U.S. patent application number 14/309308 was filed with the patent office on 2014-10-09 for methods for enhanced protein production.
The applicant listed for this patent is MEDAREX, L.L.C.. Invention is credited to Alahari Arunakumari, Xiao-Ping Dai, Javier Garcia, Richard P. Martel.
Application Number | 20140302581 14/309308 |
Document ID | / |
Family ID | 43480207 |
Filed Date | 2014-10-09 |
United States Patent
Application |
20140302581 |
Kind Code |
A1 |
Arunakumari; Alahari ; et
al. |
October 9, 2014 |
METHODS FOR ENHANCED PROTEIN PRODUCTION
Abstract
The present invention provides a method of increasing protein
production in a cell culture by growing cells that produce the
protein (e.g., the growth phase) in a perfusion cell culture to a
high cell density (i.e., at least above about 40.times.10.sup.6
cells/mL) and then switching to a protein production phase, wherein
the cells are cultured in a fed-batch cell culture. The present
invention further provides a method for clarifying a protein from a
cell culture by adjusting the pH of the cell culture to below
neutral pH (i.e., below a pH of 7) and settling the cell culture,
such that the cell culture separates to form a supernatant layer
and a cell-bed layer, wherein the protein is in the supernatant
layer.
Inventors: |
Arunakumari; Alahari;
(Pennington, NJ) ; Dai; Xiao-Ping; (Flemington,
NJ) ; Garcia; Javier; (Palmerton, NJ) ;
Martel; Richard P.; (Allentown, PA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
MEDAREX, L.L.C. |
Princeton |
NJ |
US |
|
|
Family ID: |
43480207 |
Appl. No.: |
14/309308 |
Filed: |
June 19, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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13510372 |
Jun 14, 2012 |
8765415 |
|
|
PCT/US2010/056924 |
Nov 17, 2010 |
|
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14309308 |
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61261886 |
Nov 17, 2009 |
|
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Current U.S.
Class: |
435/183 ;
530/387.1; 530/387.3; 530/388.1; 530/388.15; 530/399; 530/418 |
Current CPC
Class: |
C07K 1/30 20130101; C07K
2317/14 20130101; C07K 16/00 20130101; C12P 21/00 20130101; C12N
1/02 20130101; C12P 21/02 20130101 |
Class at
Publication: |
435/183 ;
530/418; 530/387.1; 530/388.1; 530/388.15; 530/387.3; 530/399 |
International
Class: |
C07K 1/30 20060101
C07K001/30; C07K 16/00 20060101 C07K016/00 |
Claims
1. A method for clarifying a protein from a cell culture,
comprising: (A) adjusting the pH of the cell culture to below
neutral pH; and (B) settling the cell culture, such that the cell
culture separates to form a supernatant layer and a cell-bed layer,
wherein the protein is in the supernatant layer.
2. The method of claim 1, wherein the cell culture is settled for
at least 30 minutes.
3. The method of claim 1, wherein the cell culture is settled for
between 30 and 120 minutes.
4. The method of claim 1, wherein the pH is between 4 and 7.
5. The method of claim 4, wherein the pH of the buffer is
preferably at the same pH as that the cell settling was done.
6. The method of claim 1, wherein the cell culture is an animal
cell culture.
7. The method of claim 6, wherein the cell culture is a Chinese
Hamster Ovary (CHO) cell culture.
8. The method of claim 1, wherein the protein is an antibody.
9. The method of claim 8, wherein the antibody is a monoclonal
antibody.
10. The method of claim 9, wherein the monoclonal antibody is
selected from the group consisting of a human, humanized and
chimeric antibody.
11. The method of claim 1, wherein the protein is selected from the
group consisting of enzymes, receptors, fusion proteins, cytokines,
regulatory factors, hormones, antigen-binding agents, therapeutic
proteins, and diagnostic proteins.
Description
CROSS REFERENCE TO RELATED APPLICATION
[0001] This application is a divisional of U.S. application Ser.
No. 13/510,372, filed Jun. 14, 2012, which claims the benefit of
International Application No. PCT/U.S. 2010/056924, filed on Nov.
17, 2010, which claims the benefit of 61/261,886, filed Nov. 17,
2009, the entire contents of all of which are herein incorporated
by reference.
BACKGROUND OF THE INVENTION
[0002] Animal cell culture, particularly mammalian cell culture, is
commonly used for the expression of recombinantly produced proteins
for therapeutic, prophylactic and diagnostic purposes. Although
mammalian cell culture methods are preferred over microbial
expression systems (e.g., bacterial or yeast expression systems),
because they are better suited to express high molecular weight
proteins and proteins having complex steric structures, protein
expression levels from mammalian cell culture-based systems are
generally considerably lower than those from microbial expression
systems. While numerous approaches have tried to increase protein
expression from mammalian cell culture, these methods have been
deficient in optimizing conditions for cell growth, maintaining
high cell viability and producing large volumes of high quality
protein, thereby limiting their practical application in the
biopharmaceutical industry.
[0003] As such, there is a need in the art to develop improved
large-scale animal cell culture methods for producing and purifying
proteins (e.g., antibodies and antibody fragments, peptides,
enzymes, growth factors, hormones, interleukins, interferons, and
vaccines) to achieve reliable and cost-efficient protein production
at high yields.
SUMMARY OF THE INVENTION
[0004] In certain embodiments, the present invention provides
methods for increasing production of a protein in a cell culture by
growing cells that produce the protein in perfusion to a high cell
density (e.g., at least to above about 40.times.10.sup.6 cells/mL,
more preferably above about 60 to 80.times.10.sup.6 cells/mL, and
most preferably around about 100.times.10.sup.6 cells/mL), also
referred to herein as "super high density", then switching the cell
culture to fed-batch, such that the cells enter a high protein
production phase. The present invention is based, at least in part,
on the unexpected discovery that it is possible to grow cells in
culture to a much higher density than previously thought possible.
This, in turn, yields significantly more protein than is typically
produced using known cell culture techniques. Specifically, the
maximum cell density achieved using known cell cultures techniques
is generally thought to be limited by the presence of particular
levels of waste products (e.g., lactate, ammonium, etc.), since it
is known that such waste products can be toxic to cell growth when
they accumulate to critical concentrations (see, for example,
Schumpp, B. et al., J. Cell Sci., 7(Pt 4):639-647 (Dec. 1990)). As
such, known cell culture techniques often limit the maximum density
to which cells are initially grown, so that the cells are not
adversely affected by particular concentrations of waste
products.
[0005] For example, the cell culture method described in WO
2009/023562 relies on lactate levels to signal the maximum cell
density that can theoretically be achieved before initiating
perfusion cell culture. As taught in WO 2009/023562, cells are
grown to a cell density of about 1 million to 9 million cells/mL,
which results in a lactate concentration of about 1 g/L to about 6
g/L. According to WO 2009/023562, this signals the optimum time
point to begin perfusion. After perfusion, cells are then grown to
roughly 5 to 40 million cells/mL and maintained in fed-batch cell
culture to yield antibody titers between 8-10 g/L (between days
14-17).
[0006] In contrast to such known cell culture methods, no
particular level of waste products restricts the density of cell
growth according to the methods of the present invention. Instead,
it was discovered that when cells are initially grown only in a
perfusion cell culture, the cells are able to grow to a much higher
cell density (e.g., at least above 40.times.10.sup.6 cells/mL) than
previously reported for known cell culture techniques, regardless
of the presence of waste products. In a particular embodiment, the
cells are grown to a density of at least above about
40.times.10.sup.6 cells/mL to 60.times.10.sup.6 cells/mL,
preferably above about 70.times.10.sup.6 cells/mL to
90.times.10.sup.6 cells/mL, more preferably above about
100.times.10.sup.6 to 130.times.10.sup.6, and most preferably above
about 140.times.10.sup.6 to 200.times.10.sup.6 cells/mL or more.
This "super" high density of cells, in turn, enables the production
of significantly higher quantities of protein (e.g., 13.8 g/L at
day 6) in a shorter period of time than has been previously
reported.
[0007] The present invention further provides yet another
unexpected advantage over known cell culture techniques in that it
optimizes the production of large amounts of high quality protein.
For example, in one embodiment, protein harvested according to the
methods of the present invention is obtained only from the
fed-batch cell culture. This increases the freshness, stability and
quality of the protein, in contrast to protein obtained from both
perfusion and fed-batch cultures subjected to longer periods of
culture, which is thus more susceptible to degradation and
generally of poorer quality. Notwithstanding, the present invention
also contemplates harvesting protein from both the perfusion and
fed-batch cultures (e.g., when the cells are cultured in a single
bioreactor).
[0008] In certain embodiments, the present invention employs
recombinant cells which express a protein of interest. For example,
cells are transfected with at least one nucleic acid that encodes a
protein of interest.
[0009] The methods of the present invention can be used to enhance
production of any protein of interest, including, without
limitation, enzymes, receptors, fusion proteins, cytokines,
regulatory factors, hormones, diagnostic proteins, therapeutic
proteins, and antigen-binding agents. In a particular embodiment,
the protein is an antibody (or antigen binding fragment thereof).
Similarly, a wide variety of cells can be cultured according to the
methods of the present invention. In a particular embodiment, the
cells are animal cells. In a preferred embodiment, the cells are
mammalian cells, such as CHO, NSO, BHK and Per C6 cells.
[0010] The conditions of the cell culture (e.g., pH, temperature,
media, particular vessel for growing the cultures, etc.) can be
determined and adjusted by one of ordinary skill in the art
depending on a number of factors, such as the particular cell line
and protein to be produced. In one embodiment, the perfusion cell
culture and fed-batch mode cell culture are performed in
bioreactors. This can include a single bioreactor or multiple
bioreactors (e.g., such that the perfusion cell culture and
fed-batch mode cell culture are performed in separate bioreactors).
For example, the perfusion cell culture can be performed in one
bioreactor and then the cells can be transferred into multiple
fed-batch bioreactors.
[0011] Additionally, the cell culture conditions can be optimized
to maximize protein production. For example, cell culture
parameters, such as pH, DO, temperature, feed strategies, feed
composition, etc. can be optimized.
[0012] In other embodiments, the present invention provides methods
for clarifying a protein from a cell culture. This is achieved by
adjusting the pH of the cell culture to below neutral pH (i.e.,
below a pH of 7) and settling the cell culture, such that the cell
culture separates to form a supernatant layer and a cell-bed layer,
wherein the protein is present in (and can be isolated from) the
supernatant layer. While the methods can be applied to cell
cultures of the invention, they can be applied to clarify a protein
from any cell culture, including high density cell cultures.
[0013] In one embodiment, the method involves adjusting the pH of
the cell culture to a low pH (i.e., below a neutral pH of 7 such as
pH of 4-7). In a particular embodiment, the pH is adjusted to a pH
between about 4.5 and 6.5. In other embodiment, the method involves
settling the cell culture for at least about 30 minutes, so as to
enhance clarification of the cell culture in advance of collecting
the protein. However, the cell culture can be settled for longer
periods of time at the discretion of the skilled artisan. In a
particular embodiment, the cell culture is settled for between
about 30 and 120 minutes.
[0014] Other known purification techniques can optionally be
employed in conjunction with the clarification method described
above. For example, in one embodiment, the cell culture can be
centrifuged before settling the cell culture. In another
embodiment, the cell culture can be centrifuged after settling the
cell culture. In yet another embodiment, the cell culture can be
centrifuged before and after settling the cell culture.
[0015] Another optional step that can be taken to enhance the
clarification method is washing the cell-bed layer that forms as a
result of the settling process with a low pH buffer. In a
particular embodiment, the pH of the buffer is the same as the pH
of the cell culture, i.e., when the cell culture is adjusted to a
low pH (i.e., below a neutral pH of 7).
[0016] Additionally, filtration techniques can be used to further
clarify the cell culture. For example, the cell culture can be
filtered before the cell culture is settled. In another embodiment,
the cell culture can be filtered after the cell culture is settled.
In yet a further embodiment, the cell culture can be filtered
before and after the cell culture is settled. Filtration can be
performed using any number of techniques known in the art,
including, but not limited to depth filtration and polishing
filtration.
[0017] Other features and advantages of the invention will be
apparent from the following detailed description, and from the
claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0018] FIG. 1 depicts one possible scenario for practicing the
methods of the present invention, i.e., wherein the super density
fed-batch cell culture process is performed in a single
bioreactor.
[0019] FIG. 2 depicts another possible scenario for practicing the
methods of the present invention, i.e., wherein the cells are
perfused in a perfusion bioreactor until a particular density of
cells is achieved and then transferred to multiple fed batch
reactors. Fed-batch cell culture process is performed in a single
bioreactor.
[0020] FIG. 3 is a graph showing the cell growth and protein
production profile for Experiment #1.
[0021] FIG. 4 is a graph showing the cell growth and protein
production profile for Experiment #2.
[0022] FIG. 5 is a graph depicting the perfusion bioreactor profile
(i.e., viable cell density and percent viability) of Experiment
3.
[0023] FIG. 6 is an overlay graph depicting the cell density and
productivity profiles from the two bioreactors utilized in
Experiment 3.
[0024] FIG. 7 is a graph showing the cell growth, cell viability
and protein production profiles in production bioreactor for
Experiment 4.
[0025] FIG. 8 is a graph summarizing the productivity results of
all four Experiments as a function of cell integral.
[0026] FIG. 9 is a graph depicting the effect of varying
experimental parameters (i.e., pH, filter aid, etc.) on the
clarification process.
[0027] FIG. 10 is a schematic depicting the key steps in the
clarification process, as well as optional techniques for enhancing
the clarification process.
DETAILED DESCRIPTION OF THE INVENTION
[0028] The present invention provides improved methods for
increasing protein production in a cell culture by growing cells
that produce the protein in a perfusion cell culture to a high cell
density (i.e., at least above 40.times.10.sup.6 cells/mL), and then
switching to a fed-batch cell culture, such that the cells enter a
protein production phase. The invention further provides methods
for clarifying cell cultures to facilitate collection of protein
from the cultures.
[0029] In order that the present invention may be more readily
understood, certain terms are first defined. Additional definitions
are provided throughout the detailed description.
I. Definitions
[0030] The terms "cell culture" and "culture" include any
combination of cells and medium. The methods of the present
invention contemplate, without limitation, two general types of
cell culture, i.e., perfusion cell culture and fed-batch cell
culture. The principles behind these types of cell culture are
described below.
[0031] As used herein, the terms "perfuse", "perfusion" and
"perfusion culture" are used interchangeably to refer to a method
of culturing cells, wherein additional fresh medium is provided to
the culture and spent medium is removed from the culture. Perfusion
is initiated after the culture is seeded and can occur either
continuously or intermittently, as desired, over a period of time.
The fresh medium added during perfusion typically provides
nutritional supplements for the cells that have been depleted
during the culturing process. Perfusion also allows for removal of
cellular waste products and toxic byproducts from the cell culture.
Perfusion is performed during the growth phase of the cells, but
can also be continued after the cells have been transferred to a
fed-batch cell culture (discussed below).
[0032] As used herein, the term "specific perfusion rate" (SPR)
refers to the rate at which fresh medium is provided to the cell
culture and spent medium is removed based on cell density. SPR can
be calculated using the following equation:
Specific Perfusion Rate (SPR)=(Reactor Volume/day)/(Total Cell
Density (.times.10.sup.6)).
[0033] The SPR can be determined and/or adjusted by one of ordinary
skill in the art, based on factors including, but not limited to
the nature of the particular host cells, the cell growth rate, and
the cell density. For example, the typical SPR can range from about
0.01 to about. 1.0.times.10.sup.-6 mL cell.sup.-1 day.sup.-1. In
one embodiment, the SPR is 1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3,
0.2, 0.1, 0.09, 0.08, 0.07, 0.06, 0.05, 0.04, 0.03, 0.02 or 0.01.
In one embodiment, the SPR ranges from 0.25 to
0.03.times.10.sup.-6mL cell.sup.-1 day.sup.-1. In another
embodiment, the SPR ranges from 0.07 to 0.01.times.10.sup.-6mL
cell.sup.-1 day.sup.-1. In another embodiment, the SPR ranges from
0.07 to 0.03.times.10.sup.-6mL cell.sup.-1 day.sup.-1. In a
particular embodiment, the SPR is maintained at about
0.05.times.10.sup.-6mL cell.sup.-1 day.sup.-1.
[0034] The SPR can remain constant over a period of time or it can
be altered (i.e., increased or decreased) over the course of the
period of perfusion. For example, the SPR can be steadily increased
over time, increased in a step-wise fashion over time, steadily
decreased over time, decreased in a step-wise fashion over time, or
any combination thereof The perfusion can be applied in a
continuous manner or in an intermittent manner. One of ordinary
skill in the art can determine the SPR, as well as the appropriate
timing of the initiation and cessation of the perfusion period(s),
and of any alterations to the perfusion, based upon the monitoring
of some parameter of the cell culture.
[0035] As used herein, the term "fed-batch culture" refers to a
method of culturing cells, wherein the cell culture is supplemented
with fresh medium, i.e., the cells are "fed" with new medium while
spent medium is not removed. Typically, a "fed-batch" culture
process is performed in a bioreactor and additional components
(e.g., nutritional supplements) are added to the culture at some
time after initiation of the culture process. The controlled
addition of nutrients directly affects the growth rate of the
culture and allows for avoidance of the build-up of overflow
metabolites (see, for example, Wlaschin, K. F. et al., "Fedbatch
culture and dynamic nutrient feeding," Cell Culture Engineering,
101:43-74 (2006) and Lee, J. et al., "Control of fed-batch
fermentations," Biotechnol. Adv., 17:29-48 (1999)). A fed-batch
culture is typically terminated at some point and the cells and/or
components in the medium are harvested and optionally purified.
[0036] As used herein, the term "feed percentage" is the percentage
of feed volume in the total volume of cell culture.
[0037] As used herein, the term "bolus feed" refers to one time
feed addition
[0038] As used herein, the terms "inoculation", "inoculum", and
"seeding" refer to the addition of cells to starting medium to
begin the culture.
[0039] As used herein, the term "cell density" refers to the number
of cells in a given volume of medium. A high cell density is
desirable in that it can lead to higher protein productivity. As
such, cell density is routinely monitored in cell cultures. Cell
density can be monitored by any technique known in the art,
including, but not limited to, extracting samples from a culture
and analyzing the cells under a microscope, using a commercially
available cell counting device or by using a commercially available
suitable probe introduced into the bioreactor itself (or into a
loop through which the medium and suspended cells are passed and
then returned to the bioreactor).
[0040] As used herein the terms "super high cell density" and "high
cell density" are used interchangeably and refer to a cell density
of at least above 40.times.10.sup.6 cells/mL. Known cell culture
techniques may involve growing cells to a "first critical level"
(i.e., "a point during the cell cycle growth phase when the cell
viability may be affected by the increased concentration of waste
productions (e.g., cell growth inhibitors and toxic metabolites,
e.g., lactate, ammonium, etc.)" before perfusing the cell culture
and obtaining roughly 5 to 40 million cells/mL). In contrast, cells
grown according to the methods of the present invention are not
restricted by waste products and, thus, are able to reach a super
high cell density (i.e., at least above about 40, 50, 60, 70, 80,
90, 100, 110, 120, 130.times.10.sup.6 cells/mL). Specifically, as
part of the present invention it was discovered that when cells are
initially grown in a perfusion cell culture, the cells grow to a
much higher cell density (i.e., super high cell density),
independent of the presence of waste products, such as lactate or
ammonium.
[0041] In the present invention, cells grown in perfusion cell
culture are "switched" (e.g., shifted or transferred) to a
fed-batch culture mode once the cells reach high cell density. In
one embodiment, the switch occurs at a high cell density of at
least above about 40.times.10.sup.6 cells/mL. In another
embodiment, the switch occurs at a high cell density of at least
between about 40.times.10.sup.6 cells/mL and 200.times.10.sup.6
cells/mL. In particular embodiments, the switch occurs at high cell
densities of about 41.times.10.sup.6 cells/mL, 42.times.10.sup.6
cells/mL, 43.times.10.sup.6 cells/mL, 44.times.10.sup.6 cells/mL,
45.times.10.sup.6 cells/mL, 46.times.10.sup.6 cells/mL,
47.times.10.sup.6 cells/mL, 48.times.10.sup.6 cells/mL,
49.times.10.sup.6 cells/mL, 50.times.10.sup.6 cells/mL,
51.times.10.sup.6 cells/mL, 52.times.10.sup.6 cells/mL,
53.times.10.sup.6 cells/mL, 54.times.10.sup.6 cells/mL,
55.times.10.sup.6 cells/mL, 56.times.10.sup.6 cells/mL,
57.times.10.sup.6 cells/mL, 58.times.10.sup.6 cells/mL,
59.times.10.sup.6 cells/mL, 60.times.10.sup.6 cells/mL,
61.times.10.sup.6 cells/mL, 62.times.10.sup.6 cells/mL, 63'10.sup.6
cells/mL, 64.times.10.sup.6 cells/mL, 65.times.10.sup.6 cells/mL,
66.times.10.sup.6 cells/mL, 67.times.10.sup.6 cells/mL,
68.times.10.sup.6 cells/mL, 69.times.10.sup.6 cells/mL,
70.times.10.sup.6 cells/mL, 71.times.10.sup.6 cells/mL,
72.times.10.sup.6 cells/mL, 73.times.10.sup.6 cells/mL,
74.times.10.sup.6 cells/mL, 75.times.10.sup.6 cells/mL,
76.times.10.sup.6 cells/mL, 77.times.10.sup.6 cells/mL,
78.times.10.sup.6 cells/mL, 79.times.10.sup.6 cells/mL,
80.times.10.sup.6 cells/mL, 81.times.10.sup.6 cells/mL m
82.times.10.sup.6 cells/mL, 83.times.10.sup.6 cells/mL,
84.times.10.sup.6 cells/mL, 85.times.10.sup.6 cells/mL,
86.times.10.sup.6 cells/mL, 87.times.10.sup.6 cells/mL,
88.times.10.sup.6 cells/mL, 89.times.10.sup.6 cells/mL,
90.times.10.sup.6 cells/mL, 91.times.10.sup.6 cells/mL,
92.times.10.sup.6 cells/mL, 93.times.10.sup.6 cells/mL,
94.times.10.sup.6 cells/mL, 95.times.10.sup.6 cells/mL,
96.times.10.sup.6 cells/mL, 97.times.10.sup.6 cells/mL,
98.times.10.sup.6 cells/mL, 99.times.10.sup.6 cells/mL,
100.times.10.sup.6 cells/mL, 101.times.10.sup.6 cells/mL,
102.times.10.sup.6 cells/mL, 103.times.10.sup.6 cells/mL,
104.times.10.sup.6 cells/mL, 105.times.10.sup.6 cells/mL,
106.times.10.sup.6 cells/mL, 107.times.10.sup.6 cells/mL,
108.times.10.sup.6 cells/mL, 109.times.10.sup.6 cells/mL,
110.times.10.sup.6 cells/mL, 111.times.10.sup.6 cells/mL,
112.times.10.sup.6 cells/mL, 113.times.10.sup.6 cells/mL,
114.times.10.sup.6 cells/mL, 115.times.10.sup.6 cells/mL,
116.times.10.sup.6 cells/mL, 117.times.10.sup.6 cells/mL,
118.times.10.sup.6 cells/mL, 119.times.10.sup.6 cells/mL,
120.times.10.sup.6 cells/mL, 121.times.10.sup.6 cells/mL,
122.times.10.sup.6 cells/mL, 123.times.10.sup.6 cells/mL,
124.times.10.sup.6 cells/mL, 125.times.10.sup.6 cells/mL,
126.times.10.sup.6 cells/mL, 127.times.10.sup.6 cells/mL,
128.times.10.sup.6 cells/mL, 129.times.10.sup.6 cells/mL,
130.times.10.sup.6 cells/mL, 131.times.10.sup.6 cells/mL,
132.times.10.sup.6 cells/mL, 133.times.10.sup.6 cells/mL,
134.times.10.sup.6 cells/mL, 135.times.10.sup.6 cells/mL,
136.times.10.sup.6 cells/mL, 137.times.10.sup.6 cells/mL,
138.times.10.sup.6 cells/mL, 139.times.10.sup.6 cells/mL,
140.times.10.sup.6 cells/mL, 141.times.10.sup.6 cells/mL,
142.times.10.sup.6 cells/mL, 143.times.10.sup.6 cells/mL,
144.times.10.sup.6 cells/mL, 145.times.10.sup.6 cells/mL,
146.times.10.sup.6 cells/mL, 147.times.10.sup.6 cells/mL,
148.times.10.sup.6 cells/mL, 149.times.10.sup.6 cells/mL,
150.times.10.sup.6 cells/mL, 151.times.10.sup.6 cells/mL,
152.times.10.sup.6 cells/mL, 153.times.10.sup.6 cells/mL,
154.times.10.sup.6 cells/mL, 155.times.10.sup.6 cells/mL,
156.times.10.sup.6 cells/mL, 157.times.10.sup.6 cells/mL,
158.times.10.sup.6 cells/mL, 159.times.10.sup.6 cells/mL,
160.times.10.sup.6 cells/mL, 161.times.10.sup.6 cells/mL,
162.times.10.sup.6 cells/mL, 163.times.10.sup.6 cells/mL,
164.times.10.sup.6 cells/mL, 165.times.10.sup.6 cells/mL,
166.times.10.sup.6 cells/mL, 167.times.10.sup.6 cells/mL,
168.times.10.sup.6 cells/mL, 169.times.10.sup.6 cells/mL,
170.times.10.sup.6 cells/mL, 171.times.10.sup.6 cells/mL,
172.times.10.sup.6 cells/mL, 173.times.10.sup.6 cells/mL,
174.times.10.sup.6 cells/mL, 175.times.10.sup.6 cells/mL,
176.times.10.sup.6 cells/mL, 177.times.10.sup.6 cells/mL,
178.times.10.sup.6 cells/mL, 179.times.10.sup.6 cells/mL,
180.times.10.sup.6 cells/mL, 181.times.10.sup.6 cells/mL,
182.times.10.sup.6 cells/mL, 183.times.10.sup.6 cells/mL,
184.times.10.sup.6 cells/mL, 185.times.10.sup.6 cells/mL,
186.times.10.sup.6 cells/mL, 187.times.10.sup.6 cells/mL,
188.times.10.sup.6 cells/mL, 189.times.10.sup.6 cells/mL,
190.times.10.sup.6 cells/mL, 191.times.10.sup.6 cells/mL,
192.times.10.sup.6 cells/mL, 193.times.10.sup.6 cells/mL,
194.times.10.sup.6 cells/mL, 195.times.10.sup.6 cells/mL,
196.times.10.sup.6 cells/mL, 197.times.10.sup.6 cells/mL, 198 x
10.sup.6 cells/mL, 199 x 10.sup.6 cells/mL or 200 x 10.sup.6
cells/mL, or more. In a preferred embodiment, the switch from
perfusion culture to fed-batch culture occurs at a cell density of
at least about 50.times.10.sup.6 cells/mL. In a more preferred
embodiment, the switch occurs at a cell density of at least about
100.times.10.sup.6 cells/mL.
[0042] As used herein, the term "super density fed-batch process,"
"SDF process", and "super density fed-batch cell culture process"
are used interchangeably and refer to the process of growing cells
in a perfusion cell culture and then transferring the cells to a
fed-batch culture mode, once the cells reach high cell density
(e.g., at least above 40.times.10.sup.6 cells/mL).
[0043] The transition from perfusion cell culture to fed-batch cell
culture occurs once a high cell density is achieved (as discussed
above). A high cell density may be achieved at any time after
inoculation of the cell culture, depending on the growth rate of
the cell line and the seeding density. In one embodiment, the high
density may be reached 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 23, 24 or 25 days post-inoculation. In
a preferred embodiment, the high density is reached between about 4
to 17 days post-inoculation.
[0044] As used herein, the term "viable cell density" refers to the
number of live cells present in a given volume of medium under a
given set of experimental conditions.
[0045] As used herein, the term "cell viability" refers to the
ability of cells in culture to survive under a given set of
conditions or experimental variations. The term as used herein also
refers to that portion of cells that are alive at a particular time
in relation to the total number of cells (e.g., living and dead) in
the culture at that time.
[0046] As used herein, "the growth phase" of a cell culture refers
to the phase during which the viable cell density at any time point
is higher than at any previous time point.
[0047] As used herein, the "production phase" of a cell culture
refers to the phase during which the cells produce significant
amounts of protein, which accumulates for future processing.
[0048] As used herein, the term "cell integral" refers to the
overall viable cell numbers during the course of a cell growth
profile.
[0049] As used herein, the term "titer" refers to the total amount
of protein produced by a cell culture, divided by a given amount of
medium volume. In essence, the term "titer" refers to a
concentration and is typically expressed in units of milligrams of
polypeptide per liter of medium. The methods of the present
invention have the effect of substantially increasing polypeptide
product titer, as compared to polypeptide product titer produced
from other cell culture methods known in the art.
[0050] As used herein, the terms "media", "cell culture media" and
"culture media", including grammatical variations thereof, are used
interchangeably, and refer to the nutrient solution in which cells
(preferably animal or mammalian cells) are grown in culture. Cell
culture media is the physiochemical, nutritional, and hormonal
environment for cells and typically includes at least one or more
components from the following: an energy source (e.g., in the form
of a carbohydrate such as glucose); essential amino acids,
including the twenty basic amino acids plus cysteine; vitamins
and/or other organic compounds typically required at low
concentrations; lipids or free fatty acids (e.g., linoleic acid);
and trace elements (e.g., inorganic compounds or naturally
occurring elements that are typically required at very low
concentrations, usually in the micromolar range). Media may be
solid, gelatinous, liquid, gaseous or a mixture of phases and
materials.
[0051] The cells utilized in the methods of the present invention
can be grown and maintained in any number of cell culture media
which are known in the art or are commercially available. One of
ordinary skill in the art may opt to use one or more known cell
culture media that is selected to maximize cell growth, cell
viability, and/or protein production in a particular cultured host
cell. Exemplary cell culture media include any media suitable for
culturing cells that can express a protein of interest, including,
but not limited to animal component free medium, such as
EX-CELL.RTM. TiterHigh medium (SAFC), and chemically defined media,
such as CD CHO medium (Invitrogen, Carlsbad, Calif.) and CD OptiCHO
(Invitrogen, Carlsbad, Calif.))
[0052] Additionally, the cell culture media can optionally be
supplemented to include one or more additional components, in
appropriate concentrations or amounts, as necessary or desired, and
as would be known and practiced by those of ordinary skill in the
art. Exemplary supplements include, but not limited to, chemical
gene selection agents, hormones and other growth factors, (e.g.,
insulin, transferrin, epidermal growth factor, serum, somatotropin,
pituitary extract, aprotinin); salts (e.g., calcium, magnesium and
phosphate), and buffers (e.g., HEPES
(4-[2-Hydroxethyl]-1-piperazine-ethanesulfonic acid)); nucleosides
and bases (e.g., adenosine, thymidine, hypoxanthine); protein and
hydrolysates; antibiotics (e.g., gentamycin); cell protective
agents (e.g., a
[0053] Pluronic polyol (PLURONIC.RTM. F68)) and extracellular
matrix proteins (e.g., fibronectin). Supplements that support the
growth and maintenance of particular cell cultures are able to be
readily determined by those of ordinary skill in the art, such as
is described, for example, by Barnes et al. (Cell, 22:649 (1980));
in Mammalian Cell Culture, Mather, J. P., ed., Plenum Press, NY
(1984); and in U.S. Pat. No. 5,721,121.
[0054] As used herein, the term "bioreactor" refers to any
apparatus, closed container or vessel (e.g., a fermentation
chamber) that is used for growing cell cultures. Bioreactors allow
controlling various parameters during the cell culture process
including, but not limited to, the circulation loop flow, pH, the
temperature, the overpressure and/or the medium perfusion rate.
Bioreactors include commercially available bioreactors, classical
fermenters and cell culture perfusion systems, as well as
disposable bioreactors.
[0055] The bioreactor can be of any size that is useful for
culturing cells at a desirable scale in accordance with a method of
the invention. For example, a bioreactor employed in the methods of
the present invention may be at least 0.1, 0.5, 1, 5, 10, 15, 20,
25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,
105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165,
170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230,
235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295,
300, 305, 310, 315, 320, 325, 330, 340, 350, 360, 370, 380, 390,
400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 550, 1,000,
1,500, 2,000, 2,500, 3,000, 3,500, 4,000, 4,500, 5,000, 5,500,
6,000, 6,500, 7,000, 7,500, 8,000, 8,500, 9,000, 9,500, 10,000,
10,500, 11,000, 11,500, 12,0000, 13,000, 14,000, 15,000 liters or
more, or any intermediate volume.
[0056] The methods of the present invention can employ one or more
bioreactors. For example, in one embodiment, the perfusion cell
culture and fed-batch cell culture can be performed in the same
bioreactor. In another embodiment, the perfusion cell culture can
be performed in separate bioreactors. In another embodiment, the
cells from the perfusion cell culture can be transferred to
multiple fed-batch bioreactors.
[0057] A suitable bioreactor may be composed of (i.e., constructed
of) any material that is suitable for holding cell cultures under
the culture conditions of the present invention and is conducive to
cell growth and viability. For example, a bioreactor employed in
the methods of the present invention can be made of glass, plastic
or metal. However, the materials comprising the bioreactor should
not interfere with expression or stability of the polypeptide
product. Suitable bioreactors are known in the art and commercially
available.
[0058] A perfusion bioreactor used in the methods of the present
invention can be a disposable perfusion bioreactor or any other
traditional perfusion bioreactors. The bioreactor may optionally be
equipped with any internal or external cell retention devices,
including, but not limited to, spin filters, tangential flow
membrane filters, dynamic membranes, ultrasonic separators, gravity
settlers, continuous centrifuge or acoustic cell retention device,
microfiltration devices, ultrafiltration devices, etc. In a
particular embodiment, the bioreactor is a disposable bioreactor
equipped with microfiltration membrane having a pore size of 1.2 to
10 .mu.m.
[0059] As used herein, the term "antifoam" refers to an agent that
can be added to a cell culture to prevent the build up of excess
foam. Examples of antifoam agents include, but are not limited to,
3% simethicone manufactured by Invitrogen and HyClone. Antifoams
are commercially available and can be used at the discretion of one
of ordinary skill in the art.
[0060] The cell cultures encompassed by the methods of the present
invention may be grown at any temperature appropriate for the cell
type and culture conditions. In one embodiment, it is desirable to
use a temperature between about 30.degree. C. and 38.degree. C., to
enhance protein production. In another embodiment, the temperature
is at least about 25.degree. C., 26.degree. C., 27.degree.,
28.degree. C., 29.degree. C., 30.degree. C., 31.degree. C.,
32.degree. C., 33.degree. C., 34.degree. C., 35.degree. C.,
36.degree. C., 37.degree. C., 38.degree. C., 39.degree. C.,
40.degree. C., or 41.degree. C. It may also be desirable to use
different temperatures at different times during the culture.
A. Cell Culture
[0061] As used herein, the term "cell", refers to animal cells,
mammalian cells, cultured cells, host cells, recombinant cells, and
recombinant host cells. Such cells are generally cell lines
obtained or derived from mammalian tissues which are able to grow
and survive when placed in media containing appropriate nutrients
and/or growth factors. The cells utilized in the methods of the
present invention are generally animal or mammalian cells that can
express and secrete, or that can be molecularly engineered to
express and secrete, large quantities of a particular protein into
the culture medium. In one embodiment, the protein produced by the
cell can be endogenous or homologous to the cell. Alternatively,
the protein is heterologous, i.e., foreign, to the cell.
[0062] Any eukaryotic cell that is capable of expressing the
protein of interest can be cultured according to the methods of the
present invention. Numerous cell lines are available from
commercial sources, including, but not limited to the American Type
Culture Collection (ATCC). In one embodiment of the invention, the
cell culture employs hybridoma cells. The construction of
antibody-producing hybridoma cells is well known in the art. In
another embodiment of the invention, the cell culture employs CHO
cells.
[0063] Representative cells that can be used in the methods of the
present invention include, but are not limited to, Chinese hamster
ovary cells (CHO), NSO, Per C6, HEK, COS, VERO076, BRL-3A, HepG2,
MRC 5, 293T, A431, 3T3, CV-I, C3H10T1/2, Colo205, 293, L cells,
HL-60, FRhL-2, U937, HaK, Jurkat cells, Rat2, BaF3, 32D, FDCP-I,
PC12, Mix, murine myelomas (e.g., SP2/0 and NSO) and C2C12 cells,
DG44 (Chasin et al., Som. Cell Molec. Genet., 12:555-556 (1986);
and Kolkekar et al., Biochemistry, 36:10901-10909 (1997)), CHO-K1
Tet-On cell line (Clontech), CHO designated ECACC 85050302 (CAMR,
Salisbury, Wiltshire, UK), CHO clone 13
[0064] (GEIMG, Genova, IT), CHO clone B (GEIMG, Genova, IT),
CHO-K1/SF designated ECACC 93061607 (CAMR, Salisbury, Wiltshire,
UK), RR-CHOK1 designated ECACC 92052129 (CAMR, Salisbury,
Wiltshire, UK), dihydrofolate reductase negative CHO cells
(CHO/-DHFR, Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216
(1980)), and dp12.CHO cells (U.S. Patent No. 5,721,121); monkey
kidney CV1 cells transformed by SV40 (COS cells, COS-7, ATCC.RTM.
CRL-1651); human embryonic kidney cells (e.g., 293 cells, or 293
cells subcloned for growth in suspension culture, Graham et al., J.
Gen. Virol., 36:59 (1977)); baby hamster kidney cells (BHK,
ATCC.RTM. CCL-10); monkey kidney cells (CV1, ATCC.RTM. CCL-70);
African green monkey kidney cells (VERO-76, ATCC.RTM. CRL-1587;
VERO, ATCC.RTM. CCL-81); mouse sertoli cells (TM4, Mather, Biol.
Reprod., 23:243-251 (1980)); human cervical carcinoma cells (HELA,
ATCC.RTM. CCL-2); canine kidney cells (MDCK, ATCC.RTM. CCL-34);
human lung cells (W138, ATCC.RTM. CCL-75); human hepatoma cells
(HEP-G2, HB 8065); mouse mammary tumor cells (MMT 060562, ATCC.RTM.
CCL-51); buffalo rat liver cells (BRL 3A, ATCC.RTM. CRL-1442); TRI
cells (Mather, Annals N.Y. Acad. Sci., 383:44-68 (1982)); MCR 5
cells; FS4 cells, as well as transformed primate cell lines,
hybridomas, normal diploid cells, and cell strains derived from in
vitro culture of primary tissue and primary explants.
[0065] Cells suitable for culturing in the methods of the present
invention can contain introduced (e.g., via transformation,
transfection, infection, or injection) expression vectors
(constructs), such as plasmids and the like, that harbor coding
sequences (or portions thereof), which encode a desired protein.
Such expression vectors contain the necessary elements for the
transcription and translation of the inserted coding sequence and
generally include, but are not limited to, one or more of the
following: a signal sequence, one or more marker genes, an enhancer
element, a promoter, and a transcription termination sequence.
[0066] Methods and techniques to construct expression vectors
containing sequences encoding the produced proteins, as well as the
appropriate transcriptional and translational control elements, are
well known in the art. Such methods include in vitro recombinant
DNA techniques, synthetic techniques, and in vivo genetic
recombination (see, for example, Sambrook J. et al., Molecular
Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview,
N.Y. (1989) and in Ausubel, F. M. et al., Current Protocols in
Molecular Biology, John Wiley & Sons, New York, N.Y.
(1989)).
[0067] Expression constructs can be introduced into cells by a wide
variety of routine gene transfer methods known in the art. For
example, such methods can include, but are not limited to,
conventional gene transfection methods, such as calcium phosphate
co-precipitation, liposomal transfection, microinjection,
electroporation, and infection or viral transduction (see, for
example, U.S. Pat. No. 4,399,216, Keown et al., Methods in
Enzymology (1989), Keown et al., Methods in Enzymology, 185:527-537
(1990), and Mansour et al., Nature, 336:348-352 (1988).
[0068] Any number of known expression vectors can be suitable for
eukaryotic host cells cultured according to the methods of the
invention, including, but not limited to, vectors for mammalian
host cells (e.g., BPV-1, pHyg, pRSV, pSV2, pTK2 (Maniatis); pIRES
(Clontech); pRc/CMV2, pRc/RSV, pSFV1 (Life Technologies); pVPakc
vectors, pCMV vectors, pSGS vectors (Stratagene), retroviral
vectors (e.g., pFB vectors (Stratagene)), pcDNA-3 (Invitrogen),
adenoviral vectors; Adeno-associated virus vectors, baculovirus
vectors, yeast vectors (e.g., pESC vectors (Stratagene)), or
modified forms of any of the foregoing. Vectors can also contain
enhancer sequences upstream or downstream of promoter region
sequences for optimizing gene expression.
[0069] Control elements (e.g., regulatory sequences), are those
non-translated regions of the vector, e.g., enhancers, promoters,
5' and 3' untranslated regions, that interact with host cellular
proteins to carry out transcription and translation. Such elements
vary in their strength and specificity. Depending on the vector
system and particular host cell, any number of suitable
transcription and translation elements, including constitutive and
inducible promoters, can be used. In mammalian cell systems,
promoters from mammalian genes or from mammalian viruses are
preferred. The constructs for use in protein expression systems are
designed to contain at least one promoter, an enhancer sequence
(optional, for mammalian expression systems), and other sequences
as necessary or required for proper transcription and regulation of
gene expression (e.g., transcriptional initiation and termination
sequences, origin of replication sites, polyadenylation sequences).
The selection of an appropriate vector for proper transcription,
expression, and isolation of proteins produced in eukaryotic (e.g.,
mammalian) expression systems is known and well within the ordinary
skill in the art.
[0070] Commonly used eukaryotic control sequences for use in
mammalian expression vectors include promoters and control
sequences compatible with mammalian cells, such as, for example,
the cytomegalovirus (CMV) promoter (CDM8 vector) and avian sarcoma
virus (ASV). Other commonly used promoters include the early and
late promoters from Simian Virus 40 (SV40) (Fiers et al., Nature,
273:113 (1973)), or other viral promoters such as those derived
from polyoma, Adenovirus 2, and bovine papilloma virus. An
inducible promoter, such as hMTII (Karin et al., Nature,
299:797-802 (1982)) can also be used.
B. Protein Production
[0071] As used herein, the terms "polypeptide", "polypeptide
product", "protein" and "protein product," are used interchangeably
and, as is known in the art, refer to a molecule consisting of two
or more amino acids, e.g., at least one chain of amino acids linked
via sequential peptide bonds. In one embodiment, a "protein of
interest" or a "polypeptide of interest" is a protein encoded by an
exogenous nucleic acid molecule that has been transformed into a
host cell, wherein the exogenous DNA determines the sequence of
amino acids. In another embodiment, a "protein of interest" is a
protein encoded by a nucleic acid molecule that is endogenous to
the host cell.
[0072] Numerous polypeptides can be produced by the methods of the
present invention. Exemplary polypeptides include gene products,
naturally-occurring proteins, homologs, orthologs, paralogs,
fragments, and other equivalents, variants and analogs of the
foregoing. Polypeptides may also include one or more modifications
such as, for example, a lipid moiety, a phosphate, a sugar moiety,
etc. Particular polypeptides that may be desirable for expression
in a method of the invention include, but are not limited to,
cytokines, cytokine receptors, growth factors (e.g., epidermal
growth factor (EGF), human epidermal growth factor receptor-2
(HER-2), fibroblast growth factor-alpha (FGF-.alpha..), fibroblast
growth factor-beta (FGF-.beta., transforming growth factor-alpha
(TGF-.alpha.), transforming growth factor-beta (TGF-.beta.,
platelet-derived growth factor (PDGF), insulin-like growth factor-1
(IGF-1), insulin-like growth factor-2 (IGF-2), nerve growth factor
(NGF), nerve growth factor-beta (NGF-.beta.); growth factor
receptors, including fusion or chimeric proteins, growth hormones
(e.g., human growth hormone, bovine growth hormone); insulin (e.g.,
insulin A chain and insulin B chain), proinsulin; erythropoietin
(EPO); colony stimulating factors (e.g., granulocyte
colony-stimulating factor (G-CSF), granulocyte macrophage
colony-stimulating factor (GM-CSF), macrophage colony-stimulating
factor (M-CSF)); interleukins (e.g., IL-1 through IL-12); vascular
endothelial growth factor (VEGF) and its receptor (VEGF-R);
interferons (e.g., IFN-.alpha., .beta., or .gamma.) and their
receptors; tumor necrosis factor (e.g., TNF-.alpha.and TNF-.beta.)
and their receptors, TNFR-1 and TNFR-2; thrombopoietin (TPO);
thrombin; brain natriuretic peptide (BNP); clotting factors (e.g.,
Factor VIII, Factor IX, von Willebrands factor, and the like);
anti-clotting factors; tissue plasminogen activator (TPA), e.g.,
urokinase or human urine or tissue type TPA; follicle stimulating
hormone (FSH); luteinizing hormone (LH); calcitonin; CD proteins
(e.g., CD3, CD4, CD8, CD28, CD19, etc.); CTLA proteins (e.g.,
CTLA4); T-cell and B-cell receptor proteins; bone morphogenic
proteins (BMPs, e.g., BMP-1, BMP-2, BMP-3, etc.); neurotrophic
factors, e.g., bone derived neurotrophic factor (BDNF);
neurotrophins, e.g., 3-6; renin; rheumatoid factor; RANTES
(regulated on activation normally T-cell expressed and secreted);
albumin; relaxin; relaxin A-chain; relaxin B-chain; prorelaxin;
macrophage inhibitory protein (e.g., MIP-1, MIP-2); viral proteins
or antigens; surface membrane proteins; ion channel proteins;
enzymes; regulatory proteins; antibodies; immunomodulatory
proteins, (e.g., HLA, MHC, the B7 family); homing receptors;
transport proteins; superoxide dismutase (SOD); G-protein coupled
receptor proteins (GPCRs); neuromodulatory proteins; Alzheimer's
Disease associated proteins and peptides, (e.g., A-.beta.),
parathyroid hormone; thyroid stimulating hormone; lipoproteins;
glucagon; atrial natriuretic factor; lung surfactant; bombesin;
hemopoietic growth factor; enkephalinase; a serum albumin (e g.,
human serum albumin); mullerian-inhibiting substance;
gonadotropin-associated peptide; DNase; inhibin; activin; receptors
for hormones or growth factors; integrin; protein A or D; CD
proteins such as CD-3, CD-4, CD-8, and CD-19; PD-1 and PD-L1 (B7-H1
and ligand); and B7-H4, osteoinductive factors; immunotoxins; decay
accelerating factor; and others as known in the art, fusion
proteins and polypeptides, chimeric proteins and polypeptides, and
fragments or portions, or mutants, variants, or analogues of any of
the aforementioned proteins and polypeptides.
[0073] In further embodiments, methods of the present invention can
be used to produce immunoglobulins (e.g., antibodies),
immunoglobulin-like domain-containing molecules (e.g., ankyrin or
fibronectin domain-containing molecules), and Fc-fusion proteins.
The term "Fc-fusion protein", as used herein, is meant to encompass
therapeutic proteins comprising an immunoglobulin-derived moiety
(i.e., an Fc moiety) and a moiety derived from a second,
non-immunoglobulin protein.
[0074] In a particular embodiment of the invention, the polypeptide
produced by the methods of the present invention is an antibody.
The term "antibody" is used in the broadest sense to cover any type
of known antibody, including, but is not limited to, monoclonal
antibodies (including full length monoclonal antibodies),
polyclonal antibodies, monospecific antibodies, multispecific
antibodies (e.g., bispecific antibodies), immunoadhesins,
antibody-immunoadhesin chimeras, humanized, human, chimeric,
single-chain, synthetic, recombinant, hybrid, mutated, grafted, or
in vitro generated antibodies. The antibody can be a full length
antibody or an antibody fragment. The antibody may be selected from
any of the known antibody isotypes, for example, IgA, IgG, IgD,
IgE, IgM. The antibody may be a monomer, dimer, or multimer (e.g.,
a trimer or pentamer).
[0075] The term "antibody" or "immunoglobulin," as used
interchangeably herein, includes whole antibodies and any antigen
binding fragment (i.e., "antigen-binding portion") or single chains
thereof. An "antibody" comprises at least two heavy (H) chains and
two light (L) chains inter-connected by disulfide bonds. Each heavy
chain is comprised of a heavy chain variable region (abbreviated
herein as V.sub.H) and a heavy chain constant region. The heavy
chain constant region is comprised of three domains, CH1, CH2 and
CH3. Each light chain is comprised of a light chain variable region
(abbreviated herein as V.sub.L) and a light chain constant region.
The light chain constant region is comprised of one domain, CL. The
V.sub.H and V.sub.L regions can be further subdivided into regions
of hypervariability, termed complementarity determining regions
(CDR), interspersed with regions that are more conserved, termed
framework regions (FR). Each V.sub.H and V.sub.L is composed of
three CDRs and four FRs, arranged from amino-terminus to
carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3,
CDR3, FR4. The variable regions of the heavy and light chains
contain a binding domain that interacts with an antigen. The
constant regions of the antibodies may mediate the binding of the
immunoglobulin to host tissues or factors, including various cells
of the immune system (e.g., effector cells) and the first component
(Clq) of the classical complement system.
[0076] The term "antigen-binding portion" of an antibody (or simply
"antibody portion"), as used herein, refers to one or more
fragments of an antibody that retain the ability to specifically
bind to an antigen. It has been shown that the antigen-binding
function of an antibody can be performed by fragments of a
full-length antibody. Examples of binding fragments encompassed
within the term "antigen-binding portion" of an antibody include
(i) a Fab fragment, a monovalent fragment consisting of the
V.sub.L, V.sub.H, CL and CH1 domains; (ii) a F(ab').sub.2 fragment,
a bivalent fragment comprising two Fab fragments linked by a
disulfide bridge at the hinge region; (iii) a Fd fragment
consisting of the V.sub.H and CH1 domains; (iv) a Fv fragment
consisting of the V.sub.L and V.sub.H domains of a single arm of an
antibody, (v) a dAb including VH and VL domains; (vi) a dAb
fragment (Ward et al., Nature, 341:544-546 (1989)), which consists
of a V.sub.H domain; (vii) a dAb which consists of a VH or a VL
domain; and (viii) an isolated complementarity determining region
(CDR) or (ix) a combination of two or more isolated CDRs which may
optionally be joined by a synthetic linker. Furthermore, although
the two domains of the Fv fragment, V.sub.L and V.sub.H, are coded
for by separate genes, they can be joined, using recombinant
methods, by a synthetic linker that enables them to be made as a
single protein chain in which the V.sub.L and V.sub.H regions pair
to form monovalent molecules (known as single chain Fv (scFv); see,
e.g., Bird et al., Science, 242:423-426 (1988); and Huston et al.,
Proc. Nati. Acad. Sci. USA, 85:5879-5883 (1988)). Such single chain
antibodies are also intended to be encompassed within the term
"antigen-binding portion" of an antibody. These antibody fragments
are obtained using conventional techniques known to those with
skill in the art, and the fragments are screened for utility in the
same manner as are intact antibodies. Antigen-binding portions can
be produced by recombinant DNA techniques, or by enzymatic or
chemical cleavage of intact immunoglobulins.
[0077] The term "monoclonal antibody" as used herein refers to an
antibody obtained from a population of substantially homogeneous
antibodies, i.e., the individual antibodies comprising the
population are identical except for possible naturally occurring
mutations that may be present in minor amounts. Monoclonal
antibodies are highly specific, being directed against a single
antigenic site. Furthermore, in contrast to conventional
(polyclonal) antibody preparations which typically include
different antibodies directed against different determinants
(epitopes), each monoclonal antibody is directed against a single
determinant on the antigen. For example, monoclonal antibodies can
be produced using conventional hybridoma technology first described
by Kohler et al., Nature, 256:495 (1975), or they can be made using
recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567).
Monoclonal antibodies can also be isolated from phage antibody
libraries, e.g., using the techniques described in Clackson et al.,
Nature, 352:624-628 (1991); Marks et al., J. Mol. Biol.,
222:581-597 (1991); and U.S. Pat. Nos. 5,223,409; 5,403,484;
5,571,698; 5,427,908 5,580,717; 5,969,108; 6,172,197; 5,885,793;
6,521,404; 6,544,731; 6,555,313; 6,582,915; and 6,593,081.
[0078] A "bispecific" or "bifunctional antibody" is an artificial
hybrid antibody having two different heavy/light chain pairs and
two different binding sites. Bispecific antibodies can be produced
by a variety of methods including fusion of hybridomas or linking
of Fab' fragments. See, e.g., Songsivilai et al., Clin. Exp.
Immunol., 79:315-321 (1990); Kostelny et al., J. Immunol.,
148:1547-1553 (1992).
[0079] An "isolated antibody," as used herein, is intended to refer
to an antibody which is substantially free of other antibodies
having different antigenic specificities. In addition, an isolated
antibody is typically substantially free of other cellular material
and/or chemicals. In one embodiment of the invention, multiple
"isolated" monoclonal antibodies having different binding
specificities are combined in a well defined composition.
[0080] As used herein, "isotype" refers to the antibody class
(e.g., IgM or IgG1) that is encoded by heavy chain constant region
genes. In one embodiment, an antibody or antigen binding portion
thereof is of an isotype selected from an IgG1, an IgG2, an IgG3,
an IgG4, an IgM, an IgA1, an IgA2, an IgAsec, an IgD, or an IgE
antibody isotype.
[0081] Monoclonal antibodies described herein include "chimeric"
and "humanized" antibodies in which a portion of the heavy and/or
light chain is identical with or homologous to corresponding
sequences in antibodies derived from a particular species or
belonging to a particular antibody class or subclass, while the
remainder of the chain(s) is identical with or homologous to
corresponding sequences in antibodies derived from another species
or belonging to another antibody class or subclass, as well as
fragments of such antibodies, so long as they exhibit the desired
biological activity (U.S. Pat. No. 4,816,567; and Morrison et al.,
Proc. Nati. Acad. Sci. USA, 81:6851-6855 (1984)). "Humanized" forms
of non-human (e.g., murine) antibodies are chimeric antibodies
which contain minimal sequence derived from non-human
immunoglobulin. For the most part, humanized antibodies are human
immunoglobulins (recipient antibody) in which the hypervariable
region residues of the recipient are replaced by hypervariable
region residues from a non-human species (donor antibody) such as
mouse, rat, rabbit or nonhuman primate having the desired
specificity, affinity, and capacity. In some instances, Fv
framework region (FR) residues of the human immunoglobulin are
replaced by corresponding non-human residues. Furthermore,
humanized antibodies may comprise residues which are not found in
the recipient antibody or in the donor antibody. These
modifications are made to further refine antibody performance In
general, the humanized antibody will comprise substantially all of
at least one, and typically two, variable domains, in which all or
substantially all of the hypervariable loops correspond to those of
a non-human immunoglobulin and all or substantially all of the FR
regions are those of a human immunoglobulin sequence. The humanized
antibody optionally also will comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin. For further details, see Jones et al., Nature,
321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988);
and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992). Chimeric or
humanized antibodies can be prepared based on the sequence of a
murine monoclonal antibody prepared as described above. DNA
encoding the heavy and light chain immunoglobulins can be obtained
from the murine hybridoma of interest and engineered to contain
non-murine (e.g., human) immunoglobulin sequences using standard
molecular biology techniques. For example, to create a chimeric
antibody, the murine variable regions can be linked to human
constant regions using methods known in the art (see, e.g., U.S.
Pat. No. 4,816,567 to Cabilly et al.). To create a humanized
antibody, the murine CDR regions can be inserted into a human
framework using methods known in the art (see, e.g., U.S. Pat. No.
5,225,539 to Winter, and U.S. Pat. Nos. 5,530,101; 5,585,089;
5,693,762 and 6,180,370 to Queen et al.).
[0082] The monoclonal antibodies described herein also include
"human" antibodies, which can be isolated from various sources,
including, e.g., from the blood of a human patient or recombinantly
prepared using transgenic animals. Examples of such transgenic
animals include KM-MOUSE.RTM. (Medarex, Inc., Princeton, N.J.)
which has a human heavy chain transgene and a human light chain
transchromosome (see WO 02/43478), XENOMOUSE.RTM. (Abgenix, Inc.,
Fremont Calif.; described in, e.g., U.S. Pat. Nos. 5,939,598;
6,075,181; 6,114,598; 6, 150,584 and 6,162,963 to Kucherlapati et
al.), and HUMAB-MOUSE.RTM. (Medarex, Inc.; described in, e.g.,
Taylor, L. et al., Nucleic Acids Research, 20:6287-6295 (1992);
Chen, J. et al., International Immunology, 5:647-656 (1993);
Tuaillon et al., Proc. Natl. Acad. Sci. USA, 90:3720-3724 (1993);
Choi et al., Nature Genetics, 4:117-123 (1993); Chen, J. et al.,
EMBO J., 12: 821-830 (1993); Tuaillon et al., J. Immunol.,
152:2912-2920 (1994); Taylor, L. et al., International Immunology,
6: 579-591 (1994); and Fishwild, D. et al., Nature Biotechnology,
14:845-851 (1996); U.S. Pat. Nos. 5,545,806; 5,569,825; 5,625,126;
5,633,425; 5,789,650; 5,877,397; 5,661,016; 5,814,318; 5,874,299;
and 5,770,429; 5,545,807; and PCT
[0083] Publication Nos. WO 92/03918, WO 93/12227, WO 94/25585, WO
97/13852, WO 98/24884 and WO 99/45962, WO 01/14424 to Korman et
al.). Human monoclonal antibodies of the invention can also be
prepared using SCID mice into which human immune cells have been
reconstituted such that a human antibody response can be generated
upon immunization. Such mice are described in, for example, U.S.
Pat. Nos. 5,476,996 and 5,698,767 to Wilson et al.
[0084] Another example of the type of protein that may be produced
using the methods of the present invention is a fusion protein. A
fusion protein is a protein, or domain or a protein (e.g., a
soluble extracellular domain) fused to a heterologous protein or
peptide. Representative fusion proteins include, but are not
limited to, proteins expressed as a fusion with a portion of an
immunoglobulin molecule, proteins expressed as fusion proteins with
a zipper moiety, and novel polyfunctional proteins, such as a
fusion protein of a cytokine and a growth factor. WO 93/08207 and
WO 96/40918 describe the preparation of various soluble oligomeric
forms of a molecule referred to as CD40L, including an
immunoglobulin fusion protein and a zipper fusion protein,
respectively. The techniques described in WO 93/08207 and WO
96/40918 are applicable to other proteins. Generally speaking, any
molecule can be expressed as a fusion protein including, but not
limited to, the extracellular domain of a cellular receptor
molecule, an enzyme, a hormone, a cytokine, a portion of an
immunoglobulin molecule, a zipper domain, and an epitope.
C. Cell Culture Clarification and Purification
[0085] The present invention further provides improved methods for
clarifying a cell culture e.g., so as to facilitate collection of
the expressed protein. Specifically, the present invention provides
a method for clarifying a protein from a cell culture by adjusting
the pH of the cell culture to below neutral pH (i.e., below a pH of
7) and settling the cell culture, such that the cell culture
separates to form a supernatant layer and a cell-bed layer, wherein
the protein is present in and can be isolated from the supernatant
layer. In certain embodiments, methods of the present invention
comprise steps to enhance the clarification process. For example,
after the protein is isolated from the supernatant layer, the
methods may further comprise washing the cell-bed with the same pH
buffer, additional settling, and additional filtration such that
more protein yield can be obtained from the cell culture. The
clarification methods described herein can be used in combination
with the above-described cell culture method or any other cell
culture method.
[0086] As used herein, the term "cell culture supernatant layer"
refers to the liquid fraction of the cell culture, including the
liquid phase of the cell-bed.
[0087] As used herein, the term "cell bed layer" refers to the
biomass layer of the cell culture.
[0088] As used herein, the term "settling" refers to the process of
allowing the cell culture to sit undisturbed for a period of time,
so as to facilitate separation of the supernatant from the
cell-bed. The cell culture can be settled for any period of time,
including but not limited to about 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,
57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105,
106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,
119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,
132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144,
and 145 minutes. In one embodiment, the cell culture can be settled
for between about 30-120 minutes. In another embodiment, the cell
culture can be settled for between about 30-60, 60-90 or 90-120
minutes.
[0089] Cell cultures can be clarified using the methods described
herein either alone or in combination with other known
clarification and purification techniques. Such known processes
included, but are not limited to, filtration, centrifugation,
precipitation (e.g., ethanol precipitation or ammonium sulfate
precipitation), phase separation, affinity purification, gel
filtration, ion exchange chromatography, hydrophobic interaction
chromatography (HIC; using such resins as phenyl ether, butyl
ether, or propyl ether),
[0090] HPLC, or fractionation on immunoaffinity or ion-exchange
columns, reverse SDS-PAGE, or any combination of these techniques.
A protease inhibitor such as phenyl methyl sulfonyl fluoride (PMSF)
also may be useful to inhibit proteolytic degradation during
clarification.
[0091] One skilled in the art will appreciate that clarification
methods suitable for the protein of interest may require
modification to account for changes in the character of the protein
upon expression in recombinant cell culture. Additionally, the
desired degree of clarification depends on the particular protein
and the intended use of the protein. The proteins ultimately
isolated using the methods described herein can be suitable for
therapeutic and diagnostic uses.
[0092] As used herein, the term "depth filtration" refers to a type
of filtration performed using a depth filter. A depth filter
usually has multiple layers of filtration media, each of varying
size and density, which become progressively finer and denser in
the lower layer. A depth filter traps particular within it
structure, not just on the surface.
[0093] As used herein, the term "polishing filtration" refers to a
finer grade of depth filtration and membrane filtration.
[0094] The present invention is further illustrated by the
following examples which should not be construed as further
limiting. The contents of all figures and all references, patents
and published patent applications cited throughout this application
are expressly incorporated herein by reference in their
entireties.
EXAMPLES
Example 1
Super Density Fed-Batch Cell Culture Process
A. Experimental Methods
[0095] Recombinant CHO cells (i.e., antibody producing CHOK1SV
cells) were expanded in cell culture flasks before inoculating the
Wave perfusion bioreactor. The perfusion bioreactor was operated
with the same basal medium that is used in cell expansion process.
The perfusion rate was adjusted to maintain a healthy culture with
high cell viabilities. In certain experiments, cells were
concentrated to a higher cell density, as appropriate, by adjusting
the medium in and out flow rates. Once the viable cell density
reached greater than 50.times.10.sup.6 cells/mL, fed-batch
production process was started. The culture was fed by a
combination of bolus and continuous feeding modes, so as to control
the osmolality and glucose level. The cell culture was then
harvested when cell viability decreased to approximately
60-10%.
B. Experiment 1
[0096] Cells were inoculated in a BIOSTAT Cultibag (Sartorius) at
approximately 0.84.times.10.sup.6 cells/mL. The specific perfusion
rate (SPR) ranged from 0.25 to 0.03.times.10.sup.-6 mL cell.sup.-1
day.sup.-1. Cells were concentrated about 2.6 fold when viable cell
density reached 12.6.times.10.sup.6 cells/mL. After concentration,
cells were grown up to 108.8.times.10.sup.6 cells/mL. Once the
cells reached 108.8.times.10.sup.6 cells/mL, perfusion was stopped
and the fed-batch process was started immediately. During the
fed-batch process, one or two bolus feeds at 3 to 10% (i.e.,
percentage of feed to post feed volume) were performed every day to
maintain cell viability. Glucose was also supplemented by bolus
feed to maintain a sufficient level. Cell density reached
124.66.times.10.sup.6 cells/mL with 98% viability the second day
after fed-batch process started. The total feed percentage was
about 40%. As shown in the growth and production profile depicted
in FIG. 3, a final productivity of 8.8 g/L from fed-batch process
was achieved after 6 days at 39% viability.
C. Experiment 2
[0097] Cells were inoculated in the WAVE BIOREACTOR.RTM. (GE
Healthcare, Fairfield, Conn.) at approximately 0.81.times.10.sup.6
cells/mL. The rate of specific perfusion (SPR) ranged from 0.07 to
0.01.times.10.sup.-6mL cell.sup.-1 day.sup.-1 and varied at
different time points. The cells were concentrated about 1.5 fold
overnight between days 15 and 16. On day 16, the cell density
reached up to 136.5.times.10.sup.6 cells/mL. At this point in time,
the perfusion process was stopped and the fed-batch process was
started. One or two bolus feeds at 1 to 6% were performed in the
first two days to maintain cell viability. Continuous feeding of
glucose and/or other nutrients was started on the first day of the
fed-batch process to maintain glucose level, as well as to promote
a favorable osmolality increasing trend, while providing sufficient
nutrients.
[0098] The cells grew to 142.0.times.10.sup.6 cells/mL about 7
hours after fed-batch process started and the total feed percentage
was about 28%. As shown in the growth and production profile
depicted in FIG. 4, a final productivity of 13.8 g/L was achieved
after 6 days at 61% viability from fed-batch production phase.
[0099] During this experiment, it was noted that feed components
fell out of solution in the pump tubing during the continuous
feeding process, possibly due to a slow flow rate. As such, some
modifications of feeds were made in a subsequent study (see
Experiment# 5 below) to prevent precipitation of feed components in
the pump tubing.
D. Experiment 3
[0100] Cells were inoculated in the WAVE BIOREACTOR.RTM. (GE
Healthcare, Fairfield, Conn.) at approximately 1.20.times.10.sup.6
cells/mL. The rate of specific perfusion (SPR) ranged from 0.07 to
0.03 (e.g., 0.05).times.10.sup.-6 mL cell.sup.-1 day.sup.-1 and
varied at different time points. As shown in FIG. 5, cells were
partially transferred on day 13 and day 18 to two separate 5 liter
stir tank bioreactors at a cell density of approximately
50.times.10.sup.6 cells/mL. Antifoam was also added to overcome
foaming in the bioreactors. As shown in the growth and production
profile depicted in FIG. 5, a final productivity of 6.3 g/L at
about 40% viability was achieved from the fed-batch cells
transferred on day 13 (i.e., 2391AB) (see FIG. 6). A final
productivity of 7.1 g/L at about 38% viability was achieved from
the fed-batch cells transferred on day 18 (i.e., 2391BB) (see FIG.
6).
E. Experiment 4
[0101] A further perfusion run was performed to repeat the cell
culture process of the foregoing examples in a single perfusion
bioreactor (i.e., such that both perfusion and fed-batch occurred
in the same bioreactor). Through the optimization of perfusion
process (e.g., specific perfusion rate (SPR)), the cell density
reached over 100.times.10.sup.6 cells/mL on day 8. The SPR was
maintained at a range of about 0.15 to 0.05, to keep the cells in a
stable and healthy condition. This led to a more than 100% increase
of cell growth rate, as compared to the initial perfusion runs
(Experiment #s 1 and 2). Cell density increased by about 70% per
day.
[0102] Once the cell density reached over 100.times.10.sup.6
cells/mL, the fed-batch process was started immediately and medium
perfusion was stopped. Two to three time bolus feeds at 2 to 6%
were performed every day for three days. On the second day after
the fed-batch process was started, the cell density reached
119.5.times.10.sup.6 cells/mL and 98% viability was achieved.
Continuous feeding of glucose and/or other nutrients was performed
throughout the fed-batch process to maintain glucose level and
control the osmolality increase rate. The total feed volume
percentage was about 60%.
[0103] Optimization of concentrations and ratios for feed
components led to a clear solution in the pump tubing during
continuous feeding process. No visible precipitation was observed.
However, feed volume increased significantly compared to experiment
#2, which resulted in a diluted product concentration. As shown in
FIG. 7, the final volumetric productivity was 8.9 g/L.
F. Summary of Experiments 1-4
[0104] FIG. 8 summarizes the productivity and cell integral of
Experiment #s 1-3 (i.e., wherein the fed-batch process started with
over 100.times.10.sup.6 cells/mL) and Experiment # 4 (i.e., wherein
the fed-batch process started with about 50.times.10.sup.6
cells/mL). The productivity is represented in terms of the actual
observed final titer, as well as a normalized titer (e.g.,
normalized by starting volume and final perfusion cell density per
100 million cells/mL). For example, the normalized titer can be
calculated as follows:
Normalized titer=observed titer/(starting culture
volume.times.final perfusion cell density in 10.sup.6
cells/mL).times.100
G. Optimizing Cell Culture Conditions
[0105] Various experimental parameters can be adjusted to optimize
the cell culture conditions. For example, the basal medium can be
optimized by concentrating the nutrients, so as to potentially
reduce the perfusion volume. Alternatively or additionally, the pH
buffering component in the basal medium can be optimized to handle
low pH conditions typical of traditional stir tank bioreactors.
Further, the feed composition and/or the feeding strategy can be
optimized to promote productivity and efficiency, while maintaining
good solubility.
Example 2
Clarification of Super Density Fed-Batch Cell Culture Process
[0106] Due to the super high cell densities produced in the
above-described culture methods, the resultant culture has a high
percentage of cell-bed solid volume (e.g., 20% cell bed volume for
cultures when cell density is over 100.times.10.sup.6 cells/mL by
natural settling or centrifugation) and very turbid supernatant. As
such, it can be challenging to harvest the protein. Accordingly,
several different experimental methods were tested to improve the
efficiency of the harvesting process, i.e., cell settling, filter
aid, adding CaCl.sub.2, decreasing the pH to 5.5 before cell
settling, as well as various combinations of these techniques.
[0107] Specifically, various conditions were tested using the
1201-09-29311AB run from Experiment #3 (described above). As shown
in FIG. 9, the pH was decreased to 4.5 or 5.5, with or without
adding filter aid, before settling the cell culture for 90 minutes.
All conditions tested significantly reduced the turbidity (depicted
as bars in FIG. 9) after cell settling. Compared to the control
bioreactor titer, a pH 4.5 in combination with filter aid led to
some product loss by protein A HPLC assay (depicted as diamond
symbols in FIG. 9).
[0108] Additionally, decreasing the pH or adding calcium salts
and/or filter aid prior to settling, the cell bed volume increased
to about 40-50% and produced a much clearer cell supernatant. This
enhanced clarification process was also tested for other proteins
and similar results were obtained. In sum, a low pH settling
strategy increased filtration capacity significantly and also
increased the quality of the filtrate.
[0109] Additional steps, such as washing the bed with product
compatible buffer or diluted PBS at the same pH condition that used
to settle the cells, additional settling, and additional
filtration, can optionally be performed to enhance the
clarification process, as shown in FIG. 10. However, it is to be
noted that FIG. 10 is not intended to be limiting, and the
additional optional steps (e.g., filtration, centrifugation,
washing, etc.) can occur in a different order than is depicted in
FIG. 10. For example, centrifugation can optionally be performed
prior to or after the settling process.
Equivalents
[0110] Those skilled in the art will recognize, or be able to
ascertain using no more than routine experimentation, many
equivalents of the specific embodiments of the invention described
herein. Such equivalents are intended to be encompassed by the
following claims. Any combination of the embodiments disclosed in
the dependent claims is contemplated to be within the scope of the
invention.
INCORPORATION BY REFERENCE
[0111] The contents of all references, patents and published patent
applications cited throughout this application, as well as the
figures and Sequence Listing, are expressly incorporated herein by
reference.
* * * * *