U.S. patent application number 12/126611 was filed with the patent office on 2009-01-01 for compositions comprising high concentration of biologically active molecules and processes for preparing the same.
This patent application is currently assigned to VGX PHARMACEUTICLAS, INC.. Invention is credited to Ying Cai, Ruxandra Draghia-Akli, Henry Hebel.
Application Number | 20090004716 12/126611 |
Document ID | / |
Family ID | 39669869 |
Filed Date | 2009-01-01 |
United States Patent
Application |
20090004716 |
Kind Code |
A1 |
Draghia-Akli; Ruxandra ; et
al. |
January 1, 2009 |
COMPOSITIONS COMPRISING HIGH CONCENTRATION OF BIOLOGICALLY ACTIVE
MOLECULES AND PROCESSES FOR PREPARING THE SAME
Abstract
Large scale processes for producing high purity samples of
biologically active molecules of interest from bacterial cells are
disclosed. The methods comprise the steps of producing a lysate
solution by contacting a cell suspension of said plurality of cells
with lysis solution; neutralizing said lysate solution with a
neutralizing solution to produce a dispersion that comprises
neutralized lysate solution and debris; filtering the dispersion
through at least one filter; performing ion exchange separation on
said neutralized lysate solution to produce an ion exchange eluate;
and performing hydrophobic interaction separation on said ion
exchange eluate to produce a hydrophobic interaction solution.
Further, provided are compositions comprising large scale amounts
of plasmid DNA produced by the disclosed large scale processes.
Inventors: |
Draghia-Akli; Ruxandra;
(Houston, TX) ; Hebel; Henry; (The Woodlands,
TX) ; Cai; Ying; (The Woodlands, TX) |
Correspondence
Address: |
Pepper Hamilton LLP
400 Berwyn Park, 899 Cassatt Road
Berwyn
PA
19312-1183
US
|
Assignee: |
VGX PHARMACEUTICLAS, INC.
Blue Bell
PA
|
Family ID: |
39669869 |
Appl. No.: |
12/126611 |
Filed: |
May 23, 2008 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60939792 |
May 23, 2007 |
|
|
|
Current U.S.
Class: |
435/170 ;
435/320.1 |
Current CPC
Class: |
C12N 15/1017 20130101;
C12N 1/06 20130101 |
Class at
Publication: |
435/170 ;
435/320.1 |
International
Class: |
C12P 1/00 20060101
C12P001/00; C12N 15/00 20060101 C12N015/00 |
Claims
1. A large scale process for producing high purity samples of at
least one biologically active molecule of interest from bacterial
cells, comprising the steps of: a) producing a lysate solution by
contacting a cell suspension of said plurality of cells with lysis
solution; b) neutralizing said lysate solution with a neutralizing
solution to produce a dispersion that comprises neutralized lysate
solution and debris; c) filtering the dispersion through at least
one filter; d) performing ion exchange separation on said
neutralized lysate solution to produce an ion exchange eluate; and
e) performing hydrophobic interaction separation on said ion
exchange eluate to produce a hydrophobic interaction solution.
2. The method of claim 1, wherein step a) comprises mixing said
cell suspension with lysis solution in a high shear, in-line
mixer.
3. The method of claim 1, wherein step b) comprises mixing said
lysate solution with said neutralizing solution in a bubble
mixer.
4. The method of claim any one of claims 1, wherein step e)
comprises performing hydrophobic interaction separation using a
hydrophobic interaction column or a hydrophobic interaction
membrane to form a hydrophobic interaction solution.
5. The method of any of claims 1, further comprising the step: f)
preparing a solution of at least one biologically active molecule
by ultrafiltration of said hydrophobic interaction solution.
6. The method of claims 5, further comprising the step: g)
preparing a sterile solution of at least one biologically active
molecule by sterile filtration of said solution of biologically
active molecules.
7. The method of claim 1, further comprising holding the dispersion
for a period of time to separate the neutralized lysate solution
from the debris and filtering the neutralized lysate solution
through at least one filter.
8. The method of claim 1, wherein the producing step comprises
contacting the cell suspension with the lysis solution in a mixer
over a duration of from about 1 minutes to about 20 minutes.
9. The method of claim 8, wherein the duration is from about 4
minutes to about 8 minutes.
10. The method of claim 8, wherein the duration is about 5
minutes.
11. The method of claim 1, wherein said biologically active
molecule is a plasmid.
12. The method of claim 1 wherein said ion exchange is an anion
exchange membrane.
13. The method of claim 1, wherein step e) comprises performing
hydrophobic interaction separation comprises butyl hydrophobic
interaction chromatography in order to produce a hydrophobic
interaction solution that is a butyl hydrophobic interaction
chromatography solution eluate.
14. The method of claim 1, wherein the method comprises
transitioning from one step to a subsequent step substantially
continuously and comprises separating the neutralized lysate
solution from the debris in the dispersion by collecting the lysate
in a container and passing the dispersion through a primary filter
to produce an initial crude neutralized lysate solution.
15. The method of claim 14, further comprising passing the first
crude neutralized lysate solution through a secondary filter to
produce a subsequent crude neutralized lysate solution.
16. A large scale process for producing high purity samples of at
least one biologically active molecule of interest from bacterial
cells, comprising the steps of: contacting the bacterial cells in a
dispersion of cells with lysis solution to form a lysate solution;
neutralizing the lysate solution by mixing a neutralization
solution into the lysate solution with a bubble column mixer to
form a neutralized mixture; filtering the neutralized mixture
through a primary filter and a secondary filter to form a filtered
solution; passing the filtered solution through an ion-exchange
column to form a ion-exchange solution; passing the ion-exchange
solution through a hydrophobic interaction column or a hydrophobic
interaction membrane to form a hydrophobic interaction solution;
and ultrafiltration of the hydrophobic interaction solution to form
a high purity sample of at least one biologically active molecules
of interest; wherein each transition from one step to a subsequent
step in the large scale process from the contacting step to the
passing the filtered solution step occur substantially
continuously.
17. A composition comprising of at least one biologically active
molecule of interest prepared by the method of claims 1, wherein at
least one biologically active molecule of interest is a DNA
plasmid.
18. The composition of claim 17, where the composition comprises
DNA plasmids at a quantity of about 10 mg or more in solution,
wherein the high purity of said plasmids is the plasmids being
present at greater than about 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, or 99%.
19. The composition of claim 18, wherein the purity of said plasmid
is greater than about 99%.
20. The composition of claim 18, wherein concentration of plasmid
in the solution is about 5, 6, 7, 8, 9, 10, 11, 12, or 13
mg/mL.
21. The composition of claim 18, wherein said plasmid comprises
greater than about 50% supercoiled plasmid.
22. The composition of claim 18, wherein said plasmid comprises
greater than about 80% supercoiled plasmid.
23. The composition of claim 18, wherein said solution contains
less than or equal to about 10 EU endotoxin per mg of plasmid.
24. The composition of claim 18, wherein said solution contains
less than or equal to about 1 EU endotoxin per mg of plasmid.
25. The composition of claim 18, wherein said solution contains
less than or equal to about 0.1 EU endotoxin per mg of plasmid.
26. The composition of claim 18, wherein said solution contains
less than or equal to about 1.0% RNA.
27. The composition of claim 18, wherein said solution contains
less than or equal to about 0.4% RNA.
28. The composition of claim 18, wherein said solution contains
less than or equal to about 1.0% protein.
29. The composition of claim 18, wherein said solution contains
less than or equal to about 0.20% protein.
30. The composition of claim 18, wherein said solution contains
less than or equal to about 1% genomic DNA.
31. The composition of claim 18, wherein said solution contains
less than or equal to about 0.01% genomic DNA.
Description
CROSS REFERENCE TO RELATED APPLICATION
[0001] This application claims the benefit of U.S. Provisional
Application No. 60/939,792, filed May 23, 2007, the contents of
which are incorporated herein by reference.
FIELD OF THE INVENTION
[0002] The present invention relates to bulk compositions
comprising biologically active molecules such as plasmids in high
concentrations and processes for producing such compositions.
BACKGROUND OF THE INVENTION
[0003] There are numerous uses of biologically active molecules
produced in and isolated from cells. U.S. Publication Serial No.
20050014245, which is incorporated herein by reference, discloses
devices and methods for biomaterial production. Biologically active
molecules include proteins and nucleic acid molecules. Production
of such molecules in living cells offers numerous advantages over
alternative productions methods but isolation and purification
issues arise when extracting biologically active molecules from
cells. There are various components present in cells which prevent
realization of high yields of biologically active molecules of
interest as well as representing possible unwanted contaminants to
a final product.
[0004] Plasmid production is a field of interest due to the
emergence of the non-viral gene therapy and DNA vaccine fields.
Plasmids are large and complex macromolecules, which are maintained
as supercoiled DNA structures unless disrupted. Rather then using
synthetic means, in many instances it is more cost effective to
produce them in biological systems, and subsequently isolate and
purify them from those systems. Biological production of plasmids
commonly takes the form of fermenting Escherichia coli ("E. coli")
cells containing the plasmid of interest.
[0005] Cell lysis and the subsequent treatment steps used to
prepare a process stream for purification, are the most difficult,
complex, and important steps in any plasmid process. It is in this
process where yield and quality are defined for each plasmid
production run. The search for an optimal method, one which is
continuous, scaleable, and yielding high quality product that can
be formulated at high concentration irrespective of plasmid size,
has been an obstacle in getting acceptable processes to commercial
capability.
[0006] Lysing bacteria for plasmid purification using alkali and
detergents is a common technique. Unfortunately, this method
presents significant challenges for large scale preparations (or
scaled-up production). First, thorough mixing of suspended cells
with lysis solution is easily managed at small scale by simply
vortexing or inverting the vessel containing the cells. However,
this is impractical at large scale, where volumes may be in the
range of tens or hundreds of liters. Common techniques for mixing
large volumes of liquid, such as impeller mixing, are problematic
because as some cells begin to lyse after initial mixing, they
release genomic DNA which dramatically increases solution
viscosity. This increase in viscosity significantly interferes with
further mixing. Another challenge is that excessive incubation at
high pH after addition of alkaline lysis solution can lead to
permanent denaturation of the plasmid, making it unsuitable for
most subsequent uses, especially for therapeutic purposes.
Furthermore, it is well known that mixing at this step should be
thorough but sufficiently gentle (i.e., low shear) to prevent
substantial amounts of material from the flocculent precipitate
into the plasmid-containing solution. Large amounts of host genomic
DNA and endotoxin are present in the flocculent precipitate and if
they become mixed with the plasmid they can be difficult to
separate from the plasmid during subsequent purification. Thus, the
large scale production of plasmids expose large quantities of cells
to lysis solution, mix them and neutralize the lysate in a manner
to optimize plasmid yield, minimize plasmid degradation, and
maximize removal of other cellular components so that the material
can be further purified to produce a high concentration, high
quality, high purity final product in relatively large volumes.
[0007] There are a variety of existing methods to purify plasmids;
however, these methods are not suitable for large scale
preparations. Laboratory scale purification techniques cannot
simply be scaled up for the volumes involved in large scale plasmid
preparation. Large scale preparations require the optimization of
yield and molecular integrity while maximizing removal of
contaminants and concentration of plasmid. In producing large
quantities of plasmid DNA at high concentration, a problem exists
in maintaining the plasmid as supercoiled and open circle relaxed
form. Storage conditions generally require high salt, and molecular
degradation over time remains a problem even in the presence of
salt. Many existing purification methods rely upon the use of
potentially dangerous, toxic, mutagenic or contaminated substances,
and/or expensive substances or equipment, which, again, are not
desirable for large scale preparations. Some existing purification
methods utilize the use of enzyme to digest protein for eventual
elimination and such enzymes are costly for large scale production
and can cause a risk of biologic contamination.
[0008] There remains a need for methods of large scale production
of biologically active molecules of interest, such as plasmids, in
which the final product can be produced in a cost effective manner,
such as minimal equipment and/or minimal process steps, with high
yield, at high concentration, and minimal degradation and without
the presence of impurities, contaminants and unwanted substances.
There remains a need for large quantities of plasmids solutions
having high concentration and minimal degradation and presence of
impurities, contaminants and unwanted substances and methods of
preparing such solutions. The need for large quantities of plasmids
is greater for those plasmids that are low copy number plasmids,
which require much larger quantities of cells to yield plasmid
quantities in the milligram ("mg") range and above.
SUMMARY OF THE INVENTION
[0009] An aspect of the present invention comprises large scale
processes for producing high purity samples of at least one
biologically active molecule of interest from bacterial cells. The
large scale processes comprise the steps of:
[0010] a) producing a lysate solution by contacting a cell
suspension of said plurality of cells with lysis solution;
[0011] b) neutralizing said lysate solution with a neutralizing
solution to produce a dispersion that comprises neutralized lysate
solution and debris;
[0012] c) filtering the dispersion through at least one filter;
[0013] d) performing ion exchange separation on said neutralized
lysate solution to produce an ion exchange eluate; and
[0014] e) performing hydrophobic interaction separation on said ion
exchange eluate to produce a hydrophobic interaction solution. In
some embodiments of this aspect, the large scale processes further
includes the step of preparing a solution of at least one
biologically active molecule by ultrafiltration of said hydrophobic
interaction solution.
[0015] A further aspect of the present invention comprises large
scale processes for producing high purity samples of at least one
biologically active molecule of interest from bacterial cells,
comprising the steps of: contacting the bacterial cells in a
dispersion of cells with lysis solution to form a lysate solution;
neutralizing the lysate solution by mixing a neutralization
solution into the lysate solution with a bubble column mixer to
form a neutralized mixture; filtering the neutralized mixture
through a primary filter and a secondary filter to form a filtered
solution; passing the filtered solution through an ion-exchange
column to form a ion-exchange solution; passing the ion-exchange
solution through a hydrophobic interaction column or a hydrophobic
interaction membrane to form a hydrophobic interaction solution;
and ultrafiltration of the hydrophobic interaction solution to form
a high purity sample of at least one biologically active molecule
of interest; wherein each transition from one step to a subsequent
step in the large scale process from the contacting step to the
passing the filtered solution step occur substantially
continuously.
[0016] In another aspect of the present invention, provided are
compositions comprising at least one biologically active molecule
of interest prepared by the method described and disclosed herein,
wherein at least one biologically active molecule of interest is a
DNA plasmid. In some embodiments the compositions comprise at least
one DNA plasmid at a quantity of about 10 mg or more in solution,
wherein the high purity of said plasmids is the plasmids being
present at greater than about 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, or 99%.
BRIEF DESCRIPTION OF THE DRAWINGS
[0017] The numerous objects and advantages of the present invention
may be better understood by those skilled in the art by reference
to the accompanying figures, in which:
[0018] FIG. 1 displays a schematic of one embodiment that is used
to isolate and purify biologically active molecules of interest
from bacterial cells in a continuous flow process.
[0019] FIG. 2 displays a picture of an electrophoretic gel that
includes samples from EXAMPLE 1, below. Lane 1 represents the
supercoiled plasmid ladder (Invitrogen); Lane 2 the cell lysate;
Lane 3 product after Q anion exchange; Lane 4 the product after
purification with hydrophobic interaction; and lane 5 the final
product blended after UF.
[0020] FIG. 3 displays a picture of an electrophoretic gel that
includes samples from EXAMPLE 3. Lane 1 represents the supercoiled
plasmid ladder (Invitrogen); Lane 2 represents the lysate after
primary filtration using a 48 .mu.m pleated cartridge; Lane 3
represents the filtrate after secondary filtration using a 1 .mu.m
pleated cartridge; Lane 4 represents the filtrate after a third
filtration using a C0HC Pod filter; Lane 5 represents the eluate
product fraction #1 after undergoing step of Mustang Q anion
exchange; and Lane 6 represents the secondary fraction of Q
eluate.
DESCRIPTION OF PREFERRED EMBODIMENTS
[0021] Methods of purifying biologically active molecules of
interest from cells are provided so as to purify biologically
active molecules of interest at high levels of purity and
concentrations from the cells. Preferably the biologically active
molecules of interest are plasmids or DNA plasmids. The cells may
be any cells containing biologically active molecules of interest.
In some embodiments, the cells are microbial cells such as for
example prokaryotic cells such as bacterial cells. In some
embodiments, they are E. coli cells. The cells may be produced or
generated by any means, such as for example by fermentation.
Methods for fermenting cells are well known to those skilled in the
art. The present invention may be employed to extract any
biologically active molecules of interest from cells. In some
embodiments, the present invention may be employed to extract more
than one type of biologically active molecule of interest. The
biologically active molecules of interest may be a macromolecule
such as a nucleic acid molecule or protein. In some embodiments,
the biologically active molecule of interest may be a plasmid.
[0022] The term "plasmid" or "DNA plasmid," used interchangeably,
refers to circular DNA molecules that are extra-chromosomal DNA
molecules separate from the chromosomal DNA which are capable of
replicating independently of the chromosomal DNA. An encoding
sequence or transgene is often contained within the DNA plasmid,
and when present, the DNA plasmid is referred to as an expression
plasmid or expression construct. The coding sequence, or "encoding
nucleic acid sequence," can include initiation and termination
signals operably linked to regulatory elements including a promoter
and polyadenylation signal capable of directing expression in the
cells of the individual to whom the nucleic acid molecule is
administered.
[0023] The term "large scale" as used in reference to the described
processes refers to purification processes that produce from
bacterial cells or a suspension of bacterial cells quantities of at
least one biologically active molecules, particularly DNA plasmid,
of about 1 gram or greater and/or purification processes that
requires lysis of quantities of bacterial cell paste of about 1
kilogram or greater.
[0024] The term "high purity" as used in reference to the level of
purity of biologically active molecules, particularly DNA plasmid,
refers to purification of the molecules from host bacterial cells
at a level of at least greater than or equal to about 90%; and
preferably greater than or equal to about 91%, greater than or
equal to about 92%, greater than or equal to about 93%, greater
than or equal to about 94%, greater than or equal to about 95%,
greater than or equal to about 96%, greater than or equal to about
97%, greater than or equal to about 98%, or greater than or equal
to about 99%.
[0025] The term "continuous" or "substantially continuous" as used
in reference to the processes described herein refers to a
continuous flow of materials (or solution or dispersion) between
each step of the purification process to each subsequent step,
starting from the beginning of the purification process up until
the step of loading the ion-exchange chromatography column. For
example, as bacterial cells of a dispersion contact with lysis
solution in the contacting step to form a lysate solution, such
lysate solution will directly flow into the next step of
neutralization with the neutralization solution. These continuous
transitions between steps eliminate a holding or incubating step
between the purification process steps.
[0026] The term "biologically active molecule" refers to a molecule
or a biomolecule contained within the bacteria that is in its
functional state, and, in some embodiments, particularly refers to
a DNA plasmid. Such DNA plasmids can be isolated and used to
transfect cells of interest. The compositions of the present
invention comprise at least one type of biological active molecule.
In some embodiments, the compositions of the present invention
comprise more than one type of biological active molecules.
[0027] Plasmids vary widely in their copy number depending on the
origin of replication they contain, e.g., pMB1 or pSC101, which
determines whether they are under relaxed or stringent control; as
well as the size of the plasmid and its associated inserted
sequences. Some plasmids, such as the pUC series and derivatives,
have mutations which allow them to reach very high copy numbers
within the bacterial cell. Plasmids based on pBR322 are generally
maintained at lower copy numbers. Very large plasmids are often
maintained at very low copy numbers per cell. Some embodiments of
the present invention relate to a plasmid purification process that
allows for purifying plasmids from cells, preferably bacterial
cells, in large scale to yield large quantities of plasmid, such as
gram quantities, in cost-efficient and minimal-steps manufacturing
process (in order to maintain higher yields). In some embodiments,
the plasmid is a low copy number plasmid. For purposes of the
process provided and the resulting biologically active molecules
produced, a low copy number plasmid is a plasmid that achieves a
copy number of less than or equal to about 300, less than or equal
to about 100, less than or equal to about 50, less than or equal to
about 20, less than or equal to about 10, or less than or equal to
about 5.
[0028] An aspect of the present invention comprises large scale
processes for producing high purity samples of at least one
biologically active molecule of interest from bacterial cells. The
processes comprise the steps of:
[0029] a) producing a lysate solution by contacting a cell
suspension of said plurality of cells with lysis solution;
[0030] b) neutralizing said lysate solution with a neutralizing
solution to produce a dispersion that comprises neutralized lysate
solution and debris;
[0031] c) filtering the dispersion through at least one filter;
[0032] d) performing ion exchange separation on said neutralized
lysate solution to produce an ion exchange eluate; and
[0033] e) performing hydrophobic interaction separation on said ion
exchange eluate to produce a hydrophobic interaction solution.
[0034] In an embodiment, the large scale processes comprise a
producing lysate solution step that comprises mixing said cell
suspension with lysis solution in a high shear, in-line mixer.
[0035] In some embodiments, the producing step comprises contacting
the cell suspension with the lysis solution in a mixer over a
duration of from about 1 minutes to about 20 minutes, preferably
from about 4 minutes to about 8 minutes, and more preferably for
about 5 minutes. In some embodiments, the neutralizing step
comprises mixing the lysate solution with the neutralizing solution
in a bubble mixer. In some embodiments, the performing hydrophobic
interaction separation step comprises performing hydrophobic
interaction separation using a hydrophobic interaction column or a
hydrophobic interaction membrane to form a hydrophobic interaction
solution. The hydrophobic interaction separation step can be
separation of the biologically active molecule of interest by
binding to a hydrophobic interaction membrane or column, which
enables impurities to flow through or be washed off. In some
embodiments, the biologically active molecule of interest may flow
through a hydrophobic interaction column while impurities bind. In
some embodiments, the biologically active molecules of interest
flow through a hydrophobic interaction membrane (or HIC membrane)
(referred to herein as "Method I"). In some embodiments, the
biologically active molecules of interest bind to a HIC column,
such as a butyl column (referred to herein as "Method II"). In some
embodiments, a combination of HIC membrane and HIC column, such as
a butyl column, may be used (referred to herein as "Method III") to
yield large-scale amounts of biologically active molecule of
interest with high purity, such as gram or greater quantities of
DNA plasmids. In some embodiments, the hydrophobic interaction
separation comprises separation using at least butyl hydrophobic
interaction chromatography in order to produce a hydrophobic
interaction solution that is a butyl hydrophobic interaction
chromatography solution eluate.
[0036] In some embodiments, the described large scale processes can
further include a step of preparing a solution of at least one
biologically active molecule by ultrafiltration of said hydrophobic
interaction solution. Furthermore, a step of preparing a sterile
solution of biologically active molecules by sterile filtration of
said solution of biologically active molecules can be
performed.
[0037] In some embodiments, the large scale processes include a
holding step that requires holding the dispersion for a period of
time to separate the neutralized lysate solution from the debris,
and then filtering the neutralized lysate solution through at least
one filter.
[0038] In some embodiments, the performing ion exchange separation
step is performed using an anion exchange membrane. Preferably, the
ion exchange separation step comprises use of an ion exchange
column, and preferably using a Mustang.RTM. Q cartridge.
[0039] In some embodiments, the large scale processes include
continuous processes or is referred to as a continuous large scale
process for production of high purity biologically active molecules
from bacterial cells. The method comprises transitioning from one
step to a subsequent step of the large scale process substantially
continuously and comprises separating the neutralized lysate
solution from the debris in the dispersion by collecting the lysate
in a container and passing the dispersion through a primary filter
to produce an initial crude neutralized lysate solution. In some
embodiments, the processes further comprises passing the first
crude neutralized lysate solution through a secondary filter to
produce a subsequent crude neutralized lysate solution.
[0040] In an embodiment, the present invention comprises large
scale processes for producing high purity samples of biologically
active molecules of interest from bacterial cells, comprising the
steps of: contacting the bacterial cells in a dispersion of cells
with lysis solution to form a lysate solution; neutralizing the
lysate solution by mixing a neutralization solution into the lysate
solution with a bubble column mixer to form a neutralized mixture;
filtering the neutralized mixture through a primary filter and a
secondary filter to form a filtered solution; passing the filtered
solution through an ion-exchange column to form a ion-exchange
solution; passing the ion-exchange solution through a hydrophobic
interaction column or a hydrophobic interaction membrane to form a
hydrophobic interaction solution; and ultrafiltration of the
hydrophobic interaction solution to form a high purity sample of
biologically active molecules of interest; wherein each transition
from one step to a subsequent step in the large scale process from
the contacting step to the passing the filtered solution step occur
substantially continuously.
[0041] In another aspect of the present invention, provided are
compositions comprising biologically active molecules of interest
prepared by the described large scale processes herein, wherein the
biologically active molecules of interest are DNA plasmids. In some
embodiments the compositions comprise DNA plasmids at a quantity of
about 10 mg or more in solution, wherein the high purity of said
plasmids is the plasmids being present at greater than about 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. The composition of
claim 18, wherein said concentration of plasmid is about 5, 6, 7,
8, 9, 10, 11, 12, or 13 mg/mL. Some compositions include plasmid at
a level of greater than about 50%, 55%, 60%, 65%, 70%, 75%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94% or 95% supercoiled plasmid, and preferably greater 80%
supercoiled plasmid. Some compositions contain less than or equal
to about 10 EU endotoxin per mg of plasmid, and some embodiments,
the compositions, less than or equal to about 1 EU endotoxin per mg
of plasmid. Some embodiments less than or equal to about 0.1 EU
endotoxin per mg of plasmid. In some embodiments, the compositions
include solution containing less than or equal to about 1.0% RNA or
less than or equal to about 0.4% RNA. In some preferred
embodiments, the compositions include solution containing less than
or equal to about 1.0% protein, preferably less than or equal to
about 0.20% protein. In some embodiments, the compositions include
solution containing less than or equal to about 1% genomic DNA,
preferably less than or equal to about 0.01% genomic DNA.
[0042] An example of an embodiment of the present invention which
includes many of the process steps provided herein, includes the
following steps: first step, cells of interest are produced and
harvested; second step, cells are lysed to release their contents,
including the biologically active molecules of interest, into
solution; third step, solid cell debris and precipitated cell
components are separated from the fluid containing at least one
biologically active molecule of interest; fourth step, solutions
containing the biologically active molecules of interest are
subjected to ion exchange chromatography; fifth step, the partially
purified material resulting from ion exchange chromatography is
subjected to hydrophobic interaction chromatography; sixth step,
the material resulting from hydrophobic interaction chromatography
is subjected to ultrafiltration and diafiltration, to concentrate
at least one type of biologically active molecules of interest, and
to remove excess salts from the solution; seventh step, the
concentrated and desalted product is optionally subjected to
sterile filtration, to render it suitable for pharmaceutical uses,
including, for example, intramuscular delivery, intravenous
delivery, intranasal delivery, intracardiac delivery, aerosol
delivery, transdermal delivery, in vivo electroporation facilitated
delivery to muscle, in vivo electroporation facilitated delivery to
subcutaneous or intradermal tissue, as well as other known methods
of pharmaceutical administration.
[0043] Some embodiments of the invention include the process steps
disclosed herein, including, but not limited to the operation of a
combination of steps in a continuous mode resulting in the scale of
production which is not limited by the process hold steps. Such
processes enable the production of pharmaceutical grade
biomolecules at large scale, e.g. production of about 1 gram or
more of plasmid. Some embodiments of the invention exclude the use
of any materials or processes that could prove detrimental to the
large scale production or pharmaceutical products include, for
example, the inclusion of enzymes, heat denaturation, mechanical
separation (machines that do such separation), e.g., centrifugation
apparatus, or organic or volatile solvents, e.g., isopropanol.
[0044] Cells of interest may be produced and harvested such as by
routine means of fermentation and collection. It is well within the
abilities of one skilled in the art to prepare sufficient
quantities of the cells of interest. For example, the cells may be
E. coli containing a high copy number plasmid of interest, and the
plasmid-containing cells may be fermented to high density using
batch or fed batch techniques. Methods for preparing such
plasmid-containing E. coli cells and performing such batch or
fed-batch fermentation are well known to those skilled in the art.
The cells may be harvested by routine means such as centrifugation
or filtration to form a cell paste. Such harvesting methods are
well known to those skilled in the art. Furthermore, those skilled
in the art will recognize that harvested cells or cell paste may be
processed immediately, or stored in a frozen or refrigerated state
for processing at a later date.
[0045] Harvested cells may be lysed using a lysis solution to
release their contents, including the biologically active molecules
of interest, into a lysate solution.
[0046] Generally, prior to lysing the cells, the cell paste may be
used to prepare a suspension of cells containing the biologically
active molecule of interest. The cells may be suspended in any
suitable solution. The suspension containing the cells in
suspension solution may be maintained in a tank or other storage
container. Two containers may be used wherein the second container
may be used to resuspend additional amount of cells while the first
container is used in the lysis process. The suspension solution may
in some embodiments contain a moderate concentration of buffer, a
moderate concentration of a chelating agent, or both. In some
embodiments, the suspension solution may comprise about 25 mM
Tris-hydrochloride ("Tris-HCl"), and about 10 mM edetate disodium
("Na.sub.2EDTA"), at a pH of about 8. In some embodiments, the cell
suspension may be prepared by suspending a known weight of cell
paste with a known weight of suspension buffer. For example, one
part cell paste may be resuspended in about 4-10 parts of buffer,
in some embodiments with about 6-8 parts of buffer. In some
embodiments, the optical density of the resulting cell suspension
may be about 50-80 OD.sub.600 units. In some embodiments, it may be
about 60-70 OD.sub.600 units.
[0047] A lysis solution preferably contains one or more lysis
agents, such as an alkali, an acid, an enzyme, an organic solvent,
a detergent, or a mixture thereof. However, the use of an animal
derived enzymes or organic solvent is not preferred as they are
detrimental to the production of pharmaceutical products. In some
embodiments, the lysis solution comprises an alkali, a detergent,
or a mixture thereof. Suitable alkalis include, but are not limited
to, sodium hydroxide or potassium hydroxide. Detergents may be
nonionic, cationic, or anionic. Suitable detergents include, but
are not limited to sodium dodecyl sulfate ("SDS"), Triton, Tween,
or pluronic-type agents (block-copolymers based on ethylenoxide and
propylenoxide). Selection of suitable alkali or detergent will be
well within the ordinary skill of the art. In some embodiments, the
lysis solution may comprise sodium hydroxide ("NaOH") and SDS. In
some embodiments, the concentration of NaOH may be about 0.1 to
about 0.3 N, and in some embodiments, about 0.2 N. In some
embodiments, the concentration of SDS may be about 0.1% to about
5%, and in some embodiments about 1%. In some embodiments, the
lysis solution may be maintained in a tank or other storage
container.
[0048] The cell suspension and lysis solution may be combined to
lyse the cells and produce a lysate solution. In some embodiments,
they are combined, mixed and maintained as a mixture for a time
sufficient to facilitate high levels of lysis of cells and release
of biological materials, thus forming the lysate solution.
[0049] In some embodiments, cell suspension and lysis solution are
maintained in separate tanks and retrieved from such tanks using
one or more pumps. The cell suspension and lysis solution may be
brought into contact with each other using a "Y" connector. In some
embodiments, equal volumes of cell suspension and lysis solution
may be pumped at equal flow rates using a dual head pump. However,
those of skill in the art will recognize that cell suspension and
lysis solution of different volumes may be pumped at different
rates, using individual pumps, if so desired. In some embodiment,
cell suspension and lysis solution are simultaneously pumped
through a dual head pump frp, from about 0.3 L/min to about 2
L/min, with the contacted fluids exiting the "Y" connector at a
rate from about 0.6 L/min to about 4 L/min. Those of skill in the
art will recognize that these flow rates can be easily increased or
decreased, and tubing size increased or decreased, to meet any
throughput requirement. After exiting the "Y" connector, the
contacted cell suspension and lysis solution may be passed through
a high shear, in-line mixer. The mixer may be any device that
provides rapid, high shear mixing in a flow through mode (as
opposed to a batch mode). In some embodiments, the mixer is a
rotor/stator mixer or an emulsifier. Those of skill in the art will
recognize that a variety such high shear, in-line mixers are
commercially available. Use of any such mixers is well within the
scope of the present invention. In some embodiments, the mixer is a
Silverson L4R rotor/stator mixer fitted with a standard Emulsor
screen (Silverson Machines, Inc. East Longmeadow, Mass.) and an
in-line assembly. The rotor may be operated at a speed such as from
about 500 rpm to about 900 rpm, 500-600 rpm, from about 500 rpm to
about 700 rpm, from about 500 rpm to about 800 rpm, from about 600
rpm to about 700 rpm, from about 600 rpm to about 800 rpm, from
about 600 rpm to about 900 rpm, from about 700 rpm to about 800 rpm
or from about 700 rpm to about 900 rpm. Such a mixer is suitable
for processing cell suspensions of from about 0.3 L/min to about 2
L/min. However, one skilled in the art will recognize that larger
scale mixers may be substituted for processing substantially
greater volumes of cell suspension. Such substitution will be
readily accomplished by one skilled in the art with no more than
ordinary experimentation. The use of a high shear, in-line mixer
facilitates the thorough and rapid mixing of the cell suspension
and lysis solution, bringing the cells into intimate contact with
the lysis agent(s) to achieve efficient lysis. Moreover, mixers can
readily accommodate different fluid flow rates, and provide the
flexibility of adjustable speed mixing for different flow rates.
Materials exiting the high shear, in-line mixer may then pass
through a holding coil. This coil may simply comprise a length of
tubing sufficient to provide that the fluid passes through the coil
for a determined time. The function of the coil is to provide
sufficient contact time between the cells and the lysis agent(s) to
ensure substantially complete lysis. At the same time, the coil
ensures that contact time is not so long as to have negative
consequences. In some embodiments, such as those in which the cells
are plasmid-containing cells and the lysis solution comprises an
alkali, it is desirable to ensure that exposure to alkali lasts
long enough to achieve substantially complete cell lysis as well as
substantially complete denaturation of proteins, genomic DNA, and
other cell components. However, it is also desirable that exposure
to alkali not be so prolonged as to result in substantial amounts
of permanently denatured plasmid. The coil may be one complete
tubing, or segmented into 2-10 tubings to allow for flexibility of
fluid flow rates. The holding coil allows this contact time to be
controlled. In some embodiments this contact time may be from about
2 minutes to about 10 minutes. In some embodiments this contact
time may be from about 2 minutes to about 9 minutes, from about 2
minutes to about 8 minutes, from about 2 minutes to about 7
minutes, from about 2 minutes to about 6 minutes, from about 3
minutes to about 10 minutes, from about 3 minutes to about 9
minutes, from about 3 minutes to about 8 minutes, from about 3
minutes to about 7 minutes, from about 3 minutes to about 6
minutes, from about 4 minutes to about 10 minutes, from about 4
minutes to about 9 minutes, from about 4 minutes to about 8
minutes, from about 4 minutes to about 7 minutes, from about 4
minutes to about 6 minutes, from about 5 minutes to about 10
minutes, from about 5 minutes to about 9 minutes, from about 5
minutes to about 8 minutes, from about 5 minutes to about 7
minutes, or from about 5 minutes to about 6 minutes. Preferably the
contact time is from about 4 minutes to about 8 minutes or from
about 4 minutes to about 6 minutes. In some embodiments the contact
time is about 5 minutes. In some embodiments, the length and
diameter of the holding coil are such that the desired exposure
time is achieved when lysed cells are flowed through at the desired
rate. In some embodiments, the holding coil may be from about 10
feet in length to about 150 feet in length, from about 25 feet in
length to about 100 feet in length, or from about 40 feet in length
to about 60 feet in length. In some embodiments the holding coil is
about 50 feet in length, and in some embodiments the holding coil
is about 100 feet in length. The holding coil can have an inner
diameter from about 0.5 inches to about 2 inches, and in some
embodiments 0.625 inches. Also in some embodiments, the lysed cells
may exit the high shear, in-line mixer and pass through the holding
coil at a rate of from about 100 mL/min to about 10 L/min, from
about 200 mL/min to about 8 L/min, from about 300 mL/min to about 6
L/min, from about 400 mL/min to about 4 L/min, from about 400
mL/min to about 2 L/min, or from about 600 mL/min to about 1.2
L/min. Preferably the rate through the holding coil is from about
0.6 L/min to about 10 L/min. In some preferred embodiments the rate
of passage through the holding coil is about 600 mL/min and in some
embodiments it is about 1200 mL/min. Adjustment of coil length and
diameter can be accomplished by one skilled in the art to
accommodate or adjust to the larger flow rate as biologically
active molecule production is scaled-up. The lysate solution is
collected from the holding coil.
[0050] The lysate solution is neutralized by combining it with a
neutralizing solution (which is also referred to as a neutralizing
precipitation solution) to produce a dispersion comprising
neutralized lysate solution and debris. The resultant dispersion
may then be maintained to facilitate separation of the neutralized
lysate solution from the debris.
[0051] In some embodiments, lysate solution, which comprises the
lysed cells, may be neutralized by mixing it with neutralizing
solution in a neutralizing chamber. This neutralization of lysate
solution can be facilitated by mixing in the neutralizing chamber.
In some embodiments, this neutralizing can be followed by bubble
mixing in a bubble column mixer. Preferably, the neutralization
occurs in conjunction with bubble mixing in a bubble column mixer.
In some embodiments, the lysate solution exiting the holding coil
may enter a bubble column mixer while simultaneously a pump may
deliver a neutralization/precipitation solution from another tank
into the bubble column mixer. In some examples, also
simultaneously, compressed gas from another tank may be sparged
into the bottom of the bubble column mixer. In some embodiments,
lysate solution may enter the column at the bottom from one side,
while neutralization/precipitation solution may enter at the bottom
from the opposite side. Compressed gas may be sparged in through a
sintered sparger designed to deliver gas bubbles substantially
uniformly across the column cross section. Lysate solution, which
comprises the lysed cells, and neutralization solution flow
vertically up the column and exit through an outlet port on the
side near the top. The passage of the gas bubbles through the
vertical column of liquid serves to mix the lysate solution with
the neutralization/precipitation solution. The mixing provided by
the rising gas bubbles is thorough but gentle and low shear. As the
neutralization/precipitation solution mixes with the lysed cells of
the lysate solution, cell components precipitate from the solution.
A snorkel may be provided at the top of the bubble column mixer to
vent excess gas.
[0052] In some embodiments, the lysate solution comprises
plasmid-containing cells lysed with an alkali, a detergent, or a
mixture thereof, and the neutralizing/precipitating solution
neutralizes the alkali and precipitates host cell components such
as proteins, membranes, endotoxins, and genomic DNA. In some
embodiments, the alkali may be NaOH, the detergent may be SDS, and
the neutralization/precipitation solution may comprise potassium
acetate, ammonium acetate, or a mixture thereof. In some
embodiments, the neutralization/precipitation solution may comprise
an unbuffered solution containing about 1 M potassium acetate and
from about 3 M to about 7 M ammonium acetate. Using such a
neutralization/precipitation solution produces a suspension with a
pH of from about 7 to about 8, which is preferable to an acidic pH
because acidic conditions can lead to depurination of DNA. In some
embodiments, the neutralization/precipitation solution may be
provided in a chilled form from about 2.degree. C. to about
8.degree. C.
[0053] The bubble column mixer provides mixing in a low shear
manner and thus avoids excessive release of genomic DNA and
endotoxins into the neutralized lysate solution. One skilled in the
art will be able to determine suitable rates for flowing gas
through the bubble column mixer. Gas flow rates may be used at
about 2 standard liters per minute to about 20 standard liters per
minute ("slpm"). Any suitable gas may be used, including, but not
limited to, air, nitrogen, argon, and carbon dioxide. The gas may
be filtered compressed air.
[0054] The combination of lysate solution and neutralization
solution results in the generation of a dispersion containing
neutralized lysate solution and debris. The neutralized lysate
solution may be collected in a tank or other storage container. In
some embodiments, the container is chilled to 5-10.degree. C. The
time for the holding of neutralized lysate in the container is not
mandatory, and may vary from less than 1 hour, from about 1 hour to
about 12 hours, from about 12 hours to about 15 hours, or greater
than 15 hours. In some embodiments, the time used is about 12
hours, while some examples involve a time of about 15 hours, while
in other examples the time is "overnight" (defined as being greater
than about 15 hours). In one embodiment, a sufficient hold period
was employed to achieve substantially complete separation of the
cell debris from the neutralized lysate solution, resulting the
obtained crude lysate of limited solid particles advantageous for
subsequent clarification process. However, the process scale is
limited to the crude lysate holding tank and the process time is
elongated by this hold period.
[0055] In order to achieve large scale purification of low yield
plasmid product, the period for the holding of neutralized lysate
may be reduced to lower than 1 hour. In some embodiments, the
neutralized lysate solution may be simultaneously processed at the
time it is generated, thus the holding time in the container is
negligible. In some embodiments, the lysate solution is
simultaneously processed by the following process after a period
from about 5 minutes to about 60 minutes of collecting the lysate
in the container. The reduction or elimination of lysate holding
time also removes the process capacity limit by containers as the
lysate is processed immediately at its generation.
[0056] The neutralized lysate solution may be clarified with any
approaches of solid/liquid separation, e.g. bag filtration,
cartridge filtration, batch centrifugation, continuous
centrifugation. Complete removal of the particles in the solution
is desirable to avoid the clogging of membrane or column in the
following purification processes. At the same time, the lysate may
not be subjected to excessive shear that will shred genomic DNA and
cause the release of genomic DNA, shredded genomic DNA, endotoxin
and other contaminants to be released into the plasmid-containing
solution. Batch filtration may be used for processing small volume
of lysate, but impractical at large scale. Continuous
centrifugation is also unsuitable because the precipitate may be
subjected to high shear stress and release high level of
contaminant to solution. In some embodiments a series of
filtrations employing different grade of filter media can be
utilized. The primary filtration can be used to remove a majority
of large cell floccs range in micron sizes, while the consecutive
secondary filtration retains the remaining fine particles. An
optional third filtration may be conducted when a stringent clarity
is desired for the following process and the secondary filtration
is insufficient.
[0057] In some embodiments, bag and cartridge filters can be
employed due to their high dirt holding capacity and minimal
disturbance to solution. The filter bags or cartridge may be of any
size, shape, pore size rating, configuration, and media type. The
filter media is preferred to be made of materials of pharmaceutical
grade or compliant with Food and Drug Administration (FDA)
requirements. The filter material is also preferred to have no
charge or have limited binding of the product. The particle size
limit of filter materials may vary from about 0.1 .mu.m to about a
few hundred microns, providing that it is greater than the size of
the target product that the product will not be retained by the
filter media. The bag filters and cartridge filter media may be
single-layered, multi-layered, pleated, or multi-pleated.
[0058] In some embodiments, two or more filters with similar pore
size ratings may be used in parallel to accommodate process at
large scale. The majority of solid particles in the lysate
solution, including cell wall and membrane components,
precipitates, genomic DNA, protein, lipids, lipopolysaccharides,
and other contaminants, will be removed by the filtration. However,
when the primary filtration is insufficient to deliver solution of
desired clarity, a secondary filtration with reduced pore size or
higher retention rate may be placed subsequently. In some
embodiments, two or more secondary filters may be placed in
parallel to accommodate process at large scale. Use of multiple
filters may be required in a large scale process, and one skilled
in the art will recognize that details such as the number of
filters used, as well as their particle size limits, may be readily
varied.
[0059] In some embodiments, the dispersion may be collected and
maintained in a settling tank to allow the debris to precipitate or
float. Accordingly, in some embodiments, the dispersion may be
collected as a slurry of crude cell lysate and precipitated host
cell components from the bubble column mixer and maintained in a
settling tank to allow the debris to precipitate or float. The
dispersion may be maintained, such as being held in the settling
tank, for a time sufficient to achieve substantially complete
separation of the precipitated host cell components, which make up
the debris, from the neutralized lysate solution. The precipitated
components may rise to the surface of the dispersion, aided by the
entrapped gas bubbles introduced by the bubble column mixer. In
some embodiments, the dispersion may be held in the settling tank
for about 6 to about 24 hours, in some embodiments from about 12
hours to about 18 hours. In some embodiments, the dispersion may be
chilled to less than about 15.degree. C. during the holding period,
in some embodiments from about 2.degree. C. to about 8.degree. C.,
to aid in precipitating RNA or other impurities. In some
embodiments, the dispersion may be gently mixed during the holding
period, such as by an impeller mixer operated at a very low rpm,
preferably from about 15 rpm to about 25 rpm.
[0060] In some embodiments, a vacuum may be applied to the
container which holds the dispersion, such as, for example, a
settling tank. This aids in bringing precipitated components to the
liquid surface. Furthermore, this compacts the floating flocculent
precipitate/debris, aiding its subsequent removal and also allowing
a greater percentage of neutralized lysate solution to be recovered
in later steps. Furthermore, this removes air trapped in solution
that may foul later chromatography steps. In some embodiments, the
applied vacuum may be from about 15 inches of HG to about 30 inches
of Hg (inHg), in some embodiments, from about 20 in Hg to about 30
inHg, and in some embodiments, from about 25 in Hg to about 30
inHg. In some embodiments, the vacuum may be maintained throughout
this holding period. Vacuum may be applied using a vacuum pump, or
any other available vacuum or negative pressure device available.
In some embodiments, prior to beginning solid/liquid separation,
any vacuum applied to the tank is carefully released. Crude cell
lysate, i.e., neutralized lysate solution, is then collected from
the tank using a pump and passed through a depth filter and a final
filter, and then collected in a holding tank. In some embodiments,
the settling tank is fitted with a sight glass, allowing an
operator to observe the position of the liquid level and the
compacted precipitated host cell components. Pumping of material
from the tank is monitored visually, and halted before the
precipitated host cell components enter the line. This prevents
clogging of the subsequent filters. No bag filtration (or cartridge
filtration) or centrifugation is required. Further, disturbance of
the debris is thus minimizing release of components such as genomic
DNA or endotoxins into the neutralized lysate solution. After the
neutralized lysate solution is pumped from the settling tank, it
may be passed through one or more filters to remove fine
particulates. In some embodiments, about one to about three filters
may be used in series, with the first filter removing larger
particles, and subsequent filters removing successively smaller
particles. In some embodiments, two filters may be used in series.
In some embodiments, the first filter is a pre-filtering depth
filter with a particle size limit from about 5 .mu.m to about 15
.mu.m, preferably from about 7.5 .mu.m to about 12 .mu.m, or more
preferably from about 9 .mu.m to about 11 .mu.m. In some
embodiments the pre-filtering depth filter has a particle size
limit of about 10 .mu.m. The second filter is preferably a membrane
filter with a cut-off of from about 0.01 .mu.m to about 0.25 .mu.m,
or preferably from about 0.05 .mu.m to about 0.15 .mu.m. In some
embodiments the membrane filter has a cut-off of about 0.1 .mu.m.
However, one skilled in the art will recognize that details such as
the number of filters used, as well as their particle size limits,
may be readily varied.
[0061] A large selection of filters is commercially available from
different vendors. One particular type is 720 series pleated
cartridge filters (CPI filters, Houston, Tex.), which demonstrated
a large dirt holding ability and superior processing capacity. High
efficiency multi-layer filter bags such as 300 series and 500
series (Knight Corporation, Houston, Tex.) have showed considerable
retention to fine particles. PROGAF.TM. filter bags (Eaton
Filtration, Cleveland, Ohio) with progressive density design of up
to 12 layers of media may deliver high efficiency in the removal of
particles with a variety of sizes. In some embodiments, a
combination of pleated cartridge filtration followed by multilayer
or pleated cartridge filtration may deliver best performance for
the clarification of particles in the neutralized lysate
solution.
[0062] The cartridge filters or bag filters are preferred to be
assembled in the filter housings or filter vessels for the ease of
operation and higher process capacity. The vessel material may be
type 304 or 316 stainless steel, or carbon steel, while all plastic
housing with a choice of polyvinyl chloride (PVC), chlorinated
polyvinyl chloride (CPVC), polyester plastic (PPL) or
polyvinylidene fluoride (PVDF) construction may be advantageous for
ultra-pure or corrosive applications. The filter vessels may be
custom-designed or readily available from several manufacturers.
For example, Eaton Filtration (Cleveland, Ohio) provides a wide
selection of housings/vessels designed to meet any demanding
applications, such as TOPLINE, SIDELINE, DUOLINE, MODULINE,
POLYLINE, FLOWLINE, ECOLINE, MAXILINE series. One skilled in the
art will be able to determine the construct and features of filter
housing to accommodate the process requirements.
[0063] Optionally, an additional depth filter or membrane filter
may be implemented after the secondary filtration. The filter is
preferred to have a cut-off of from about 0.1 m to about 0.2 .mu.m
for further removal of fine particles in the neutralized lysate
solution. Cartridge filters, such as Vangard PP and Alpha PP from
Meissner (Camarillo, Calif.), Clarigard from Millipore (Billerica,
Mass.), HP and PreFlow from Pall (East Hills, N.Y.), may be
contemplated as disposable or with the aid of housings. However,
most of these cartridge filters are limited by their process
capacity, especially in the disposable formats. Preferable is the
use of disposable components which may offer scalable format to
accommodate applications at large scale. Millipore (Billerica,
Mass.) has developed a high-performance disposable depth filter
system, Millistak+Pod, for the applications in either the lab or
process-scale. The filter media in the pod filters is composed of
select grade cellulose fiber and diatomaceous earth, and is
demonstrated to have large contaminant holding and superior
retention. The stacked disc design of pod format aid by the
stainless holder enabled large surface area filtration in tight
spaces. One skilled in the art may determine the media grade and
membrane area of the Pod filter to meet specific operation
needs.
[0064] The clarified neutralized lysate solution, which contains
the biologically active molecules of interest, can then be
subjected to ion exchange chromatography, including column
chromatography or membrane based. Preferably, a membrane-based
approach may be used, such as anion exchange membrane
chromatography. For example, the neutralized lysate solution can be
applied to an ion exchange membrane. According to some embodiments,
the biologically active molecule of interest may contacted with a
membrane whereby the biologically active molecule of interest may
bind to the membrane, while impurities flow through or are washed
off of the membrane, thus separating the biologically active
molecule of interest from the impurities. Alternatively, the
biologically active molecule of interest may flow through the
membrane, while impurities are retained. In some embodiments, the
biologically active molecule of interest binds to the membrane and,
after washing to remove weakly bound impurities, the biologically
active molecule of interest is eluted from the membrane. The
elution may be accomplished by flowing a salt solution through the
membrane. The salt solution has a strength, concentration, or
conductivity sufficient to overcome the binding of the biologically
active molecule of interest to the membrane. The biologically
active molecule of interest is thus recovered in the ion exchange
eluate.
[0065] Although any ion exchange membrane may be suitable, in some
embodiments an anion exchange membrane such as a strong anion
exchange membrane, comprising quaternary amine groups, may be used.
Examples of such membranes include, but may not be limited to the
Mustang Q (Pall Corporation, East Hills, N.Y.), Sartobind Q
(Sartorius, Edgewood, N.Y.), and Intercept Q (Millipore Corporate,
Billerica, Mass.).
[0066] In some embodiments, plasmid-containing cells are lysed and
neutralized to produce a neutralized lysate solution that may be
processed by anion exchange membrane purification that comprises
purification using a Pall Mustang Q cartridge (Pall Corporation,
East Hills, N.Y.). In some embodiments, the neutralized lysate
solution may be adjusted to a conductivity of about less than 95
mS/cm, or about 85 mS/cm, by dilution with a suitable amount of
purified water. The conductivity may be adjusted to from about 80
mS/cm to about 85 mS/cm in some embodiments. Purified water equal
to about 1.5-times the lysate volume can be used for dilution to
achieve the desired conductivity. The Mustang.RTM. Q cartridge may
be conditioned by flowing a suitable salt solution through it. In
some embodiments, the solution may comprise from about 0.5 M sodium
chloride to about 1.0 M sodium chloride ("NaCl") and in some other
embodiments 0.67 M NaCl. The equilibration solution may also
include a buffering agent, a chelating agent, or a combination
thereof. In some embodiments, this equilibration/wash solution may
comprise, in addition to 0.67 M NaCl, 10 mM Tris-HCl, 1 mM
Na.sub.2EDTA, with a pH of 8. In some embodiments,
equilibration/wash solution may be pumped through the cartridge at
about 800 mL/min to about 1500 mL/min. Diluted neutralized lysate
solution may be pumped onto the cartridge, in some embodiments at
less than about 4800 mL/min, in some embodiments at from about 2000
mL/min to about 20,000 mL/min. The loaded cartridge may be washed
with equilibration/wash buffer, preferably at a flow rate from
about 800 mL/min to about 1500 mL/min. Washing may in some
embodiments be continued until the absorbance at 260 nm (A.sub.260)
of the effluent returns to approximately baseline. Plasmid may be
eluted with a solution that comprises 1 M NaCl, 10 mM Tris-HCl, 1
mM Na.sub.2EDTA, and pH 8. Elution may in some embodiments be
performed at a flow rate of from about 500 mL/min to about 9000
mL/min, from about 500 mL/min to about 8000 mL/min, from about 500
mL/min to about 7000 mL/min, from about 500 mL/min to about 6000
mL/min, from about 500 mL/min to about 5000 mL/min, from about 500
mL/min to about 4000 mL/min, from about 500 mL/min to about 3000
mL/min, from about 500 mL/min to about 2000 mL/min, from about 600
mL/min to about 5000 mL/min, from about 600 mL/min to about 4000
mL/min, from about 600 mL/min to about 3000 mL/min, from about 600
mL/min to about 2000 mL/min, or from about 600 mL/min to about 1500
mL/min. In some embodiments elution is continued until the
A.sub.260 of the eluate returns to about baseline. Those of skill
in the art will recognize that flow rates can be easily increased
by using large membrane areas and that the specific salts
concentrations of the solutions listed can be altered to maximize
the yield and purity of specific biomolecules using no more than
ordinary experimentation. The eluate collected is ion exchange
eluate and is used in subsequent purification by hydrophobic
interaction steps.
[0067] The ion exchange eluate recovered from the ion exchange
membrane is subjected to purification by hydrophobic interaction
chromatography (herein, "HIC"). In some embodiments, the
biologically active molecule of interest may bind to the HIC
membrane or column, while impurities flow through or are washed
off. In some embodiments, the biologically active molecule of
interest may flow through while impurities bind. In some
embodiments, the biologically active molecule of interest flow
through a HIC membrane (referred to herein as "Method I"). In some
embodiments, the biologically active molecules of interest bind to
a HIC column, such as a butyl column (referred to herein as "Method
II"). In some embodiments, a combination of HIC membrane and HIC
column, such as a butyl column, may be used (referred to herein as
"Method III") to yield large-scale amounts of biologically active
molecule of interest with high purity.
[0068] The ion exchange eluate may be conditioned prior to flow
onto the hydrophobic interaction membrane. Typically, the
conditioning consists of adding a desired amount of a desired salt.
In some embodiments, ammonium sulfate may be used in an amount
suitable to provide binding of the product or the impurities, as
desired. Typically, in methods III, no conditioning may be
necessary for the HIC filtrate before loading to butyl column.
[0069] In some embodiments, ion exchange eluate is produced by
anion exchange chromatography using a Pall Mustang.RTM. Q cartridge
and further purified by hydrophobic interaction. In some
embodiments, a HIC membrane such as a Pall Kleenpak.TM. Nova
capsule (Pall Corporation, East Hills, N.Y.) with Supor PES filters
may be used. The cartridge may be conditioned by flowing an
equilibration/wash solution comprising concentration ammonium
sulfate through it. In some embodiments, the equilibration/wash
solution comprises from about 1 M ammonium sulfate to about 3 M
ammonium sulfate and in some embodiments comprises 2.4 M ammonium
sulfate and 10 mM Tris-HCl at about pH 8. In some embodiments, the
conductivity of the equilibration/wash solution is from about 240
mS/cm to about 260 mS/cm. In some embodiments, the conductivity of
the equilibration/wash solution is from about 240 mS/cm to about
300 mS/cm, in some embodiments and equilibration/wash solution is
from about 250 mS/cm to about 270 mS/cm, and in some embodiments
the equilibration/wash solution is from about 245 mS/cm to about
255 mS/cm. In some embodiments, a HIC column employed may be a
column that is packed with resin Toyopearl butyl resin 650M (Tosoh
Bioscience LLC, Montgomeryville, Pa.). In some embodiments, the
column may be equilibrated with a solution comprised of about 1.5 M
ammonium sulfate to about 3.0 M ammonium sulfate. In some
embodiments, the column may be equilibrated with a solution
comprised of 2.5 M ammonium sulfate and 10 mM Tris-HCl.
[0070] Hydrophobic interaction membranes may be any such membrane
that binds either biologically active molecules of interest or
impurities based primarily on hydrophobic interactions. Examples of
HIC membranes include, but are be limited to Pall supor
polyethersulfone ("PES") filters, PVDF filters, GE PES capsule
filters, and similar hydrophilic membranes with low protein binding
and broad chemical compatibility. Typical HIC resins include, but
not limited to butyl, hexyl, phenyl, octyl, propyl, neopentyl,
hydroxypropyl, benzyl, methyl and derivatives thereof.
[0071] In some embodiments, the ion exchange eluate may be
conditioned by diluting it with 3 M or 4.1 M ammonium sulfate to
bring up the conductivity between from about 240 mS/cm to about 290
mS/cm, and in some embodiments, from about 245 mS/cm to about 255
mS/cm. When using HIC method I, the diluted ion exchange eluate may
flow through the conditioned HIC cartridge, at a flow rate, in some
embodiments, of from about 100 mL/min to about 200 mL/min. The
flow-through may be collected for subsequent
ultrafiltration/diafiltration. Optionally, the HIC cartridge may be
washed with water, and the wash solution recovered to analyze the
contaminants removed from the product. When using method II, the
diluted ion exchange eluate may be loaded to the column at the flow
rate 10-20 bed volume/minute (BV/min). The biologically active
molecule of interest may be washed, such as from about 1.0 M
ammonium sulfate to about 2.5 M ammonium sulfate until the
absorbance returns to baseline, then eluted with for example 0.5 to
2.0 M ammonium sulfate. The impurities may be stripped with sterile
water for injection (WFI) so that the column can be regenerated for
repeatable use. Method III uses a HIC membrane as described in
method I, followed by HIC column as described in method II. The
choice for method I, II or III is dependent on the product property
and quality requirements, which can be determined by one skilled in
the art. Using any HIC method, an HIC eluate is generated which
contains the biologically active material of interest. Those of
skill in the art will recognize that flow rates can be easily
increased by using large membrane areas or column diameters and
that the specific salts concentrations of the solutions listed can
be altered to maximize the yield and purity of specific
biomolecules using no more than ordinary experimentation.
[0072] Optionally, the biologically active material of interest,
which is present in the HIC eluate, may be further purified. In
some embodiments, the HIC eluate may be subjected to
ultrafiltration/diafiltration to concentrate the biologically
active material of interest, remove excess salts, and if desired,
change the composition of the diluent. Methods for performing
ultrafiltration/diafiltration are well known to those of skill in
the art. In some embodiments, tangential flow filtration is used.
In some embodiments, batch methods are used.
[0073] Ultrafiltration/diafiltration membranes may be selected
based on nominal molecular weight cut-off ("NMWCO") so as to retain
the biologically active material of interest in the retentate,
while allowing low molecular weight materials such as salts to pass
into the filtrated. One skilled in the art will be able to select
such membranes based on the size and nature of the product of
interest, coupled with no more than ordinary experimentation. In
some embodiments, such as some embodiments when the biologically
active material of interest is a plasmid,
ultrafiltration/diafiltration may be performed using either a Pall
Centramate unit (Pall Corporation, East Hills, N.Y.) or Millipore
Pellicon.RTM. XL unit (Millipore Corporate, Billerica, Mass.) or an
unit with similar characteristics, and the membranes used may be
either Pall Omega.TM. suspended screen membrane cassettes (Pall
Corporation, East Hills, N.Y.) or Millipore medium screen membrane
cassettes (Millipore Corporate, Billerica, Mass.) or a similar
cassette known in the art with a NMWCO of 100 kD or 50 kD. In some
embodiments, plasmid may be concentrated to at least about 2.5
mg/mL, in some embodiments to at least about 5.0 mg/mL, in some
embodiments to at least about 10.0 mg/mL, while in other
embodiments the concentration is at least 12.5 mg/mL, and in other
embodiments the concentration is at least 15 mg/mL or more. In some
embodiments, the conductivity of the concentrated plasmid solution
is less than about 50 mS/cm.
[0074] Concentrated desalted biologically active material of
interest recovered in the retentate from the
ultrafiltration/diafiltration may optionally be subjected to
sterile filtration, if a sterile product is desired. Methods for
sterile filtration are well known to those of skilled in the art,
and any such method may be selected. The resulting material
consists of substantially purified biologically active product. The
product may be used for a variety of purposes, including, but not
limited to, pharmaceutical, veterinary, or agricultural
applications. Thus, the methods provide for a bulk preparation of
substantially purified, biologically active molecules. These
molecules may be plasmids. In some embodiments, they may be
plasmids that are substantially free of genomic DNA, RNA, protein
and endotoxin.
[0075] In some embodiments, such as the embodiments where the
biologically active molecule is a plasmid, sterile filtration may
preferably be performed using a Pall AcroPak.TM. 200 filter (Pall
Corporation, East Hills, N.Y.) with a 0.22 .mu.m cut-off.
[0076] The plasmid DNA produced by the process provided has shown a
high purity and extremely low contaminations. In some embodiments,
the high purity of plasmid DNA is plasmid DNA being present at
levels greater than or equal to 90%, greater than or equal to 91%,
greater than or equal to 92%, greater than or equal to 93%, greater
than or equal to 94%, greater than or equal to 95%, greater than or
equal to 96%, greater than or equal to 97%, greater than or equal
to 98%, or greater than or equal to 99%. It is readily apparent
that purity can be characterized by a low level of contaminants,
including low levels of RNA, genomic DNA, endotoxin, and protein.
In some embodiments, the plasmid DNA may be in quantities of about
10 mg or more, 20 mg or more, 30 mg or more, 100 mg or more, 200 mg
or more, 300 mg or more, 500 g or more, 1 g or more, 10 g or more,
20 g or more, 30 g or more, 100 g or more, 200 g or more, 300 g or
more, 1 kg or more, or 2 kg or more. In some embodiments, the
plasmid DNA may be in a concentration 1 mg/mL or more FIG. 1 shows
a schematic of one embodiment of the manufacturing process.
[0077] The embodiment shows a continuous process that is used to
take a given sample of cells and have same undergo steps of
purification processes starting from beginning, including lysis and
neutralization steps, up until the separation steps (i.e., start of
ion-exchange chromatography) in a continuous flow of sample. The
cells are resuspended in resuspension solution contained in a cell
suspension tank 101. The lysis solution is contained in a lysis
solution tank 102. The cell suspension and lysis solution are
pumped into the two inlets of an "Y" connector with pump 104 or
105, respectively. The solution exiting the "Y" connector was mixed
by a high shear, in-line mixer 107. The lysate solution exiting the
mixer 107 passes through a holding coil 108 for an holding period
of 4-6 minutes. The lysis solution/cell mixture exiting the holding
coil enters a bubble column mixer 109 while simultaneously a pump
106 delivers neutralization/precipitation (NP) solution from
another tank, NP solution tank 103, into the bubble column mixer.
Simultaneously, compressed gas from compressed gas tank 110, is fed
into the sparger which is located at the bottom of the bubble
column mixer 109. The neutralized lysate solution is collected in a
container 111. The lysate solution is simultaneously processed by
the following process after a period of 1-60 minutes of collecting
the lysate in the container 111. A pump for primary filtration 112
delivers the crude lysate solution through a primary filter 113.
The primary filtered solution after filter 113 is simultaneously
pumped into a secondary filter 115 via pump 114. The filtered
solution resulting from 115 is filtered through a third filter 117
via pump 116. A pump for clarified lysate 118 drives flow from a
container for clarified lysate 119 to a mixer 121, which mixes with
water from water tank 120. The mixed and diluted solution is
collected in a container for diluted lysate 122. Diluted
neutralized lysate solution is pumped to pre-conditioned
Mustang.RTM. Q cartridge 124, which is accomplished by pump
123.
[0078] In some embodiments, the product of the process provided
herein is a purified, concentrated, desalted, sterile-filtered
plasmid can be substantially free of impurities such as protein,
genomic DNA, RNA, and endotoxin. Low levels of these impurities or
contaminants, preferably substantial free amounts, are provided
herein, with the most preferred levels being undetectable amounts
of such impurities or contaminants. In some embodiments, the
residual protein, as determined by BCA (bicinchoninic acid) Protein
assay (Pierce Biotechnology, Inc., Rockford, Ill.), in the solution
of biologically active molecule, preferably plasmid, produced by
provided production methods may be less than or equal to about 1%
(by weight), less than or equal to 0.9%, less than or equal to
0.8%, less than or equal to 0.7%, less than or equal to 0.6%, less
than or equal to 0.5%, less than or equal to 0.4%, less than or
equal to 0.3%, less than or equal to 0.2%, or less than or equal to
about 0.1%. In some embodiments, the residual protein is less than
or equal to 0.2% and, more preferably, less than or equal to 0.1%.
In some embodiments, the residual endotoxin in the solution of
biologically active molecule, preferably plasmid, produced by
provided production methods may be less than about 100 endotoxin
units per milligram of plasmid (EU/mg), less than about or equal to
about 20 EU/mg, less than about or equal to about 10 EU/mg, less
than or equal to about 1.0 EU/mg, less than or equal to about 0.9
EU/mg, less than or equal to about 0.8 EU/mg, less than or equal to
about 0.7 EU/mg, less than or equal to about 0.6 EU/mg, less than
or equal to about 0.5 EU/mg, less than or equal to about 0.4 EU/mg,
less than or equal to about 0.3 EU/mg, less than or equal to about
0.2 EU/mg, or less than or equal to about 0.1 EU/mg. Preferably, in
some embodiments, the endotoxin level is less than or equal to
about 0.2 EU/mg, and more preferably, less than or equal to about
0.1 EU/mg. In some embodiments, residual RNA, as determined by
hydrophobic interaction HPLC, in the solution of biologically
active molecule, preferably plasmid, produced by provided
production methods may be less than or equal to about 5% (by
weight), less than or equal to about 1%, less than or equal to
0.9%, less than or equal to 0.8%, less than or equal to 0.7%, less
than or equal to 0.6%, less than or equal to 0.5%, less than or
equal to 0.4%, less than or equal to 0.3%, less than or equal to
0.2%, or less than or equal to about 0.1%. Preferably, in some
embodiments, the amount of RNA is less than or equal to about 0.5%,
and more preferably, less than or equal to about 0.4%. In some
embodiments, residual genomic DNA, as determined by qPCR, in the
solution of biologically active molecule, preferably plasmid,
produced by provided production methods may be less than or equal
to about 5% (by weight), less than or equal to about 1%, less than
or equal to 0.9%, less than or equal to 0.8%, less than or equal to
0.7%, less than or equal to 0.6%, less than or equal to 0.5%, less
than or equal to 0.4%, less than or equal to 0.3%, less than or
equal to 0.2%, less than or equal to about 0.1%, less than or equal
to about 0.01%, less than or equal to about 0.001%, less than or
equal to about 0.0001%, less than or equal to about 0.00001%, or
less than or equal to about 0.000001%. Preferably, in some
embodiments, the amount of genomic DNA is less than or equal to
about 0.1%, and more preferably less than about 0.001%, and most
preferably less than or equal to about 0.000001%.
[0079] Large quantities of plasmid DNA in high yields and at high
concentrations can be produced by the methods provided herein. The
plasmid DNA produced by the process provided include solutions of
plasmid DNA of high purity. In some embodiments, the high purity of
plasmid DNA is greater than or equal to about 90%, greater than or
equal to about 91%, greater than or equal to about 92%, greater
than or equal to about 93%, greater than or equal to about 94%,
greater than or equal to about 95%, 5 mg/mL or more, 6 mg/mL or
more, 7 mg/mL or more, 8 mg/mL or more, 9 mg/mL or more, 10 mg/mL
or more, 11 mg/mL or more, 12 mg/mL or more, 13 mg/mL or more, 14
mg/mL or more, 15 mg/mL or more. In some embodiments, the plasmid
DNA may be in a concentration from about 5 mg/mL to about 15 mg/mL,
from about 5 mg/mL to about 14 mg/mL, from about 5 mg/mL to about
13 mg/mL, from about 5 mg/mL to about 12 mg/mL, from about 5 mg/mL
to about 11 mg/mL, from about 5 mg/mL to about 10 mg/mL, from about
5 mg/mL to about 9 mg/mL, from about 5 mg/mL to about 8 mg/mL, a
concentration from about 6 mg/mL to about 15 mg/mL, from about 6
mg/mL to about 14 mg/mL, from about 6 mg/mL to about 13 mg/mL, from
about 6 mg/mL to about 12 mg/mL, from about 6 mg/mL to about 11
mg/mL, from about 6 mg/mL to about 10 mg/mL, from about 6 mg/mL to
about 9 mg/mL, from about 6 mg/mL to about 8 mg/mL, a concentration
from about 7 mg/mL to about 15 mg/mL, from about 7 mg/mL to about
14 mg/mL, from about 7 mg/mL to about 13 mg/mL, from about 7 mg/mL
to about 12 mg/mL, from about 7 mg/mL to about 11 mg/mL, from about
7 mg/mL to about 10 mg/mL, from about 7 mg/mL to about 9 mg/mL,
from about 8 mg/mL to about 15 mg/mL, from about 8 mg/mL to about
14 mg/mL, from about 8 mg/mL to about 13 mg/mL, from about 8 mg/mL
to about 12 mg/mL, from about 8 mg/mL to about 11 mg/mL, from about
8 mg/mL to about 10 mg/mL, from about 9 mg/mL to about 15 mg/mL,
from about 9 mg/mL to about 14 mg/mL, from about 9 mg/mL to about
13 mg/mL, from about 9 mg/mL to about 12 mg/mL, from about 9 mg/mL
to about 11 mg/mL, from about 10 mg/mL to about 15 mg/mL, from
about 10 mg/mL to about 14 mg/mL, from about 10 mg/mL to about 13
mg/mL, from about 10 mg/mL to about 12 mg/mL, from about 11 mg/mL
to about 15 mg/mL, from about 11 mg/mL to about 14 mg/mL, from
about 11 mg/mL to about 13 mg/mL, from about 12 mg/mL to about 15
mg/mL, from about 12 mg/mL to about 14 mg/mL, or from about 13
mg/mL to about 15 mg/mL. In some embodiments, the plasmid DNA may
be in such concentration as set forth with a percent of supercoiled
of greater than about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%,
83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% or 95%
supercoiled plasmid, and preferably greater 80% supercoiled
plasmid. In some embodiments, the plasmid DNA may be in such
concentration as set forth with a percent of supercoiled of 50-90%,
50-80%, 50-75%, 50-70%, 50-65%, 50-60%, 60-90%, 60-80%, 60-75%,
60-70%, 65-90%, 65-80%, 65-75%, 65-70%, 70-90%, 70-80%, 70-75%,
80-90%, 85-90%, 90-95%, or more. In some embodiments, the plasmid
DNA may be in such concentration as set forth with a percent of
supercoiled and relaxed (open circle non-degraded) of 90% or more,
95% or more, or 98% or more. In some embodiments, the plasmid DNA
may be in such concentration as set forth with a percent of
supercoiled of 50% or more with essentially the remainder as
relaxed (open circle non-degraded) plasmid after storage for 2
years or more, 60% or more with essentially the remainder as
relaxed (open circle non-degraded) plasmid after storage for 2
years or more, 65% or more with essentially the remainder as
relaxed (open circle non-degraded) plasmid after storage for 2
years or more, 85% or more with essentially the remainder as
relaxed (open circle non-degraded) plasmid after storage for 2
years or more, wherein the storage below the freezing point of
water. In some embodiments, the plasmid DNA may be in such
concentration as set forth with a percent of supercoiled and
relaxed (open circle non-degraded) of 90% or more, 95% or more, 98%
or more after storage for 2 years or more, wherein the storage is
below the freezing point of water. Such plasmid preparations as
described herein may be produced as products by the processes
described herein.
EXAMPLES
[0080] The present invention is further illustrated in the
following Examples, in which parts and percentages are by weight
and degrees are Celsius, unless otherwise stated. It should be
understood that these Examples, while indicating preferred
embodiments of the invention, are given by way of illustration
only. From the above discussion and these Examples, one skilled in
the art can ascertain the essential characteristics of this
invention, and without departing from the spirit and scope thereof,
can make various changes and modifications of the invention to
adapt it to various usages and conditions. Thus, various
modifications of the invention in addition to those shown and
described herein will be apparent to those skilled in the art from
the foregoing description. Such modifications are also intended to
fall within the scope of the appended claims.
Example 1
[0081] Escherichia coli ("E. coli") cells containing a plasmid A
were fermented to high density of an optical cell density
("OD.sub.600") at 72 when harvested by centrifugation. Plasmid A
has a size of 6549 bp. The plasmid typically replicates at a low
copy number of .about.250 copies/cell. Approximately 3.1 kg wet
cell weight ("WCW") of cell paste was suspended in a resuspension
buffer consisting of 25 mM Tris-hydrochloride ("Tris-HCl", J. T.
Baker, Phillipsburg, N.J.), 10 mM edetate disodium ("Na.sub.2EDTA",
Fisher Scientific, Fair Lawn, N.J.), pH 8, to a final volume of
approximately 21.5 L. This cell suspension was pumped at 300 mL/min
into one side of a "Y" connector. Simultaneously, lysis solution
consisting of 0.2 N sodium hydroxide ("NaOH", J. T. Baker,
Phillipsburg, N.J.), 1% sodium dodecyl sulfate ("SDS", J. T. Baker,
Phillipsburg, N.J.) was pumped at 300 mL/min into the other side of
the "Y" connector. The combined fluids exiting the "Y" connector
were immediately passed through a Silverson Model L4R rotor/stator
mixer fitted with a standard Emulsor Screen (Silverson Machines,
Inc. East Longmeadow, Mass.) and an in-line assembly. The mixer was
operated at a rotor speed of 800 rpm.
[0082] The fluid exiting the rotor/stator mixer was passed through
a 50-foot, 0.625 inch (internal diameter) holding coil. At a total
flow rate of approximately 600 mL/min, transit time through the
holding coil was approximately 5 minutes to allow for complete cell
lysis.
[0083] Cell lysate (lysate solution) exiting the holding coil was
passed into a bubble column mixer. Simultaneously, cold
(approximately 4.degree. C.) neutralization/precipitation solution
consisting of 1 M potassium acetate (J. T. Baker, Phillipsburg,
N.J.), 7 M ammonium acetate (EMD Chemicals, Inc., Bibbstown, N.J.)
was independently pumped into the bubble column mixer at 600
mL/min. The lysate solution and neutralization/precipitation
solutions were flowed vertically up the mixing column and through
the outlet near the top. While the solutions passed through the
mixing column, compressed air was introduced into the bottom of the
column at a rate of approximately 3.0 slpm through a sintered
sparger designed to provide a constant stream of fine bubbles
throughout the diameter of the mixing. Excess air was vented
through the top of the column. As the lysate solution and
neutralization/precipitation solutions passed through the column,
they were continuously mixed by the gentle turbulence of the rising
bubbles. This was evidenced by the formation of a white, flocculent
precipitate (debris components) consisting of potassium SDS,
denatured cellular proteins, bound lipids and cell wall components,
and associated genomic DNA.
[0084] The neutralized precipitated lysate (dispersion of
neutralized lysate solution and debris) exiting the bubble column
mixer was collected in a settling container. This process was
operated in a continuous mode until the entire suspension of cell
paste had been lysed, neutralized and precipitated, and collected
in the settling tank. Total solution volumes were 21.5 L of cell
suspension plus a 5 L wash of the resuspension tank with
resuspension buffer, 26.5 L of lysis solution, and 53 L of
neutralization solution, for a total volume of approximately 106
L.
[0085] After collection, the material in the settling tank was
observed through a sight glass. The flocculent precipitate could be
seen rising to the surface of the liquid, aided by clearly visible
air bubbles that were entrapped in the solids. A vacuum of
approximately 28 inHg was applied to the settling tank, leading to
significant and visible compaction of the floating precipitate.
[0086] The material was held under vacuum in the settling tank at
room temperature for approximately 16 hours. The vacuum was then
slowly vented to avoid disrupting the compacted precipitate. The
plasmid-containing liquor (neutralized lysate solution) was
carefully pumped from the tank through a sanitary fitting at the
bottom. The liquid and precipitate levels in the tank were
continuously monitored, and pumping was halted in time to ensure
that the precipitate did not exit the tank. This was subjected to a
10 .mu.m depth filtration, followed by 0.1 .mu.m final filtration.
A portion of the neutralized lysate solution was lost during
filtration, due to clogging of the filters. As a result,
approximately 69 L of cleared neutralized lysate solution was
obtained. The neutralized lysate solution was then diluted with
approximately 93 L of purified water achieving a total volume of
162 L and approx. conductivity of 97 mS/cm, in preparation for
further processing with anion exchange. Plasmid concentration in
the filtered neutralized lysate solution was estimated to be about
17 .mu.g/mL, corresponding to approximately 1170 mg of total
plasmid.
[0087] The cleared, diluted neutralized lysate solution was further
purified by anion exchange. A 260 mL bed volume Pall Mustang Q
cartridge was equilibrated with 4 L of 0.67 M Sodium Chloride
("NaCl", J. T. Baker, Phillipsburg, N.J.) in 1.times. Tris-EDTA
("TE") buffer composed of 10 mM Tris-HCl (J. T. Baker,
Phillipsburg, N.J.) and 1 mM EDTA (Fisher Scientific, Fair Lawn,
N.J.) at pH 8. The volume of 162 L of diluted neutralized lysate
solution was pumped onto the Q cartridge at a flow rate of 1.2
L/min. Ultraviolet ("UV") absorbance of the cartridge effluent at
260 nm was monitored and recorded using a strip-chart recorder.
After loading, the cartridge was washed with equilibration buffer
at 1.2 L/min until the A.sub.260 of the effluent approached
baseline. Plasmid was then eluted from the cartridge with
1.times.TE buffer containing 1 M NaCl (J. T. Baker, Phillipsburg,
N.J.), pumped at 1.2 L/min. Elution was terminated with the
A.sub.260 returned to baseline. Total eluate volume was
approximately 4.8 L and contained a total of approx. 915 mg of DNA
based on A.sub.260. The yield of the Q anion exchange is
approximately 78%. Contaminants including protein, the majority of
RNA, genomic DNA and endotoxin were removed in the flow through and
wash at this step.
[0088] The Q eluate was further purified by hydrophobic interaction
via method II of butyl column. A K5/15 Amersham (Piscataway, N.J.)
column was packed with 290 mL bed volume ("BV") of Toyopearl butyl
resin 650M (Tosoh Bioscience LLC, Montgomeryville, Pa.). A volume
of 24 L 3 M ammonium sulfate (EMD Chemicals, Inc., Gibbstown, N.J.)
was mixed with 4.8 L Q elute before loading. The column was
equilibrated with 2 L of 2.5 M ammonium sulfate (EMD Chemicals,
Inc., Gibbstown, N.J.), pumped at 43 mL/min. The conditioned Q
eluate was loaded to the butyl column at 43 mL/min, followed by
washing with 5 L of 2.5 M ammonium sulfate (EMD Chemicals, Inc.,
Gibbstown, N.J.) at 43 mL/min, and the product was eluted with 1.5
L of 1.8 M ammonium sulfate (EMD Chemicals, Inc., Gibbstown, N.J.)
at 43 mL/min. The column was stripped with sterile water for
injection ("WFI", Baxter Healthcare, Deerfield, Ill.) to remove
bound contaminants including RNA and endotoxin, and was regenerated
for repeatable use. The eluate achieved approx. 870 mg of plasmid
with the yield of 95%, while the supercoiled percentage of plasmid
was enriched from 66% after Q to more than 80% after the butyl
column step.
[0089] The eluate from butyl HIC was concentrated and desalted by
ultrafiltration/diafiltration ("UF/DF"), using a Pall
Centramate.TM. cassette holder fitted with one Pall Omega suspended
screen membrane cassettes (Pall Corporation, East Hills, N.Y.),
with an area of 1 ft.sup.2 and a nominal molecular weight cut-off
of 50 kDa. A volume of 41.2 mL of bulk retentate was recovered,
with a DNA concentration of 9.026 mg/mL (by A.sub.260). First wash
of WFI for the UF/DF rig yielded 46.9 mL with the concentration of
1.6 mg/mL. Second wash of WFI yielded 65.8 mL with the
concentration of 0.268 mg/mL. Combined DNA recovery after UF was
approximately 47 6 mg with the yield of 55%. The final supercoiled
percentage of plasmid achieved was more than 87% after UF.
[0090] Samples from EXAMPLE 1 were subjected to analysis by agarose
gel electrophoresis, which is displayed as FIG. 2. Three major
bands are present in all sample lanes (lane 2-5), while the lowest
band is the supercoiled format of target plasmid A (6.5 kb). Lane 1
represents the supercoiled plasmid ladder (Invitrogen). Lane 2
represents the cell lysate containing a 6.5 kb plasmid product,
while a large amount of RNA was also present in the sample. Lane 3
represents the product after Q anion exchange, which showed that
the plasmid was concentrated with less RNA. Lane 4 displayed the
product after purification with hydrophobic interaction, and lane 5
represents final product blended after UF. The contaminant RNA in
the lysate was removed and the purity of the desired supercoiled
plasmid was substantially increased from 60% to >85%.
Example 2
[0091] An amount of 3140 gram E. coli cells containing plasmid B
was resuspended in resuspension buffer consisting of 25 mM Tris-HCl
(J. T. Baker, Phillipsburg, N.J.) at the pH of 8 and 10 mM
Na.sub.2EDTA, to a final volume of 18.8 L. Plasmid B has a size of
4.7 kb. The resuspended cells were mixed with the lysis solution
consisting of 0.2 N NaOH (J. T. Baker, Phillipsburg, N.J.) and 1%
SDS (J. T. Baker, Phillipsburg, N.J.) at an equal flow rate of 300
mL/min by a Silverson Model L4R rotor/stator mixer, which was
operated at a rotor speed of 800 rpm. The lysate effluent from
mixer retained 5-minute holding time in the holding coil before
entering the bubble column to mix with the pre-chilled (4-5.degree.
C.) neutralization/precipitation (NP) solution. The NP solution
containing 1 M potassium acetate (J. T. Baker, Phillipsburg, N.J.)
and 3 M ammonium acetate (EMD Chemicals, Inc., Bibbstown, N.J.) was
fed to the bubble column mixer at 600 mL/min, simultaneously, the
compressed air was introduced from the bottom sparger at a flow
rate of 3-5 slpm.
[0092] The neutralized cell lysate was first received by a woven
mesh bag of 200-400 .mu.m hanging below the outlet port of the
bubble column. Large cell flocculent was retained in the bag,
whereas the crude lysate solution containing the plasmid DNA and
reduced cell debris was collected in the pre-chilled (5.degree. C.)
settling tank. Simultaneously, the generated crude lysate was
pumped to a 48 .mu.m pleated cartridge filter (CPI filters,
Houston, Tex.) fitted in an ECOLINE filter vessel (Eaton
Filtration, Iselin, N.J.) at a flow rate of 2 L/min. The primary
filtered lysate was collected in a container with a total volume of
75 L recovered. A second filtration was performed afterwards. The
primary filtered lysate was pumped to a 523 multi-layer bag filter
(Knight Corporation, Barrington, Ill.) fitted in an ECOLINE filter
vessel (Eaton Filtration, Iselin, N.J.) at a flow rate of 2 L/min.
The recovered solution was collected in a container with total
volume of 65 L recovered. Finally, a depth filtration was conducted
with Millistak Pod disposable depth filter system (Millipore,
Bellerica, Mass.). The filter media had a pore size distribution of
0.2-2.5 .mu.m. A Pod filter with the membrane area of 0.11 m.sup.2
was used to clarify the secondary filtered lysate at a flow rate of
0.5 L/min. A volume of 60 L final clarified lysate was achieved,
which demonstrated a high clarity of NTU value lower than 2. The
plasmid purity and forms in the lysate samples at each stage of
filtration were indistinguishable.
Example 3
[0093] E. coli cells containing a plasmid C (plasmid size of 3.5
kb) were fermented to high cell density and harvested by
centrifugation. A wet cell weight of 24.4 kg cells were recovered
from 400-L working volume of fermentation. The cells were
resuspended with 171 L of resuspension buffer consisting of 25 mM
Tris-HCl (J. T. Baker, Phillipsburg, N.J.) at the pH of 8 and 10 mM
Na2EDTA (Mallinckrodt Baker, Phillipsburg, N.J.) for a period of 3
hours. The resuspended cells were mixed with fresh lysis solution
by Silverson high shear mixer at the same flow rate of 600 ml/min,
and held for approximately 5 min accomplished by a holding loop.
The neutralization/precipitation solution consisting of 1 M
potassium acetate (J. T. Baker, Phillipsburg, N.J.) and 3 M
ammonium acetate (EMD Chemicals, Inc., Bibbstown, N.J.) were pumped
to the bubble mixer at a flow rate of 1.2 L/min to mix with lysed
cells. Compressed air fed at a gas flow rate of 5-6 slpm served as
the mixing force and transporting the neutralized lysate to a
collecting tank. An approximate period of 5 hour was used for the
lysis process. The neutralized cells exiting the bubble mixing
device were diverted to a collecting tank and subject to following
filtration continuously.
[0094] The neutralized crude lysate was processed with three
sequential filtrations upon its generation and these clarification
processes were operated simultaneously with the lysis process. The
initial filtration was performed by pumping the crude lysate
containing cell flocculents into a TOPLINE filter vessel (Eaton
Filtration, Iselin, N.J.) fitted with a 48 .mu.m pleated cartridge
filter (CPI filters, Houston, Tex.) at a flow rate of 2.4 L/min.
The primary filtration was employed to remove the majority of large
particles such as cell floccs, and a pleated membrane offers more
filtration area, thus higher flow rate and larger process capacity
than a single layer or multi-layer construct. Four pleated
cartridges were used to process a volume of 680 L neutralized crude
lysate containing cell floccs, while recovered primary filtered
lysate was estimated at 600 L. The solution exiting the 48 .mu.m
pleated cartridge filter was directly pumped to a secondary ECOLINE
filter vessel (Eaton Filtration, Iselin, N.J.) fitted with a 1
.mu.m multi-layer cartridge filter (CPI filters, Houston, Tex.) at
a flow rate of 2.4 L/min. This step removed a majority of small
particles ranged between 1 .mu.m and 50 .mu.m in the secondary
filtered lysate. The subsequent Mustang Q has a pore size
equivalent to 0.2 .mu.m, and thus a third depth filtration by a
filter with the absolute based pore size of 0.2 .mu.m or lower was
performed. The depth filter Millitak+Pod filter system is able to
achieve both large process volume and a high retention to fine
particles. The Millistak COHC filter (Millipore, Bellerica, Mass.)
fitted in a stainless steel Pod holder was used to reduce the
turbidity of lysate to 2 Nephelometric Turbidity Unit (NTU). A
membrane area of 1.1 m.sup.2 C0HC filter processed a volume of 400
L secondary filtered lysate.
[0095] The filtered lysate exiting Millistak filter was collected
in a container. A fraction of solution from this container was
pumped to a "Y" connector at a flow rate of 2.2 L/min to mix with
water which was pumped to the same "Y" connector at a flow rate of
0.7 L/min. The mixture was flowed into a Kenics in-line mixer
leading into another holding tank. The conductivity of such diluted
lysate in the holding tank had a range of 90-95 mS/cm. A volume of
400 L diluted lysate was loaded to a 10 inch Mustang Q (Pall, East
Hills, N.Y.) which had a bed volume of 260 ml. The Q capsule was
saturated before 200 L of Q load. An approximate 3 g of plasmid DNA
was recovered in the Q eluate. The supercoiled percentage of Q
product was between 80%-90%, and the RNA content in the Q eluates
was not noticeable by gel analysis.
[0096] Samples from EXAMPLE 3 were subjected to analysis by agarose
gel electrophoresis, which is displayed in FIG. 3. The band of the
highest intensity in each lane represents the supercoiled (SC) form
of plasmid, which is present at a percentage ranging between
80-90%. Lane 1 represents the supercoiled plasmid ladder
(Invitrogen). Lane 2 represents the lysate after primary filtration
using a 48 .mu.m pleated cartridge, and shows a high RNA content.
Lane 3 represents the filtrate after secondary filtration using a 1
.mu.m pleated cartridge, and also shows a high RNA content. Lane 4
represents the filtrate after a third filtration using a C0HC Pod
filter, and shows a reduced RNA ratio. Lane 5 represents the eluate
product fraction #1 after undergoing step of Mustang Q anion
exchange, which demonstrated a high purity with limited RNA. Lane 6
represents the secondary fraction of Q eluate, with similar purity
to eluate #1.
Example 4
[0097] A wet cell weight of 25 kg of E. coli cells containing
plasmid C was resuspended in 105 L of resuspension buffer
consisting of 25 mM Tris-HCl (J. T. Baker, Phillipsburg, N.J.) at
the pH of 8 and 10 mM Na.sub.2EDTA, for a total period of 3 hours.
Plasmid C has a size of 3.5 kb. The resuspended cells were pumped
to a Silverson Model L4R rotor/stator mixer at a flow rate of 1500
ml/min, simultaneously, the lysis solution consisting of 0.2 N NaOH
(J. T. Baker, Phillipsburg, N.J.) and 1% SDS (J. T. Baker,
Phillipsburg, N.J.) was delivered to the same mixer at a flow rate
of 1500 ml/min. The mixture containing lysed cells passages through
a holding coil with the inner diameter (ID) of 1 inch and length of
100 feet. The approximate retention time was 5 minutes for the
lysate from entering the mixer until exiting the holding coil. The
lysed cells then entered the bubble column to be in contact with
the pre-chilled (4-5.degree. C.) neutralization/precipitation (NP)
solution. The NP solution containing 1 M potassium acetate (J. T.
Baker, Phillipsburg, N.J.) and 3 M ammonium acetate (EMD Chemicals,
Inc., Bibbstown, N.J.) was fed to the bubble column mixer at 3000
mL/min. Simultaneously, compressed air was introduced from the
bottom sparger at a flow rate of 6-10 slpm to serve as the mixing
force and facilitate the neutralized solution into a diverting pipe
directing to a crude lysate tank.
[0098] After collecting the crude lysate for a period of 20
minutes, the solution was pumped from the bottom of crude lysate
tank to a TOPLINE filter vessel (Eaton Filtration, Iselin, N.J.)
fitted with a 48 .mu.m pleated cartridge filter (CPI filters,
Houston, Tex.) at a flow rate of 6 L/min. Simultaneously, the
filtrate from primary filter vessel was pumped to a secondary
TOPLINE filter vessel (Eaton Filtration, Iselin, N.J.) fitted with
a 1 .mu.m pleated cartridge filter (CPI filters, Houston, Tex.) at
a flow rate of 6 L/min. The primary filtration removed 99% of
particles greater than 48 .mu.m, and five of 10 inch cartridge
filters clarified the total volume of 700 L of crude lysate. Use of
three 10 inch 1 .mu.m cartridge filters enabled the completion of
secondary filtration to remove 99% of particles greater than 1
.mu.m. The filtrate from the secondary vessel was collected in a
clarified lysate tank with the aid of a pump at a flow rate of 5-6
L/min. A third filter system of Millitak+COHC Pod filter
(Millipore, Bellerica, Mass.) fitted in a stainless steel pilot
scale Pod holder was employed to achieve a high clarity for
subsequent Mustang Q purification. The solution from the clarified
lysate tank was pumped to the pod filter at a flow rate of 6 L/min.
A membrane area of 2.2 m.sup.2 C0HC filter processed a volume of
650 L secondary filtered lysate before the inlet pressure reached
10 psi. The filtrate by the third Pod filter was collected in the
filtered lysate container.
[0099] The filtered lysate was delivered to a "Y" connector and mix
with water at a ratio of 0.3-0.4 V water/V lysate via a Kenics
in-line mixer before loading to a Mustange Q. The lysate was pumped
at a flow rate of 5 L/min, while the water was fed at a flow rate
of 1.75-2 L/min. The mixture was collected in the diluted lysate
tank. The conductivity of such diluted lysate in the holding tank
had a range of 90-95 mS/cm. An approximate volume of 800 L diluted
lysate was loaded to a Mustang Q XT5000 (Pall, East Hills, N.Y.)
which had a bed volume of 5000 ml. An approximate 25 g of plasmid
DNA was recovered in the Q eluate. The recovered Q eluate exhibited
high percentage of supercoiled form and limited levels of
contaminations.
Example 5
[0100] The following table I represents fourteen plasmid
preparations produced using Method II with plasmid A, a low copy
plasmid, and some purity parameters detected therein. The protocols
for production were that discussed in Example 3, above.
Analysis of Plasmid Samples
[0101] Plasmid C has a size of 3.5 kb (as in Example 3 and Example
4). Plasmid D1-D3 ranges from 4.4-4.7 kb, having similar construct
except of expression genes. Plasmid E1-E2 has a size of 3.8 kb,
with similar construct other than expression genes. Plasmid F has a
size of 2.5 kb.
TABLE-US-00001 TABLE I Plasmid C Plasmid C Plasmid C Plasmid C
Plasmid D Assay Units Lot #1 Lot #2 Lot #3 Lot #4 Lot #1
Concentration by mg/mL 2.5 2.5 2.4 3.0 4.4 A260 Host Cell RNA % 0.4
0.63 0.31 0.62 .ltoreq.0.1 Host Cell Protein % .ltoreq.0.1
.ltoreq.0.12 .ltoreq.0.13 .ltoreq.0.1 .ltoreq.0.07 Host Cell DNA %
0.0000002 .ltoreq.0.000002 .ltoreq.0.000002 .ltoreq.0.000002
.ltoreq.0.0000003 Endotoxin EU/mg 1 3.76 .ltoreq.1.25 1.383 0.4 pH
7.1 6.87 5.70 6.22 5.2 Osmolality mOsm/kg 19 19 11 15 15 H2O
Plasmid D1 Plasmid D2 Plasmid D3 Plasmid E1 Plasmid E2 Assay Units
Lot #1 Lot #1 Lot #1 Lot #1 Lot #1 Concentration by mg/mL 9.2 8.1
8.5 6.0 6.0 A260 Host Cell RNA % .ltoreq.0.06 .ltoreq.0.08
.ltoreq.0.07 .ltoreq.0.1 1 Host Cell Protein % .ltoreq.0.03
.ltoreq.0.04 .ltoreq.0.04 .ltoreq.0.1 .ltoreq.0.1 Host Cell DNA %
0.00000005 0.00000005 .ltoreq.0.0000005 .ltoreq.0.0000000001
.ltoreq.0.0000000001 Endotoxin EU/mg 1.1 1.2 1.9 .ltoreq.0.1
.ltoreq.0.1 pH 6.2 5.8 6.0 6.5 5.5 Osmolarity mOsm/kg 58 32 47 10
32 H2O
* * * * *