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Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5608_Библиотеки_им_академика_М_И_Перельмана.pdf
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80
G. W. Hiller
100% cell retention perfusion with the use of an ultraltration (UF) membrane of the appropriate molecular weight cutoff. In such a process (also called concentrated fed-batch) no, or very little, protein product or cells leave in the permeate that exits the system. Oftentimes such a process will operate at around 1 vessel volume per day (VVD) rate of continuous or semi-continuous perfusion. Since waste products are removed and nutrients are easily provided in the perfusion media, very high cell densities can be achieved, and culture duration can be longer than a typical fed­batch. Because of the very high cell densities achieved (commonly greater than one-quarter by volume cells), care must be taken in considering the volume of the cells in the nal calculation of productivity of such a culture as there is no signi­cant product typically recovered from the cell’s cytoplasm. Such a concentrated fed-batch process typically ends in a single discrete harvest, although there may be value in minimizing the size of the downstream process by taking several smaller, discrete harvests towards the end of the culture.
Other variants on this process include the alternating use of two different forms of cell retention device for the perfusion: one being microltration (MF) and the other ultraltration (UF). When the UF lter is used, no product comes out of the bioreactor with the exiting perfusion medium and protein product builds up in the bioreactor. The MF lter is then used for the perfusion when a harvest is desired as it allows the protein to ow across the membrane. Thus, it is possible to switch back and forth between the two forms of cell retention device and even use different per­fusion rates, on alternate days as desired, taking harvests whenever might be most appropriate for the downstream process that is designed [11].
4.2.6 Intensication ofClassical Perfusion
Many of the continuous perfusion processes developed over the past several decades have attempted to achieve a steady-state operation. Possibly because many of the cell culture scientists working in the industry were originally classically trained chemical engineers, there has long been a fondness for the type of steady-state con­tinuous (and highly efcient) process that is very common in the petroleum rening industry. The problem with this approach, however, is that cells have a certain amount of “memory” for what they have seen before [12]. Unlike hydrocarbons, they do not necessarily immediately revert to the same behavior when placed under the same conditions as had previously been encountered. Minor perturbations in culture can sometimes lead to instabilities in the process that can be difcult to predict, reliably prevent, or easily recover from. Additionally, increasing metabolic efciency as nutrient levels drop below certain critical levels can cause cell densities to slowly increase and also slow the progress towards a steady-state condition.
Ideally, perfusion culture process development is performed in a fairly standard manner. There is an initial decision made perhaps on ideal maximal cell density that can be sustained by the bioreactor system, or some productivity target is used. A decision is also commonly made as to the practical perfusion rate that can be
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maintained. That perfusion rate is typically in the 1–2 VVD range, but ideally should always try to be minimized due to the costs and logistics of supplying the massive amounts of liquid media that will need to be continuously available during the process.
A somewhat conventional cell culture perfusion process then starts usually with a day or so of batch growth, followed by a slow ramp up of the perfusion rate to match the rate of growth of cells. This is the concept of a xed cell-specic perfu­sion rate used at least during the expansion phase to maintain cells in exponential growth in order to increase the cell density in the bioreactor as quickly as possible (maximize the IVCD). Once the peak perfusion rate chosen is reached, if no other interventions are taken the cell density will typically peak at a very high and poten­tially unsustainable cell density and subsequently signicant cell death will occur. Provided perfusion media with a sufcient nutrient concentration is used, and other standard cell culture parameters are controlled (pH, DO, etc.), the cell death is usu­ally due to waste product accumulation. If the perfusion continues long enough in this theoretical perfusion process, eventually the bioreactor would be a solid mass of dead or dying cells.
Just as a bleed of inert materials is required in many continuous industrial chemi­cal processes, so too is a cell bleed required in most cell culture perfusion processes to reach a “steady-state.” Perfusion processes commonly use cell bleeds of 5–20% of the bioreactor volume per day. The cell bleed does not usually distinguish between live and dead cells and is taken directly from the bulk of the cell culture bioreactor. Sometimes the cell bleed rate will be varied and used to directly control the sustained viable cell density of the bioreactor. This can be achieved with ofine cell counts and manual manipulations of the cell bleed, or some method of continu­ous online measurement or approximation of cell mass (commonly using capaci­tance probes) and a continuous computer-controlled variable cell bleed.
Because different downstream operating conditions/unit operations and poten­tially an entirely different downstream process would be required, most perfusion processes do not attempt to purify protein product from the cell bleed as this cell­containing stream is different from that in the cell-free permeate coming through the main cell-retention lter. Thus, the cell bleed represents a continuous loss of prod­uct and attempts to minimize the necessary cell bleed are typically a signicant effort during process development [13]. As an example, if the perfusion rate was 1 VVD and the cell bleed rate was 20% per day (or 0.2 VVD), the loss of product would be close to 20% (potentially less since the cells will occupy a fraction of the volume). However, there is another phenomenon at play that very often signicantly increases the product loss in the cell bleed far above what would be estimated merely using volume ratios. When MF cell retention membranes begin to plug with cellular debris, they start to slowly transform into UF membranes with a continu­ously changing (decreasing) molecular weight cutoff. When this molecular weight cutoff gets low enough, product protein is concentrated in the bioreactor and the cell bleed can become a much larger source of product loss.
If a therapeutic protein-producing cell line is sufciently stable both with respect to its cellular productivity and its phenotypic nature, a steady-state perfusion
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process with an appropriate cell bleed might be able to operate continuously for weeks or even months [14]. The efciency of such long-term operations can be very high and the exibility of running a process as long as necessary to produce the required amount of protein is desirable. However, proving the stability and consis­tency of a very long duration process for validation or process characterization pur­poses can be daunting. As mentioned in the previous paragraph, it is desirable to minimize the required cell bleed in a continuous steady-state, or one might say “sustainable,” perfusion process. The cell bleed is usually used to control the viable cell density at some predetermined value. In such a process where the viable cell density is not changing, there is a balance between the fraction of viable cells con­tinuously dying, the new viable cells being created by division, and the viable cells that are leaving the system in the cell bleed. The number of cells dying is usually small compared to the division rate and thus the cell bleed rate is nearly equivalent to the growth rate.
While not rigidly true for all mammalian cell processes, it is generally accepted and observed that high growth rates are usually linked to lower per cell, or specic productivity rates [15]. When cells are focusing their metabolic precursors and cel­lular energy on biomass production (division), rates of recombinant protein produc­tion are generally lower. This is part of the reason that in fed-batch cultures the majority of protein production occurs in the last several days of the batch after most division is complete, and the cell density is much higher than earlier in the culture. So, these two constraints are actually somewhat synergistic. Minimizing the cell bleed once the target steady-state cell density is reached can minimize product losses, and simultaneously maintaining a lower cellular growth rate can help keep per cell productivity high. Low cell growth rate=low cell bleed rate. By increasing the nutrient content of the perfusion media and checking the culture for residual nutrient levels occasionally, one can ensure that sufcient nutrients are always avail­able to the cells [16]. In this case then the growth rate of cells in a perfusion culture is directly controlled by the rate of removal of metabolic wastes and other inhibitors of cell division. Lower perfusion rates lead to more accumulation of inhibitors of cell growth which ultimately leads to lower cellular growth rates. A slow reduction in perfusion rate during process development can then lead to a slow reduction in growth rate, increased productivity and reduced medium usage. However, the dif­culty of continuously decreasing the perfusion rate (while increasing the available nutrients in that perfusion medium) is that the most signicant benets in per cell productivity tend to come at very low growth rates which may be difcult to main­tain [17]. A minor process deviation, even one that might not be readily detectable, might be sufcient to push cells into a no-growth state, out of the steady-state condi­tion, and result in a culture with a changing and decreasing cell density. Additionally, mammalian cells in culture are continuously undergoing slight epigenetic changes as they continuously adapt to environmental factors [18], making their long-term responses to culture conditions slightly unpredictable.
For many of the reasons stated in the previous paragraph, while a sustainable, or true steady-state perfusion process has many advantages, there are considerable challenges in the design and operation of such a process with a high cell-specic
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productivity. To add to the difculty, the low cellular growth rates that are usually encountered in such a process also result in more fragile cells which are oftentimes less capable of withstanding the shear stresses that may be encountered in the cell retention system [19]. The additional shear death results in additional cellular debris/small particles which more quickly plug the small pores of most membrane­based cell retention devices, complicating scale up since ever larger surface areas, or frequent change outs of the cell retention membrane are ultimately required.
4.2.7 Dynamic Perfusion Processes
In an effort to solve some of the undesirable features of “sustainable” or steady-state perfusion, various groups in recent years have been experimenting with a more dynamic perfusion process in which cell densities, perfusion rates, and most culture conditions are expected to change during the process [8, 17, 20]. Since the goal of attaining steady state is abandoned, the cell bleed is entirely eliminated. Cell den­sity, however, still reaches some controlled peak, but that peak is typically deter­mined by the timing of the start of perfusion, how long and at what rates the perfusion is performed, and the nature of the medium or solutions used for the per­fusion. Again, the goal is to never limit the culture for nutrient availability, but also accept that growth inhibitory metabolic by-products are accumulating and will eventually slow and ultimately halt cell division in a manner analogous to that which occurs towards the end of a fed-batch process.
The initial goal of such a dynamic perfusion process is identical to that of a con­ventional perfusion process: grow the cells to high cell density as quickly as possi­ble by using perfusion to remove waste products and supply nutrients. The approximate linear timeline of one such dynamic perfusion process developed in our laboratory, the high-intensity low-volume perfusion process (HILVOP) [17] is depicted in the gure below (Fig. 4.1). For the HILVOP dynamic perfusion process, perfusion starts within a day or so of inoculation depending upon the inoculation density. This initial perfusion phase (the rst stage) is generally conducted as a continuous increase in perfusion rate that closely matches the increase in cell den­sity (therefore a nearly constant cell-specic perfusion rate). Since the product con­centration in the permeate at this stage is quite low, generally the perfusate is sent to
Fig. 4.1 Stages of perfusion
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waste. Our laboratory developed a unique method of “cell-controlled” perfusion that can be utilized in this rst stage of perfusion that minimizes the overall require­ments for perfusion volumes by eliminating the net production of lactic acid [9]. The perfusion control method also does not require constant counting or estimation of the viable cell density, but still maintains a nearly constant cell-specic perfusion rate (picoliters/cell/day) allowing for the maintenance of a nearly exponential growth rate. More details on cell-controlled perfusion will be discussed in the sec­tion on metabolism.
During the second stage of perfusion, the goal of the perfusion is no longer to maintain exponential growth, but mainly to supply the cells with nutrients for the production of the recombinant protein and for any additional cellular division. Since we are no longer attempting to dilute out inhibitory compounds, the perfusion media used during the rst part of the second stage of perfusion is extremely concentrated, perhaps over 700mM amino acids combined with additional nutrients. However, since the cell density is so high, and the cells so metabolically active, the osmotic strength in the bioreactor does not rise much above the normal physiological range even while delivering the perfusion media at the relatively low rate of around
0.2–0.3 VVDs.
Even if lactic acid is well controlled at this point in the culture (during the begin­ning of the second stage), other cell-produced metabolic by-products quickly accu­mulate, and division slows as the cells reach their peak cell density. The length of time the perfusion continues in the rst stage controls the ultimate trajectory and peak viable cell density eventually achieved later in the culture. In approximately the second half of the second stage of perfusion, the perfusion rate is slowly ramped up by adding an ever-larger fraction of a saline diluent to the perfusion medium. Cellular division does not resume, but the large volumes of saline ushing the bio­reactor facilitate the transport of the majority of the produced protein out of the bioreactor/cell retention system and into the downstream process. If a continuous downstream process is integrated directly with the upstream process, then the ramp up of saline delivery to the bioreactor can be used to help control the mass per day of product delivered to the downstream operation. Keeping the mass/day within a fairly narrow range allows for the protein A capture chromatography columns and the other associated columns and equipment throughout the purication train to be much smaller than would typically be needed with a fed-batch process. Such an integrated downstream and upstream process utilizing a pair of protein A columns operated in a simple bind and elute manner allows for highly efcient column utili­zation, achieving two to six column cycles per day and 40–80cycles over the course of a 14–18-day dynamic perfusion process.
Our laboratory has found that this dynamic perfusion/HILVOP process achieves specic productivity (per cell) rates near that of an optimized fed-batch process and signicantly higher than sustainable perfusion processes that we have explored for several cell lines [17]. The overall volumes of perfusion media used are moderate and signicantly lower than most sustainable “steady-state” perfusion processes. Because the cell density is much higher than fed-batch and the specic productivity (picograms/cell/day) is usually similar to a fed batch, the overall volumetric
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productivity of the process is also increased proportionally, typically three to four­fold higher than an optimized fed-batch process.
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4.3 Pragmatic Control ofCellular Metabolism
When in a highly proliferative state and therefore dividing quickly, most mamma­lian cell lines in exvivo culture tend to exhibit some degree of “aerobic glycolysis,” meaning that in spite of readily available oxygen, cells shift to metabolize signi­cant amounts of glucose directly to lactic acid [21]. This metabolic state may have advantages during fast growth as large amounts of various biochemicals may be drawn off from the glycolytic pathway for the production of needed precursors of DNA, RNA, lipids or other cellular building blocks required for accelerated bio­mass production. One can imagine that in tumorigenic growth, there would be sig­nicant competitive advantages to fast growth in that the tumor cells themselves do not have to trouble with the lactic acid produced as it is merely carried away to other tissues, including liver and muscle, by the nearly endless supply of fresh blood pro­vided by the host organism.
In ask or bioreactor culture however, without some form of pH control, the rapid buildup of lactic acid oftentimes drives pH quickly below that at which the cells can continue fast division (6.3–6.8) [22]. Employing pH control via the addi­tion of a base titrant to the culture tied to a continuous pH measurement effectively restores growth. In some cultures, however, even with pH control the production of lactic acid is so signicant that the lactate ion accumulates to an extent that eventu­ally the culture growth stops due to both the level of lactate ion and the accumula­tion of osmolality from the lactate ion in addition to the sodium or potassium counter ions from the base titrant [23].
4.3.1 The Development ofpH or Temperature Shifts
In a batch or fed-batch process, any ion added to the culture or chemical that is produced by the cells accumulates in the culture unless it is later taken up by the cells or degraded via some extracellular chemical or enzymatic process. Within the normal pH operating ranges of a bioreactor (6.9–7.2), lactic acid output by cells in culture is usually directly proportional to the pH of the culture [22]. To an extent, higher pH (up to about 7.3) may result in faster cell growth, but also result in higher rates of lactic acid production, and therefore lactate accumulation. To control lactic acid production rates, some researchers have found it advantageous early in the culture to reduce the pH control set point closer to neutral or slightly lower pH [22,
24, 25]. While such a practice might slow cell growth, the slower accumulation of
lactate sometimes allows the growth phase to be extended longer, resulting ulti­mately in a higher IVCD, or at a minimum a healthier biomass than would have
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been achieved with a higher pH set point. It was also discovered that while culture temperatures below the normal mammalian body temperature of about 37°C slow cellular division, sometimes a decrease in temperature several degrees below 37°C (30–35°C) at the optimum time will also slow or even completely stop the net pro­duction of lactic acid [24, 26].
When culture conditions are sufciently conducive, it is even possible for cells to begin to take up lactate from the bulk culture uid. This usually occurs several days into a batch or fed-batch culture when cell growth has slowed and some signi­cant amount of lactate has formed [27]. Sometimes facilitated by decreasing culture temperature below 37°C, when this “metabolic shift” occurs the lactate is taken up from the culture in the form of lactic acid, and the uptake rate can be rapid enough to be detected by an increase in bulk culture pH by conventional pH probes. Under such conditions lactate in the culture can sometimes be consumed down to nearly undetectable levels. It should be noted, however, that while the cells can effectively completely consume the lactate ion from the culture, sodium or potassium ions also were entering the culture as a result of the use of the base titrant to control the pH near neutrality early in the culture. These sodium or potassium ions are not appre­ciably consumed by the cells and therefore contribute to the osmotic strength (the gift that keeps on giving!) of the culture in what might be called the “base titrant ion penalty.” In some cases, so much lactate is produced early in culture that when the lactate is consumed as lactic acid, it can actually drive the pH so high (>7.4) that some processes add pH control on the high end by sparging gaseous carbon dioxide (sometimes leading to its own problems) [28] or other forms of acid (phos­phoric, etc.).
4.3.2 Glucose Limitation
Uptake of lactic acid by mammalian cells, or at a minimum a lactic acid production rate of zero, also can occur when the level of glucose in the culture drops below about 2–3mM, but the exact threshold where this occurs might be quite variable. This phenomenon was recognized several decades ago, oftentimes in continuous cultures (chemostats) [22], or perfusion cultures [29] in which the glucose concen­tration would slowly decrease but cells had time to adapt to the conditions, and there was always a low, but continuous rate of glucose addition. Some researchers attempted to determine the precise, optimal glucose level to maintain during culture in order to prevent lactate production, but also to not overly starve the cells and slow proliferation [30, 31]. Others resorted to very frequent glucose measurement via ofine analytical instruments and then sophisticated control algorithms to attempt to keep the glucose at the precise level thought to be ideal [32]. Another experimen­tal feedback control method for glucose delivery was based on the continuous mea­surement of oxygen uptake rate [33]. If the oxygen uptake rate dropped, additional glucose containing feed was added as it was assumed cells had depleted the avail­able glucose.
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While these techniques proved to be moderately successful in controlling the lactate production in a research environment at the bench scale, frequent sampling and accurate glucose quantitation at very low levels, combined with precise feeding of glucose, were generally considered to be too difcult to implement in large-scale commercial bioreactor operations [34]. Additionally, while cultures were actively growing, the length of time between sampling, accurate determination of the glu­cose level, and then a change in the glucose feeding rate may have been too long. Likely this resulted in some level of continuous glucose starvation which resulted in sub-optimal growth rates when compared with non-glucose limited cells.
Other groups have experimented with alternative carbon sources to glucose such as galactose, fructose, or mannose, but while those substitutions often do reduce the formation of lactate it is usually at the expense of fast growth rates and results in considerably reduced peak cell densities [3538]. Additional researchers tried to slow the rate of six-carbon sugar membrane transport with chemical inhibitors or genetic engineering techniques such as amplication, suppression, addition, or silencing of enzymes or substrate membrane transporters [3941]. Because in most cases the cells eventually reverted to their original wild-type metabolism, practical success with these techniques was not achieved.
Experimentation in our laboratory with additions of galactose to CHO cell cul­tures in the presence and absence of glucose lead us to the conclusion that in the presence of glucose, galactose might be competing for available membrane trans­porters and potentially slowing the transport of glucose across the cell membrane [23]. At that point we decided to investigate other methodologies to achieve a slow glucose uptake rate without slowing cellular growth rates.
4.3.3 The Development ofHiPDOG Control Methodology
After experiments in our laboratory demonstrated that the accumulation of lactate in our CHO cell fed-batch cultures was the primary factor suppressing continued cell division and productivity [23], we built on controlled glucose feeding experiments conducted earlier [25]. After realizing that the uptake of lactic acid from the bulk culture uid was sufcient to result in a signicant rise in pH detectable by conven­tional in-situ pH probes, we developed a feedback control system for lactate that would prove to be easy to manage and implement even in the largest bioreactors in common use (13,000L) in our production facilities. It was discovered that cells in culture would “signal” a low level of glucose in the bulk culture by taking up lactic acid from the surrounding culture uid. The switch to consumption of lactic acid was fast enough and of sufcient magnitude that the bulk culture increase in pH was enough to trigger a feed pump to add a small amount of glucose to the culture before the cells were overly starved for glucose. Starting with a low level of glucose in the initial medium in the production bioreactor, this control loop strategy, later given the acronym HiPDOG, for Hi-end pH delivery of glucose (shown as a hypothesized sequence of events in Fig.4.2 below) would then turn on and off the glucose feed
88
Fig. 4.2 HiPDOG sequence of events
G. W. Hiller
pump periodically throughout the growth phase of the culture. Somewhat surpris­ingly, with a sufciently tuned system, the growth rate of a fed-batch culture utiliz­ing the HiPDOG control strategy was found to be nearly identical to that of parallel cultures which never experienced glucose limitation. The net effect of the glucose/ lactic acid control scheme resulted in zero net lactic acid formation during the growth phase once the control system rst activated as the glucose concentration rst fell into a limiting range. Additionally, since little to no titrant is added in such a process, the “base titrant ion penalty” mentioned above never occurs.
One would expect that if the HiPDOG control strategy worked as simply as explained above (lactic acid produced, then almost immediately consumed again, ion for ion), when operating in a fed-batch culture there would be a very slow decrease in the lactate level of the bioreactor as the culture was slightly diluted by the glucose solution, or other feeds. However, it was found during experimentation that the rate of decrease of the culture’s lactate concentration was actually signicantly faster than could be accounted for by dilution alone. It was hypothesized and later con­rmed by additional experiments that CHO cells in a highly proliferative state are producing many other by-products of metabolism, albeit at lower levels, a signicant fraction of which are acidic in nature [42]. As these acids are secreted into the culture medium, they depress the culture pH slightly and result in a partial decoupling of the predominant glucose/lactic acid pH control and thereby slightly over-limit the cells for glucose, resulting in a slow reduction in the concentration of lactate in the culture.
Because a rapidly expanding fed-batch culture requires many other nutrients, it was found to be useful to also include these nutrients in the glucose feed being delivered by the HiPDOG control scheme. In this way, cells in a fed-batch culture would precisely control their own rate of feeding without any operator intervention. The amount of nutrients delivered would of course depend upon the glucose con­centration in the feed since only the delivery of glucose was actually being con­trolled by the culture. The higher the concentration of glucose in the feed, the less volume of feed that would be delivered, and vice-versa. Finding the right ratio of glucose to other nutrients allowed for an optimum delivery rate to the culture, main­taining all amino acids and other components above growth limiting concentrations, yet not leading to excess accumulation which could lead to toxicity, excess ammo­nium production if amino acids were used as a carbon source, or merely high osmotic strength.
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The HiPDOG control scheme was found to be widely applicable to most CHO cell lines that produced even modest amounts of lactic acid, and particularly valu­able for those with inherent high levels of lactic acid production. Many cell lines grew to much higher peak cell densities and maintained higher specic productivi­ties even late in culture because of the reduced level of lactate that had accumulated in the culture. Additionally, when utilizing HiPDOG, cell lines in which the previ­ous practice had been to decrease the pH set point during the growth phase to mini­mize lactate formation could now be grown at whatever higher pH was found to be optimum to allow for faster accumulation of IVCD.
While accumulations of ammonium ion can sometimes limit growth in CHO fed­batch cultures, oftentimes with HiPDOG controlling lactate (particularly with cell lines utilizing the glutamine synthetase expression system), growth inhibitory con­centrations of ammonium are not reached [42]. For expression systems that utilize glutamine in the cell culture media, limiting its availability in the production biore­actor with a lower starting concentration, or substituting the majority of it with a glutamine-alanine dipeptide, or asparagine, glutamate, or aspartate can help to limit the accumulation of ammonia [4345]. Glutamate and aspartate may be preferred in some cases over asparagine as these two amino acids only contribute one amine group if the carbon skeleton of the amino acid is utilized by the cells as an energy source.
Even when lactic acid and ammonia production are well controlled, cells still eventually cease division even if all necessary nutrients are available and the osmotic strength of the culture is not in a growth-inhibitory range. Other metabolic by­products accumulate in these cultures and eventually reach growth inhibitory levels after many days in culture [42]. As growth slows in this environment, it is generally no longer necessary to utilize the HiPDOG control scheme and the culture can be allowed to return to a non-glucose limited state for the remainder (usually the last half) of the culture. After working with dozens of cell lines, our lab was never able to detect any problematic features of the product quality (of particular concern was glycosylation) of protein produced during the HIPDOG phase of a culture. Additionally, since the vast majority of the recombinant protein product in a fed­batch process is produced late in culture when glucose was no longer limiting, this theoretical concern was further minimized. In many cases, the improved health of the culture as a whole when using HiPDOG resulted in superior product quality for many programs.
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4.3.4 Extension ofControlled Glucose Limitation
toPerfusion Cultures
As mentioned in the above sections, even in a very carefully fed culture with meth­ods to minimize lactic acid and ammonia production being utilized, eventually a variety of other growth-inhibitory metabolic by-products will accumulate which slow and eventually stop cellular division. The logical progression of CHO cell