accumulation to even multi-gram/liter concentrations has a negligible inu­ence on the osmotic strength of the culture. As cultures become ever more produc­tive with very high cell densities, it is sometimes no longer practical to add nutrients to the culture as discrete bolus feeds because even once daily feeds can start to impart a signicant osmotic shock of more than 30–70mOsm/kg. Frequent osmotic shocks of such magnitude may become detrimental to the health of the culture and may contribute to amino acid misincorporation should the level of any particular
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amino acid fall too low between bolus feeds [6]. In such cases, a continuous or semi-continuous feeding system may be required.
With a highly efcient fed-batch cell culture process, it is quite feasible to feed the equivalent of 400–700mOsm/kg of feeds over the course of 10–18days. With such a process, feeds must be quite concentrated in order to minimize the total vol­ume of liquid added to the culture. Many industrial-scale bioreactors have limits on the total volume that can be fed due to the placement of mixing impellers and the desire not to transition the liquid level through this zone of increased shear with its ensuing potential for increased foam formation. The science (or art!) of preparing very concentrated feed mixtures often relies on the careful order of addition of chemicals, manipulation of pH (up and down) and temperature, and separate prepa­ration of certain concentrated solutions before addition to the bulk feed mixture. In some cases, it may even be necessary or efcient to separate the components into multiple distinct feeds that might not be sufciently stable together in a single solu­tion. Furthermore, the pH manipulations often necessary to get all the components into solution will in turn introduce additional ions to the solution that are not con­sumed by the cells. Such ions, sodium and chloride being the most common of these, will ultimately accumulate in the culture. Some fed-batch culture processes then also need to manage the accumulation of these ions and other cell-produced waste products that might not be toxic in and of themselves, but do contribute to the continuous slow increase in the osmotic strength of the culture until the high osmotic strength itself becomes detrimental to cell health and productivity. While probably not yet necessary for the vast majority of fed-batch cultures, our laboratory, in con­sultation with drug product formulation experts, has also experimented with the lyophilization and even sterile spray-drying of cell culture feed media. Lyophilization was found to be largely impractical due to the amounts of high osmotic strength excipients that need to be added to facilitate stable cake formation. Aseptic spray drying, however, was found to produce a very stable and incredibly fast dissolving, uniform particle size powder that can be added directly to the surface of a produc­tion bioreactor. Naturally, methods of addition of an aseptic dry powder to the liquid surface of a bioreactor would then need to be worked out before practical imple­mentation. Should much higher efciency cell lines and cell culture processes be developed in the future, dry feeds might inevitably increase overall bioreactor pro­ductivity by minimizing culture volume increases.
Thus far we have only discussed the requirement to add nutrients to the cell cul­ture. Simultaneously, of course, cells in culture are producing certain waste prod­ucts. Cells in culture undoubtedly lack the life-supporting systems that a whole organism enjoys. Individual cells in culture cannot control glucose levels, remove and process most metabolic waste products, or manage pH, dissolved oxygen, car­bon dioxide, or temperature. Most of these parameters are reasonably easily con­trolled to the degree necessary by basic bioreactor operations that have been in existence for decades. The removal of waste products, however, is not so simple; think of the complexity of chemical processes occurring in the kidney or liver of an intact mammal. We will discuss in more detail methods to reduce the formation of waste products in a later section on control of cellular metabolism. Clearly however,
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for the state-of-the-art fed-batch process today, the buildup of waste products is the most important factor that ultimately limits the productivity of the fed-batch mode of operations.
4.2.3 Perfusion—Or theSolution toPollution Is Dilution!
When it becomes difcult to either add sufcient nutrients to a culture, or control the level of inhibitory metabolic by-products, or merely control the ever-increasing osmotic strength of the culture, many cell culture scientists have resorted to perfu­sion. Perfusion culture solves all of these problems simultaneously, depending upon how it is implemented and is somewhat analogous to the processes that occur for cells within an organ in the body. In an animal’s body, the cells in an organ do not exit the organ but are continuously supplied with nutrients and have waste products washed away by virtue of the blood supply.
In perhaps its most widely used and recognized form, perfusion cell culture uti­lizes a device to maintain all, or nearly all cells within the bioreactor (a lter or other cell retention device), while nutrient medium (perfusion medium) ows in and out of the bioreactor and thus the bioreactor maintains a constant volume.
Many early cell culture processes produced key enzymes or blood factors miss­ing in small populations of humans due to genetic abnormalities. These proteins tended to be susceptible to biochemical or enzymatic breakdown or form high molecular weight aggregates under cell culture conditions, and therefore it was advantageous to produce them by perfusion culture. In perfusion culture the average residence time in the bioreactor of the newly secreted protein could be controlled and reduced to a few days or even a few hours if necessary. Early perfusion mam­malian cultures often used cells grown on microcarriers or immobilized between the bers of a microltration hollow-ber bioreactor. Freely suspended cells are inher­ently easier to scale up but are more difcult to separate from uid leaving a biore­actor. After the “low hanging fruit” products of the nascent biotechnology industry were developed and supplied for clinical use (e.g., enzymes and blood component replacements), many companies started to produce protein therapeutics (antibodies and fusion proteins) that were more stable in the cell culture bioreactor environ­ment. Additionally, scientists became better at providing nutrients or controlling waste product formation in a batch or fed-batch format, and perfusion processes seemed to fall out of favor for a time in the 1990s and early 2000s. Eventually how­ever, as the inherent limitations of fed-batch culture mentioned before were reached, and better designed methods for cell retention became commercially available, the bioprocessing community exhibited a resurgence of interest in the process intensi­cation capabilities afforded by perfusion.
There have been a large number of clever devices designed as cell retention sys­tems [7], but the more commonly utilized today consist of external-to-the- bioreactor microltration membranes, principally hollow-ber ltration devices for scales up to about 1000 L, and tangential ow ltration devices in a stacked plate
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conguration (Prostak™) for larger bioreactors. Cells are recirculated at consider­able owrates through the tube side of these ltration cartridges, or through the open channels of the stacked plate systems, by several different forms of low-shear pumps (tangential ow ltration). Compared with batch or fed-batch processes, per­fusion processes can reach much higher cell densities. Provided sufcient oxygen transfer into and carbon dioxide removal from the culture can be maintained, it is possible in perfusion cultures to come very close to the theoretical maximum cell density which would approximate close packed spheres [8]. Such very high cell densities, and the corresponding productivities that can be achieved, are primarily possible because of the capacity of waste product removal that perfusion can pro­vide. Even with a poorly designed perfusion process, using low nutrient content media and conditions that do not reduce the formation of cell-produced inhibitory metabolic by-products, extremely high cell densities are possible if sufcient cell retention capacity is available (i.e., high ltration area). As mentioned earlier, near close packed spheres or tissue density is possible provided one is willing to use vast quantities of perfusion media and the viscosities of the resulting culture do not overly inhibit the recirculation of the uid though any cell retention device. Perfusion systems that recirculate culture using diaphragm pumps may be constrained in this regard because vacuum (negative 14.7 psig, or ~1bar) is the maximum driving force they can provide for moving the culture into the hollow-ber ltration device unless the bioreactor itself was under pressure (difcult for single-use vessels) [8].
It should be mentioned that reliable sterilization of large external microltration devices for cell retention can sometimes be problematic. Precise protocols must be established and strictly adhered to for cleaning and steam sterilization of stacked plate systems. The advent of gamma-irradiated, pre-sterilized hollow ber devices has simplied and increased the success rate of moderate scale perfusion, but ster­ilization by radiation may not be feasible for very large hollow ber cartridges.
4.2.4 Hybrid Processes
Our laboratory introduced the concept of “hybrid perfusion fed-batch” for CHO cell culture several years back [9]. This mode of operation uses several days of 100% cell retention perfusion (the perfusate is discarded) followed by several days of conventional fed-batch operations culminating in a single drug substance harvest. Utilizing perfusion at the optimal time and performing it in a manner that mini­mized the volumes of media required, we were able to boost the overall productivity of a number of cell lines/processes to more than double that achieved in optimized fed-batch processes without increasing the length of the processes. Additionally, since the perfusion only occurs for a short time at the beginning of the culture when the cells are at very high viability, the surface area of the cell retention membrane can be minimized. Because the early perfusate was discarded in such a process, and the cell densities reached could be very high, we hypothesized at the time that such a process could also theoretically be used for moderately labile proteins since the
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fed-batch portion of the process could be as short as 2–3days, yet produce product titers in the 3–6g/L range. Finally, the perfusion volumes needed for such a process were quite reasonable at between 1 and 2 reactor volumes total for the perfusion portion of the operation.
One of the essential features of this hybrid process, and many intensied cell culture processes, is the concept of maximizing integrated viable cell density (IVCD). IVCD in units of cells * time/volume is a term that is dened very simply as the area under a graph of the viable cell density versus time for any process. If we assume for a moment that the per cell, or specic productivity (picograms/cell/day) of any cell line remains relatively constant if we can provide healthy culture condi­tions, we can quickly see that any increase in the IVCD directly leads to a propor­tional increase in overall culture productivity.
Part of the reason the hybrid perfusion fed-batch process worked well with mini­mal development effort is likely due to a phenomenon of cell division that might be called “division momentum.” If at the beginning of the culture conditions are main­tained sufciently favorable, for instance with a nearly constant cell-specic perfu­sion rate (commonly in picoliters/cell/day), cells will continue to divide near their exponential growth rate. When the perfusion is suddenly stopped, the cell division does not stop immediately, likely because a fraction of cells at any point are already “committed” to cell division due to their instantaneous position in the cell cycle. Additionally, it likely takes a day or so of fed-batch conditions to accumulate the metabolic by-products to levels that inhibit further growth. Because of this phenom­enon, if sufcient nutrients are made available through appropriate timed additions of highly concentrated feed media, an additional near doubling of cell density can occur on the days immediately following the termination of perfusion.
While generally the loss of product to the perfusion stream at the beginning of the hybrid perfusion fed-batch process is a small fraction of the total produced over the time in culture, an ultra-ltration membrane of the appropriate molecular weight cutoff to retain protein in the bioreactor could be used in place of the more com­monly used micro-ltration membranes for cell retention. Such a replacement would result in near 100% capture of all protein produced during the process [10].
4.2.5 Concentrated Fed-Batch or Perfusion withUltraltration
A fed-batch process or the hybrid process described above inherently terminates with a discrete, single harvest. There are of course advantages and disadvantages to a single harvest when it comes to sizing and efciency of the downstream purica­tion process. Perfusion processes, as mentioned previously, are oftentimes used with labile proteins because of the necessity of quickly purifying the protein away from the cell culture uid. Fed-batch processes are limited by the volume of feeds possible before the bioreactor reaches its maximum working volume, and there are signicant disadvantages in taking a partial harvest prior to the end of the culture. In instances of lower productivity of stable proteins, there may be value in performing