US20140080180A1 - Harvest operations for recombinant proteins - Google Patents

Harvest operations for recombinant proteins Download PDF

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Publication number
US20140080180A1
US20140080180A1 US13/826,166 US201313826166A US2014080180A1 US 20140080180 A1 US20140080180 A1 US 20140080180A1 US 201313826166 A US201313826166 A US 201313826166A US 2014080180 A1 US2014080180 A1 US 2014080180A1
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recombinant protein
host cell
prokaryotic host
antibodies
maintained
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Michael W. Laird
Richard St. John
Jane V. Gunson
Kim Kaleas
Deepa Nadarajah
Rachel Adams
Bradley R. Snedecor
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Genentech Inc
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Genentech Inc
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Priority to US13/826,166 priority Critical patent/US20140080180A1/en
Publication of US20140080180A1 publication Critical patent/US20140080180A1/en
Priority to US14/734,848 priority patent/US20160130624A1/en
Priority to US15/908,526 priority patent/US20180291411A1/en
Priority to US16/270,494 priority patent/US20200199639A1/en
Priority to US17/067,059 priority patent/US20210171997A1/en
Priority to US17/864,255 priority patent/US20230069966A1/en
Priority to US18/419,368 priority patent/US20240158825A1/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P21/00—Preparation of peptides or proteins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M41/00—Means for regulation, monitoring, measurement or control, e.g. flow regulation
    • C12M41/40—Means for regulation, monitoring, measurement or control, e.g. flow regulation of pressure
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M41/00—Means for regulation, monitoring, measurement or control, e.g. flow regulation
    • C12M41/42—Means for regulation, monitoring, measurement or control, e.g. flow regulation of agitation speed
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli

Definitions

  • the invention relates to improved methods for culturing recombinant proteins in prokaryotic host cells.
  • proteins are produced by cell culture, using either mammalian or bacterial cell lines engineered to produce the protein of interest by insertion of a recombinant plasmid containing the gene for that protein. Since the cell lines used are living organisms, they must be fed with a complex growth medium which usually contains a mixture of salts, sugars, amino acids, vitamins, trace elements and peptones. Separation of the desired protein from the mixture of compounds fed to the cells and from the by-products of the cells themselves to a purity sufficient for use as a human therapeutic poses a daunting challenge.
  • Recombinant therapeutic proteins are commonly produced in several host cell lines including mammalian host cells, such as, for example, murine myeloma NSO and Chinese Hamster Ovary (CHO) cells (Anderson, D. C. and Krummen, L. (2002) Curr. Opin. Biotech. 13: 117-123; Chu, L. and Robinson, D. K. (2001) Curr. Opin. Biotechnol. 12:180-187) and bacterial host cells including Escherichia coli ( E. coli ).
  • mammalian host cells such as, for example, murine myeloma NSO and Chinese Hamster Ovary (CHO) cells (Anderson, D. C. and Krummen, L. (2002) Curr. Opin. Biotech. 13: 117-123; Chu, L. and Robinson, D. K. (2001) Curr. Opin. Biotechnol. 12:180-187) and bacterial host cells including Escherichia coli ( E. coli ).
  • Heterologous proteins expressed by E. coli may accumulate as soluble product or insoluble aggregates.
  • the cells may be subjected to treatments for periplasmic extraction or be lysed to release intracellular products that are otherwise inaccessible. Advances in fermentation and cell culture techniques have greatly increased the titers of targeted recombinant proteins.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dissolved oxygen (dO 2 ) levels are greater than 0%, and (c) purifying said recombinant protein to a filtered bulk for storage (FBS), wherein said filtered bulk does not contain detectable 1,4-dihydroxy-2-naphthoate (DHNA)-recombinant protein adduct, as measured by an ion exchange chromatography (IEC) assay at 310 nm.
  • the analytical assay is by HPLC, RP HPLC, HIC HPLC, NMR, mass spectrometry, or UV spectroscopy.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO 2 levels are greater than 0%, and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, wherein said recombinant protein is a recombinant polypeptide or an isolated antibody.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO 2 levels are greater than 0%, and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, wherein the fermentation is scale-independent.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO 2 levels are greater than 0%, and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, wherein said prokaryotic host cell is Escherichia coli ( E.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO 2 levels are greater than 0%, and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, wherein said dO 2 is maintained at levels greater than 0% continuously throughout the harvest operations of step (b).
  • the harvest operations comprise a homogenization stage.
  • the dO 2 is maintained at about 30% to about 75% prior to homogenization.
  • the dO 2 is maintained at levels greater than 75% prior to homogenization.
  • the dO 2 is maintained at about 50% after homogenization.
  • the dO 2 is maintained at levels greater than 50% after homogenization.
  • the dO 2 is maintained for a period of greater than or equal to 1.5 hours.
  • the dO 2 is maintained for a period of greater than or equal to 2 hours.
  • the present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO 2 levels are greater than 0%, and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, wherein the dO 2 is maintained with overlay or sparged air, with increased back-pressure, or with agitation (i.e. stirring).
  • the overlay air is from about 0.4 vvm to about 0.8 vvm. In another embodiment, the overlay air is targeted at 0.6 vvm. In another embodiment, the increased backpressure is between about 1.0 to about 30 psi. In one embodiment, the increased backpressure is targeted at 19 psi. In still another embodiment, the agitation rate is from about 6 Watts/L to about 8 Watts/L. In yet another embodiment, the agitation rate is at least 6 Watts/L. In another embodiment, the agitation rate is targeted at 6 Watts/L.
  • a method of producing a recombinant protein comprising (a) fermenting a menE gene-deleted prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, (b) harvesting said recombinant protein; and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, is contemplated.
  • the recombinant protein yield is increased by about 20% or greater, by about 30% or greater, by about 40% or greater, by about 50% or greater, by about 60% or greater, as compared to the yield using a control prokaryotic host cell.
  • a method of producing a recombinant protein comprising (a) fermenting a menE gene-deleted prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, (b) harvesting said recombinant protein; and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, is contemplated, wherein the recombinant protein yield is increased by about 20% or greater, by about 30% or greater, by about 40% or greater, by about 50% or greater, by about 60% or greater, as compared to the yield using a control prokaryotic host cell, wherein the fermentation is scale-independent.
  • a method of producing a recombinant protein comprising (a) fermenting a menE gene-deleted prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, (b) harvesting said recombinant protein; and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, is contemplated, wherein the recombinant protein yield is increased by about 20% or greater, by about 30% or greater, by about 40% or greater, by about 50% or greater, by about 60% or greater, as compared to the yield using a control prokaryotic host cell, wherein said recombinant protein is a recombinant polypeptide or an isolated antibody.
  • a method of producing a recombinant protein comprising (a) fermenting a menE gene-deleted prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, (b) harvesting said recombinant protein; and (c) purifying said recombinant protein to a FBS, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm, is contemplated, wherein the recombinant protein yield is increased by about 20% or greater, by about 30% or greater, by about 40% or greater, by about 50% or greater, by about 60% or greater, as compared to the yield using a control prokaryotic host cell, wherein said prokaryotic host cell is Escherichia coli ( E.
  • FIG. 1 shows the COC assay results of three manufacturing runs of a product in which two runs, Run 2 and Run 3, did not meet the expected results for the COC assay.
  • PW purified water
  • C development run control
  • 3 Run 3.
  • FIG. 2A shows the UV/vis Spectra (10 cm) for Runs 1-3 —Near UV, where Runs 1-3 are represented. New absorbance peaks were observed approximately at 320 nm and at 460 nm which were not apparent for Run 1.
  • FIG. 2B shows the UV/vis spectra for Run 3 minus Run 1, in which the difference of the absorbance peaks for Runs 2 and 3 can be distinguished from Run 1.
  • FIG. 3A shows an IEC assay monitored at 280 nm and FIG. 3B shows an IEC assay monitored at 310 nm for Runs 1-3. A slight shoulder peak behind the main peak was observed for Runs 2 and 3, while the profile for Run 1 was comparable to the Reference Material.
  • FIG. 4 shows a 2D LC-MS analysis of intact Runs 1-3, monitored at 280 nm and 310 nm. An expected mass was observed for Run 1, while the expected mass and an additional mass at 157 Da were observed for Runs 2 and 3.
  • FIG. 5 shows a 2D-LC MS and mass identification by tryptic peptide map with MS detection of a collected fraction of the brown adduct—a minor peak from the IEC assay was collected. From the 2D LC-MS analysis, in addition to the expected mass, a +156 Da mass was observed for the fractionated shoulder peak.
  • FIG. 6 shows the LC-MS-MS analysis of the novel brown adduct peak observed at 48.8 minutes at 310 nm was determined to be T20 peptide with Cys182 modified with +154.006 Da. Modified (at cysteine, +154.006 Da) and free T6 and T16 peptides were also detected by mass extraction.
  • FIG. 7 compares 1H-15N HSQC data of product to a synthetic peptide (NH 2 -IVQCR-COOH) and showed a Cys NH correlation was missing in the product sample.
  • FIG. 8 shows the proposed structure confirmed by strong nOe observed between the CH of Cys and the NH of arginine.
  • FIG. 10 shows the biosynthesis pathway in prokaryotic cells to make menaquinones.
  • FIG. 11 shows a representative filtered bulk recombinant product tested for brown adduct formation by ion exchange chromatography at 310 nm and showed no measurable adduct formation.
  • FIG. 12 shows an exemplary schematic of the Hi-dO process enhancements implemented around the harvest operations.
  • FIG. 13 shows a schematic that shows the three major stages of a typical harvest operation: post-fermentation stage, a homogenization stage, then a post-homogenization stage.
  • agitation rate is mixing of the culture broth or of the homogenate, which is typically measured as revolutions per minute (rpm).
  • agitation rate can be measured by a “power per unit volume”. For example, at 200 rpm in a 1,000 liter fermentor, the agitation rate has a value of approximately 6 Watts/L.
  • antibody herein is used in the broadest sense and specifically covers monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, so long as they exhibit the desired biological activity. Antibodies may be murine, human, humanized, chimeric, or derived from other species.
  • antibody also refers to a full-length immunoglobulin molecule or an immunologically active portion of a full-length immunoglobulin molecule, i.e., a molecule that contains an antigen binding site that immunospecifically binds an antigen of a target of interest or part thereof, such targets including but not limited to, cancer cell or cells that produce autoimmune antibodies associated with an autoimmune disease.
  • the immunoglobulin disclosed herein can be of any type (e.g., IgG, IgE, IgM, IgD, and IgA), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of immunoglobulin molecule.
  • the immunoglobulins can be derived from any species. In one aspect, however, the immunoglobulin is of human, murine, or rabbit origin.
  • Antibody fragments comprise a portion of a full length antibody, generally the antigen binding or variable region thereof.
  • Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies, CDR (complementary determining region), ECD (extracellular domain), and epitope-binding fragments of any of the above which immunospecifically bind to cancer cell antigens, viral antigens or microbial antigens, single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
  • COC Color, Opalescence and Coloration Assay
  • DHNA 1,4-dihydroxy-2-naphthoate
  • dissolved oxygen is a relative measure of the amount of oxygen that is dissolved or carried in a given medium. It can be measured with a dissolved oxygen probe such as an oxygen sensor in liquid media.
  • fixment or “fermenting” as used herein means the process of culturing prokaryotic host cells that have been transformed to induce the production of a recombinant protein of interest.
  • filtered bulk or “filtered bulk substance (FBS)” means the recombinant protein of interest product after harvest and purification, wherein the protein has been released from the host cell, centrifuged and/or filtered to remove any cell debris, purified over suitable chromatography columns, and subsequently concentrated by a filtration process.
  • FBS filtered bulk substance
  • Cell culture is the process by which either prokaryotic or eukaryotic cells are grown under controlled conditions.
  • the term “cell culture” refers to the culturing of cells derived from multicellular eukaryotes, including animal cells or monocellular prokaryotes, including bacteria and yeast.
  • Eukaryotic cell cultures include mammalian cells such as Chinese Hamster Ovary cells, hybridomas, and insect cells. With an appropriate cell culture vessel, secreted proteins can be obtained from anchorage dependent cells or suspension cell lines.
  • Mammalian cell cultures include Chinese Hamster Ovary (CHO) cells or NSO cells.
  • slaughter operations means, without limitation, a process comprising the lysing or homogenization, and then centrifugation and/or filtration of a fermented prokaryotic host cell culture that has been transformed to produce a recombinant protein of interest, in order to begin isolating and purifying said protein of interest.
  • Hi-dO refers to an enhanced process as described herein which is the maintenance of a dissolved oxygen level greater than 0% during harvest operations.
  • the present invention contemplates a combination of overlay air, backpressure and agitation rate that can be used to maintain the dO 2 level at or above a set-point, i.e., above 0%, or at about 30% to about 75%, or at levels greater than 75%, or at about 50%, or at levels greater than 50%.
  • those skilled in the art could also sparge air or pure oxygen into the broth directly to achieve Hi-dO of dissolved oxygen levels greater than 0%.
  • homogenization means a process of lysing or the mechanical cell lysis of prokaryotic host cells transformed with a recombinant protein of interest in order to release said protein from the host cell.
  • the term “increased back-pressure” is used to increase the oxygen transfer rate through the culture broth. Back-pressure is typically measured either in psi or bar.
  • MK menaquinones
  • MenE is a gene in the biosynthesis pathway to make menaquinones.
  • microbial fermentation means cell culture of bacteria or yeast which is genetically engineered to produce proteins and small molecules (e.g. secondary metabolites). Fermentation is used to propagate recombinant bacteria and yeast as well as other microorganisms and produce proteins of value. The cell productivity and growth of these organisms are maximized by supplying particular growth media and controlling and various environmental factors (such as pH, temperature, and aeration). Bacterial fermentation fluid may be derived from E. coli cultures.
  • the term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations which include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies.
  • the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al (1975) Nature 256:495, or may be made by recombinant DNA methods (U.S. Pat. No. 4,816,567).
  • the “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described for example in Clackson et al (1991) Nature, 352:624-628; Marks et al (1991) J. Mol. Biol., 222:581-597.
  • overlay air means air blown in from the top of the fermentor which contains the culture broth.
  • oxygen is supplied to a fermentor by bubbling air through the liquid culture medium, often accompanied by vigorous agitation to effect a fine bubble dispersion.
  • prokaryotic host cell should encompass those that utilize the menaquinone biosynthesis pathway.
  • prokaryotic host cells encompass, for example, Archaebacteria and Eubacteria , such as gram-negative or gram-positive organisms.
  • useful bacteria include Escherichia (e.g., E. coli ), Bacilli (e.g., B. subtilis ), Enterobacteria, Pseudomonas species (e.g., P. aeruginosa ), Salmonella typhimurium, Serratia marcescans, Klebsiella, Proteus, Shigella, Rhizobia, Vitreoscilla , or Paracoccus .
  • E. coli cells are used as hosts for the invention (Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D.C.: American Society for Microbiology, 1987), pp. 1190-1219; ATCC Deposit No. 27,325) and derivatives thereof, including strain 33D3 having genotype W3110 ⁇ fhuA ( ⁇ tonA) ptr3 lacIq lacL8 ⁇ ompT ⁇ (nmpC-fepE) degP41 kan R (U.S. Pat. No. 5,639,635).
  • E. coli 294 ATCC 31,446
  • E. coli B E.
  • E. coli ⁇ 1776 (ATCC 31,537) and E. coli RV308 (ATCC 31,608) are also suitable. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al. (1990) Proteins, 8: 309-314. It is, of course, necessary to select the appropriate bacteria taking into consideration replicability of the replicon in the cells of a bacterium. For example, E. coli, Serratia , or Salmonella species can be suitably used as the host when well known plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • recombinant protein refers generally to peptides and proteins, including antibodies. Such recombinant proteins are “heterologous,” i.e., foreign to the host cell being utilized, such as a human protein produced by E. coli .
  • the polypeptide may be produced as an insoluble aggregate or as a soluble polypeptide in the periplasmic space or cytoplasm.
  • scale-independent means the volume capacity of the fermentation process of the present invention can be accomplished using any scale, such as, for example, from about 1 liter or greater, or about 10 liters or greater, or about 100 liters or greater, or about 500 liters or greater, or about 1,000 liters or greater, or about 10,000 liters or greater, or about 100,000 liters or greater.
  • the present invention concerns improved methods of recombinant production of proteins in a prokaryotic system.
  • the invention is based on preventing a brown adduct formation discovered during the manufacturing of a recombinant protein which caused certain lots of the product to not meet specifications.
  • the problem of the brown adduct resulted from an inconsistent redox potential during the harvest operations. It has now been surprisingly discovered that the brown adduct formation can be prevented by maintaining a dissolved oxygen environment greater than zero during the harvest operations or alternatively, by genetically deleting the menE gene in the prokaryotic host cell genome used to recombinantly produce the recombinant protein of interest.
  • the heterologous nucleic acid (e.g., cDNA or genomic DNA) used to produce the recombinant protein of interest, is suitably inserted into a replicable vector for expression in the bacterium under the control of a suitable promoter for bacteria.
  • a replicable vector for expression in the bacterium under the control of a suitable promoter for bacteria.
  • Many vectors are available for this purpose, and selection of the appropriate vector will depend mainly on the size of the nucleic acid to be inserted into the vector and the particular host cell to be transformed with the vector.
  • Each vector contains various components depending on its function (amplification of DNA or expression of DNA) and the particular host cell with which it is compatible.
  • the vector components for bacterial transformation may include a signal sequence for the heterologous polypeptide and will include a signal sequence and will also include an inducible promoter for the heterologous polypeptide. They also generally include an origin of replication and one or more marker genes, described herein.
  • the DNA encoding the heterologous polypeptide of interest herein contains a signal sequence, such as one at the N-terminus of the mature heterologous polypeptide.
  • the signal sequence may be a component of the vector, or it may be a part of the heterologous polypeptide DNA that is inserted into the vector.
  • the heterologous signal sequence selected should be one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell. For bacterial host cells that do not recognize and process the native heterologous polypeptide signal sequence, the signal sequence is substituted by any commonly known bacterial signal sequence.
  • Expression vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria. The origin of replication from the plasmid pBR322 is suitable for most gram-negative bacteria.
  • Selection genes also generally contain a selection gene, also termed a selectable marker. This gene encodes a protein necessary for the survival or growth of transformed host cells grown in a selective culture medium. Host cells not transformed with the vector containing the selection gene will not survive in the culture medium.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli .
  • One example of a selection scheme utilizes a drug to arrest growth of a host cell. Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen.
  • the expression vector for producing a heterologous polypeptide also contains an inducible promoter that is recognized by the host bacterial organism and is operably linked to the nucleic acid encoding the heterologous polypeptide of interest. It also contains a separate inducible or low-basal-expression promoter operably linked to the nucleic acid encoding the lytic enzymes.
  • Inducible promoters suitable for use with bacterial hosts include the .beta.-lactamase and lactose promoter systems (Chang et al., Nature, 275: 615 (1978); Goeddel et al., Nature, 281: 544 (1979)), the arabinose promoter system, including the araBAD promoter (Guzman et al., J. Bacteriol., 174: 7716-7728 (1992); Guzman et al., J. Bacteriol., 177: 4121-4130 (1995); Siegele and Hu, Proc. Natl. Acad. Sci.
  • bacterial inducible promoters and low-basal-expression promoters are suitable. Their nucleotide sequences have been published, thereby enabling a skilled worker operably to ligate them to DNA encoding the heterologous polypeptide of interest or to the nucleic acids encoding the lytic enzymes (Siebenlist et al., Cell, 20: 269 (1980)) using linkers or adaptors to supply any required restriction sites. If a strong and highly leaky promoter, such as the trp promoter, is used, it is generally used only for expression of the nucleic acid encoding the heterologous polypeptide and not for lytic-enzyme-encoding nucleic acid. The tac and P L promoters could be used for either, but not both. In one embodiment, the alkaline phosphatase (phoA) promoter is used for the product and the arabinose (ara) promoter for the lytic enzymes.
  • phoA alkaline phosphatase
  • ara arabi
  • Promoters for use in bacterial systems also generally contain a Shine-Dalgarno (SD) sequence operably linked to the DNA encoding the heterologous polypeptide of interest.
  • SD Shine-Dalgarno
  • the promoter can be removed from the bacterial source DNA by restriction enzyme digestion and inserted into the vector containing the desired DNA.
  • the phoA promoter can be removed from the bacterial-source DNA by restriction enzyme digestion and inserted into the vector containing the desired DNA.
  • Plasmids containing one or more of the above-listed components employs standard ligation techniques commonly known to those of skill in the art. Isolated plasmids or DNA fragments are cleaved, tailored, and re-ligated in the form desired to generate the plasmids required.
  • Suitable prokaryotic host cells for the claimed invention include any which utilize the biosynthesis pathway to make menaquinones, as defined herein.
  • Some non-limiting examples may include, for example, Escherichia coli ( E. coli ), Enterobacter, Azotobacter, Erwinia, Bacillus, Pseudomonas, Klebsiella, Proteus, Salmonella, Serratia, Shigella, Rhizobia, Vitreoscilla , and Paracoccus.
  • Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant.
  • transformation is done using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers.
  • Another method for transformation employs polyethylene glycol/DMSO.
  • Yet another technique used is electroporation.
  • Prokaryotic cells used to produce the polypeptides of the invention are grown in media known in the art and suitable for culture of the selected host cells.
  • suitable media include Luria-Bertani (LB) broth plus necessary nutrient supplements.
  • the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector.
  • LB Luria-Bertani
  • the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector.
  • ampicillin is added to media for growth of cells expressing ampicillin resistant gene.
  • Any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source.
  • the host cell For accumulation of an expressed gene product, the host cell is cultured under conditions sufficient for accumulation of the gene product.
  • conditions include, e.g., temperature, nutrient, and cell-density conditions that permit protein expression and accumulation by the cell.
  • conditions are those under which the cell can perform basic cellular functions of transcription, translation, and passage of proteins from one cellular compartment to another for the secreted proteins, as are known to those skilled in the art.
  • the prokaryotic host cells are cultured at suitable temperatures.
  • the typical temperature ranges from about 20° C. to about 39° C. In one embodiment, the temperature is from about 25° C. to about 37° C. In another embodiment, the temperature is at about 30° C.
  • the pH of the culture medium may be any pH from about 5-9, depending mainly on the host organism.
  • the pH is from about 6.8 to about 7.4, or about 7.0.
  • the cells are cultured until a certain optical density is achieved, e.g., an A 550 of about 80-100, at which point induction is initiated (e.g., by addition of an inducer, by depletion of a repressor, suppressor, or medium component, etc.) to induce expression of the gene encoding the heterologous polypeptide.
  • a certain optical density e.g., an A 550 of about 80-100, at which point induction is initiated (e.g., by addition of an inducer, by depletion of a repressor, suppressor, or medium component, etc.) to induce expression of the gene encoding the heterologous polypeptide.
  • the broth lysate is incubated for a period of time sufficient to release the heterologous polypeptide contained in the cells.
  • the cells present in culture may be lysed mechanically, using any mechanical means known in the art, which may include, for example, chemical lysis or osmotic shock in order to release said protein from the host cell.
  • the lysate or homogenate may be transferred to a hold tank where it can await the addition of more batches of lysate/homogenate and/or where further processing may occur, such as, for example, dilution with water, addition of buffers or flocculants, pH adjustment, or altering or maintaining the temperature of the lysate/homogenate in preparation for subsequent recovery steps.
  • the heterologous polypeptide as a soluble or insoluble product released from the cellular matrix, is recovered from the lysate, or homogenate, in a manner that minimizes co-recovery of cellular debris with the product.
  • the recovery may be done by any means, but in one embodiment, can comprise sedimenting refractile particles containing the heterologous polypeptide or collecting supernatant containing soluble product.
  • An example of sedimentation is centrifugation.
  • the recovery takes place, before expanded bed adsorption (EBA) or sedimentation, in the presence of an agent that disrupts the outer cell wall to increase permeability and allows more solids to be recovered.
  • EBA expanded bed adsorption
  • EDTA ethylenediaminetetraacetic acid
  • ZWITTERGENT 316TM detergent examples of such agents.
  • the recovery takes place in the presence of EDTA.
  • the relative centrifugal force is an important factor.
  • the RCF is adjusted to minimize co-sedimentation of cellular debris with the refractile particles released from the cell wall at lysis.
  • the specific RCF used for this purpose will vary with, for example, the type of product to be recovered, but is at least about 3000 ⁇ g, more preferably about 3500-6000 ⁇ g, or about 4000-6000 ⁇ g.
  • the duration of centrifugation will depend on several factors.
  • the sedimentation rate will depend upon, e.g., the size, shape, and density of the retractile particle and the density and viscosity of the fluid.
  • the sedimentation time for solids will depend, e.g., on the sedimentation distance and rate. It is reasonable to expect that the continuous disc-stack centrifuges would work well for the recovery of the released heterologous polypeptide aggregates or for the removal of cellular debris at large scale, since these centrifuges can process at high fluid velocities because of their relatively large centrifugal force and the relatively small sedimentation distance.
  • the heterologous polypeptide captured in the initial recovery step may then be further purified from the contaminating protein.
  • the aggregated heterologous polypeptide is isolated, followed by a simultaneous solubilization and refolding of the polypeptide, as disclosed in U.S. Pat. No. 5,288,931.
  • the soluble product is recovered by standard techniques as described below.
  • the following procedures are exemplary of suitable purification procedures for the soluble heterologous polypeptide released from the periplasm or the cytoplasm, and are well known in the art: fractionation on immunoaffinity or ion-exchange columns; ethanol precipitation; reversed-phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; and gel filtration using, for example, SEPHADEXTM G-75.
  • the antibody production is conducted in large quantity by a fermentation process.
  • Various large-scale fed-batch fermentation procedures are available for production of recombinant proteins.
  • Large-scale fermentations have at least 1000 liters of capacity, preferably about 1,000 to 100,000 liters of capacity. These fermentors use agitator impellers to distribute oxygen and nutrients, especially glucose (the preferred carbon/energy source).
  • Small-scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 20 liters in volumetric capacity.
  • the claimed invention can be used to produce recombinant proteins, including, for example, peptides and proteins, including antibodies.
  • recombinant peptides and proteins that can be produced by the method of the invention include, but are not limited to, molecules such as, e.g., renin, a growth hormone, including human growth hormone; bovine growth hormone; growth hormone releasing factor; parathyroid hormone; thyroid stimulating hormone; lipoproteins; ⁇ 1-antitrypsin; insulin A-chain; insulin B-chain; proinsulin; thrombopoietin; follicle stimulating hormone; calcitonin; luteinizing hormone; glucagon; clotting factors such as factor VIIIC, factor IX, tissue factor, and von Willebrands factor; anti-clotting factors such as Protein C; atrial naturietic factor; lung surfactant; a plasminogen activator, such as urokinase or human urine or tissue-type plasminogen activator (t-PA); bombesin; thrombin; hemopoietic growth factor; tumor necrosis factor-alpha and—beta;
  • Antibodies produced by the claimed invention may be monoclonal antibodies that are homogeneous populations of antibodies to a particular antigenic determinant (e.g., a cancer cell antigen, a viral antigen, a microbial antigen, a protein, a peptide, a carbohydrate, a chemical, nucleic acid, or fragments thereof).
  • a monoclonal antibody (MAb) to a target-of-interest can be prepared by using any technique known in the art which provides for the production of antibody molecules by continuous cell lines in culture.
  • Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, and IgD and any subclass thereof.
  • the hybridoma producing the MAbs of use in this invention may be cultivated in vitro or in vivo.
  • Useful monoclonal antibodies include, but are not limited to, human monoclonal antibodies, humanized monoclonal antibodies, antibody fragments, or chimeric human-mouse (or other species) monoclonal antibodies.
  • Human monoclonal antibodies may be made by any of numerous techniques known in the art (Teng et al (1983) Proc. Natl. Acad. Sci. U.S.A. 80:7308-7312; Kozbor et al (1983) Immunology Today 4:72-79; and Olsson et al (1982) Methods in Enzymology 92:3-16).
  • the antibody can also be a bispecific antibody.
  • Bispecific antibodies may have a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm.
  • This asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation (WO 94/04690; Suresh et al (1986) Methods in Enzymology, 121:210; Rodrigues et al (1993) J.
  • bispecific antibodies can be prepared for conjugation as an antibody drug conjugate (ADC) in the treatment or prevention of disease as defined herein.
  • ADC antibody drug conjugate
  • the antibody can be a functionally active fragment, derivative or analog of an antibody that immunospecifically binds to cancer cell antigens, viral antigens, or microbial antigens or other antibodies bound to tumor cells or matrix.
  • “functionally active” means that the fragment, derivative or analog is able to elicit anti-anti-idiotype antibodies that recognize the same antigen that the antibody from which the fragment, derivative or analog is derived recognized.
  • the antigenicity of the idiotype of the immunoglobulin molecule can be enhanced by deletion of framework and CDR sequences that are C-terminal to the CDR sequence that specifically recognizes the antigen.
  • synthetic peptides containing the CDR sequences can be used in binding assays with the antigen by any binding assay method known in the art, e.g. the BIA core assay (Kabat et al, (1991) in Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, Md.; Kabat et al (1980) J. of Immunology 125(3):961-969).
  • BIA core assay Karl et al, (1991) in Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, Md.; Kabat et al (1980) J. of Immunology 125(3):961-969.
  • Other useful antibodies include fragments of antibodies such as, but not limited to, F(ab′)2 fragments, which contain the variable region, the light chain constant region and the CH1 domain of the heavy chain can be produced by pepsin digestion of the antibody molecule, and Fab fragments, which can be generated by reducing the disulfide bridges of the F(ab′)2 fragments.
  • Other useful antibodies are heavy chain and light chain dimers of antibodies, or any minimal fragment thereof such as Fvs or single chain antibodies (SCAs) (e.g., as described in U.S. Pat. No. 4,946,778; Bird (1988) Science 242:423-42; Huston et al., (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5879-5883; and Ward et al (1989) Nature 334:544-54), or any other molecule with the same specificity as the antibody.
  • SCAs single chain antibodies
  • the antibody may be a fusion protein of an antibody, or a functionally active fragment thereof, for example in which the antibody is fused via a covalent bond (e.g., a peptide bond), at either the N-terminus or the C-terminus to an amino acid sequence of another protein (or portion thereof, such as at least 10, 20 or 50 amino acid portion of the protein) that is not the antibody.
  • a covalent bond e.g., a peptide bond
  • the antibody or fragment thereof may be covalently linked to the other protein at the N-terminus of the constant domain.
  • the monoclonal antibodies herein specifically include “chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al (1984) Proc. Natl. Acad. Sci. U.S.A., 81:6851-6855).
  • a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from murine monoclonal and human immunoglobulin constant regions (U.S. Pat. Nos. 4,816,567; 4,816,397).
  • Chimeric antibodies include “primatized” antibodies comprising variable domain antigen-binding sequences derived from a non-human primate (e.g., Old World Monkey, Ape etc) and human constant region sequences.
  • Chimeric and humanized monoclonal antibodies comprising both human and non-human portions, can be made using standard recombinant DNA techniques (WO 87/02671; EP 184,187; EP 171496; EP 173494; WO 86/01533; U.S. Pat. No. 4,816,567; EP 12023; Berter et al (1988) Science 240: 1041-1043; Liu et al (1987) Proc. Natl. Acad. Sci. U.S.A. 84: 3439-3443; Liu et al (1987) J. Immunol. 139: 3521-3526; Sun et al (1987) Proc. Natl. Acad. Sci. U.S.A.
  • Therapeutic monoclonal antibodies that may be produced by the methods of the invention include, for are not limited to, trastuzumab (HERCEPTIN®, Genentech, Inc., Carter et al (1992) Proc. Natl. Acad. Sci. U.S.A., 89:4285-4289; U.S. Pat. No. 5,725,856); anti-CD20 antibodies such as chimeric anti-CD20 “C2B8” (U.S. Pat. No. 5,736,137); rituximab (RITUXAN®), ocrelizumab, a chimeric or humanized variant of the 2H7 antibody (U.S. Pat. No.
  • trastuzumab HERCEPTIN®, Genentech, Inc., Carter et al (1992) Proc. Natl. Acad. Sci. U.S.A., 89:4285-4289; U.S. Pat. No. 5,725,856
  • anti-CD20 antibodies such as chi
  • anti-IL-8 St John et al (1993) Chest, 103:932, and WO 95/23865
  • antibodies targeting other interleukins such as IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, IL-10, IL-12, IL-13
  • anti-VEGF antibodies including humanized and/or affinity matured anti-VEGF antibodies such as the humanized anti-VEGF antibody huA4.6.1 bevacizumab (AVASTIN®, Genentech, Inc., Kim et al (1992) Growth Factors 7: 53-64, WO 96/30046, WO 98/45331); anti-PSCA antibodies (WO 01/40309); anti-CD40 antibodies, including S2C6 and humanized variants thereof (WO 00/75348); anti-CD11a (U.S.
  • anti-CD25 or anti-tac antibodies such as CHI-621 SIMULECT® and ZENAPAX® (U.S. Pat. No. 5,693,762)
  • anti-CD4 antibodies such as the cM-7412 antibody (Choy et al (1996) Arthritis Rheum 39(1): 52-56); anti-CD52 antibodies such as CAMPATH-1H (Riechmann et al (1988) Nature 332: 323-337); anti-Fc receptor antibodies such as the M22 antibody directed against Fc gamma RI as in Graziano et al (1995) J. Immunol.
  • anti-carcinoembryonic antigen (CEA) antibodies such as hMN-14 (Sharkey et al (1995) Cancer Res. 55(23 Suppl): 5935s-5945s; antibodies directed against breast epithelial cells including huBrE-3, hu-Mc 3 and CHL6 (Ceriani et al (1995) Cancer Res. 55(23): 5852s-5856s; and Richman et al (1995) Cancer Res. 55(23 Supp): 5916s-5920s); antibodies that bind to colon carcinoma cells such as C242 (Litton et al (1996) Eur J. Immunol.
  • anti-CD38 antibodies e.g. AT 13/5 (Ellis et al (1995) J. Immunol. 155(2): 925-937); anti-CD33 antibodies such as Hu M195 (Jurcic et al (1995) Cancer Res 55(23 Suppl): 5908s-5910s and CMA-676 or CDP771; anti-CD22 antibodies such as LL2 or LymphoCide (Juweid et al (1995) Cancer Res 55(23 Suppl): 5899s-5907s); anti-EpCAM antibodies such as 17-1A (PANOREX®); anti-GpIIb/IIIa antibodies such as abciximab or c7E3 Fab (REOPRO®); anti-RSV antibodies such as MEDI-493 (SYNAGIS®); anti-CMV antibodies such as PROTOVIR®); anti-HIV antibodies such as PRO542; anti-hepatitis antibodies such as the anti-Hep B antibody
  • the degree of opalescence may also be determined by instrumental measurement of the light absorbed or scattered on account of submicroscopic optical density in homogeneities of opalescent solutions and suspensions. Such techniques are nephelometry and turbidimetry. For turbidity measurement of coloured samples, ratio turbidimetry and nephelometry with ratio selection are used. The light scattering effect of suspended particles can be measured by observation of either the transmitted light (turbidimetry) or the scattered light (nephelometry). Ratio turbidimetry combines the principles of both nephelometry and turbidimetry. Turbidimetry and nephelometry are useful for the measurement of slightly opalescent suspensions.
  • High Performance Liquid Chromatography also known as High Pressure Liquid Chromatography, abbreviated as HPLC
  • HPLC High Pressure Liquid Chromatography
  • the analyte is forced through a column of the stationary phase in a liquid (mobile phase) at high pressure, which decreases the time the separated components remain on the stationary phase and thus the time they have to diffuse within the column. This leads to narrower peaks in the resulting chromatogram and thence to better resolution and sensitivity as compared to LC.
  • the mobile phase is chosen to ensure solubility of the sample solutes.
  • the stationary phase preferably microparticulate silica (bare or chemically modified) is used, because its high surface area accentuates the differences in solute-stationary phase interactions.
  • a stationary phase that interacts strongly with solutes relative to solute mobile-phase interactions will result in very long retention times, a situation which is not analytically useful.
  • the stationary phase must be selected so as to provide weak to moderate solute interactions relative to those in the mobile phase.
  • the nature of the solute governs the type of LC selected. The stronger interactions should occur in the mobile phase to ensure sample solubility and ready elution, while the stationary phase should be responsive to more subtle differences among the solutes.
  • polar neutral compounds are usually better analyzed using a polar mobile phase together with a nonpolar stationary phase that distinguishes subtle differences in the dispersive character of the solutes.
  • HPLC high-density lipoprotein
  • Modifiers can be added to the mobile phase to control retention.
  • pH is an important variable in aqueous mobile phases.
  • Reversed-phase chromatography calls for the use of a non-polar stationary phase and a polar mobile phase (composed of one or more of the polar solvents, e.g. water, methanol, acetonitrile, and tetrahydrofuran).
  • a polar mobile phase composed of one or more of the polar solvents, e.g. water, methanol, acetonitrile, and tetrahydrofuran.
  • Hydrophobic interaction chromatography HPLC: This chromatographic method is good for analyzing proteins or antibody/protein bioconjugates based on their hydrophobicity.
  • the theory behind hydrophobic interaction chromatography is that proteins are bound to the resin by employing an aqueous high salt mobile phase. The salt conditions contribute to a lyotropic effect which allows the proteins to bind to the lower surface coverage of a hydrophobic ligand. Proteins are eluted by the simple technique of decreasing the salt concentration. Most therapeutic targets are eluted in a low salt or a no salt buffer. Thus, the compound can be eluted in a more polar and less denaturing environment. For example, HIC has been used extensively to analyze drug loading in antibody-drug or protein-drug conjugates.
  • Nuclear magnetic resonance (NMR) detection is based on the fact that certain nuclei with odd-numbered masses, including H and 13C, spin about an axis in, a random fashion. However, when placed between poles of a strong magnet, the spins are aligned either parallel or anti-parallel to the magnetic field, with the parallel orientation favored since it is slightly lower in energy. The nuclei are then irradiated with electromagnetic radiation which is absorbed and places the parallel nuclei into a higher energy state; consequently, they are now in “resonance” with the radiation. Each H or C will produce different spectra depending on their location and adjacent molecules, or elements in the compound, because all nuclei in molecules are surrounded by electron clouds which change the encompassing magnetic field and thereby alter the absorption frequency.
  • Mass spectrometry is an analytical technique used to measure the mass-to-charge ratio (m/z or m/q) of ions. It is most generally used to analyze the composition of a physical sample by generating a mass spectrum representing the masses of sample components.
  • the technique has several applications including identifying unknown compounds by the mass of the compound and/or fragments thereof determining the isotopic composition of one or more elements in a compound, determining the structure of compounds by observing the fragmentation of the compound, quantitating the amount of a compound in a sample using carefully designed methods (mass spectrometry is not inherently quantitative), studying the fundamentals of gas phase ion chemistry (the chemistry of ions and neutrals in vacuum), and determining other physical, chemical or even biological properties of compounds with a variety of other approaches.
  • a mass spectrometer is a device used for mass spectrometry, and it produces a mass spectrum of a sample to analyze its composition. This is normally achieved by ionizing the sample and separating ions of differing masses and recording their relative abundance by measuring intensities of ion flux.
  • a typical mass spectrometer comprises three parts: an ion source, a mass analyzer, and a detector.
  • Electron ionization and chemical ionization are used for gases and vapors.
  • chemical ionization sources the analyte is ionized by chemical ion-molecule reactions during collisions in the source.
  • Two techniques often used with liquid and solid biological samples include electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI).
  • Other techniques include fast atom bombardment (FAB), thermospray, atmospheric pressure chemical ionization (APCI), secondary ion mass spectrometry (SIMS), and thermal ionisation.
  • UV-Vis or UV/Vis refers to absorption spectroscopy or reflectance spectroscopy in the ultraviolet-visible spectral region. This means it uses light in the visible and adjacent (near-UV and near-infrared (NIR)) ranges. The absorption or reflectance in the visible range directly affects the perceived color of the chemicals involved. In this region of the electromagnetic spectrum, molecules undergo electronic transitions. This technique is complementary to fluorescence spectroscopy, in that fluorescence deals with transitions from the excited state to the ground state, while absorption measures transitions from the ground state to the excited state.
  • a UV spectrometer is an instrument that uses a beam of light from a visible and/or UV light source (colored red) is separated into its component wavelengths by a prism or diffraction grating. Each monochromatic (single wavelength) beam in turn is split into two equal intensity beams by a half-mirrored device.
  • One beam, the sample beam (colored magenta) passes through a small transparent container (cuvette) containing a solution of the compound being studied in a transparent solvent.
  • the other beam, the reference passes through an identical cuvette containing only the solvent.
  • the intensities of these light beams are then measured by electronic detectors and compared.
  • the intensity of the reference beam which should have suffered little or no light absorption, is defined as I0.
  • the intensity of the sample beam is defined as I.
  • the spectrometer automatically scans all the component wavelengths in the manner described.
  • the ultraviolet (UV) region scanned is normally from 200 to 400 nm, and the visible portion is from 400 to 800 nm.
  • the concentrated samples were compared against all the Standard color solutions listed in the U.S. Pharmacopeia 2012 (USP Monograph 631, Color and Achromicity) or in the European Pharmacopoeia 5.0 (EP Method 2.2.2, Degree of Coloration of Liquids) for confirmation of the appropriate color assignment.
  • the samples were compared in diffused daylight 5 min after preparation of the reference sample, viewing vertically against a black background. The diffusion of light must be such that reference sample I can readily be distinguished from water and that reference suspension II can readily be distinguished from reference suspension I. A liquid was considered clear if its clarity was the same as that of water R or of the solvent used when examined under the conditions described above, or if its opalescence was not more pronounced than that of the reference sample I.
  • Runs 1-3 were analyzed using ultraviolet and visible (UV/vis) spectroscopy with a 1 cm path length cuvette.
  • UV spectra 200-600 nm did not display any significant differences in the observance profile for the samples analyzed.
  • the experiment was repeated using a 10 cm path length cuvette.
  • the 10 cm cuvette offers increased sensitivity to the 1 cm cuvette due to the absorbance of a sample is proportional to the number of absorbing molecules in the spectrophotometer meter light beam.
  • the samples were scanned between 200-700 nm to determine the absorption spectrum of Runs 1-3.
  • the shape of the spectra for Runs 2 and 3 was different than Run 1: new absorbance peaks were observed approximately at 320 nm and at 460 nm which were not apparent for Run 1 ( FIG. 2A ). This difference can be observed more clearly when the spectrum of Run 1 is subtracted from the spectrum of Run 3 ( FIG. 2B ).
  • the peak observed at 460 nm for Runs 2 and 3 is consistent with a flavin (e.g., vitamin) fingerprint.
  • Intact samples were submitted for 2D LC-MS and monitored at both 280 and 310 nm.
  • the 2D LC-MS analysis consists of two parts—first dimension is separation by RP-HPLC with the second dimension as fractionated peaks for mass spectrometry analysis. From this experiment, the expected mass was observed for Run 1 while the expected mass and an additional mass of approximately +157 Da were observed for Runs 2 and 3 ( FIG. 4 ).
  • Run 3 was selected for fractionation (the minor peak from the IEC assay ( FIG. 3 ) was collected) and further analyzed by 2D-LC MS and mass identification by tryptic peptide map with MS detection.
  • TOCSY creates correlations between all protons that are coupled to each other as well as all other protons within a given spin system.
  • HSQC experiment correlates chemical shifts of directly bound nuclei (i.e. two types of chemical nuclei) while HMBC experiment correlates chemical shifts of two types of nuclei separated from each other with two or more chemical bonds.
  • the 1H-13C HSQC chemical shifts for the collected peptide in the aromatic region are a close match to those observed for the synthetic model compound bound to naphthalene-1,4-dione.
  • TOCSY data assigns the Q, V, and R resonances in the product. Comparing 1H-15N HSQC data of product to a synthetic peptide (NH 2 -IVQCR-COOH) showed a Cys NH correlation was missing in the product sample as shown in FIG. 7 .
  • the proposed structure is confirmed by strong nOe observed between the CH of Cys and the NH of Arg ( FIG. 8 ). Based on the NMR data collected, the proposed structure is presented in FIG. 9 .
  • DHNA 1,4-dihydroxy-2-naphthoate
  • a control strategy was developed to prevent the generation of a product's free thiols and the subsequent formation of the DHNA-product adduct.
  • the cause of the color formation was determined to be the result of a low redox environment during the harvest operations because Runs 2 and 3 exhibited the highest titers and cell densities, both were subjected to longer hold times for their diluted homogenates, endured longer durations for the homogenates to achieve less than the 15° C. target temperature and had suboptimal homogenate mixing times and rates (data not shown). These factors contributed to generating a low oxygen environment which promoted the reduction of the product disulfide bonds and permitted the opportunity for DHNA to attach to the free thiols of the protein product.
  • DHNA-protein adduct was formed during the low redox environment during the harvest operations which led to reduced disulfide bonds (i.e. free thiols)
  • an approach was developed to prevent the generation of free thiols and the formation of the DHNA-product adduct.
  • This enhanced process control called Hi-dO, maintains the dissolved oxygen levels in the harvest operations at greater than zero (>0%) to eliminate the reducing environment (i.e. no free thiol generation).
  • the formation of the DHNA-product adduct is a complex biological reaction that requires the combination of multiple events across the fermentation and harvest operations.
  • the output of the fermentation process is the production of considerable levels and/or availability of DHNA.
  • the schematic of the three major stages of a typical harvest operation is shown on FIG. 13 .
  • the menE gene deleted host cells were generated as an in-frame, single-gene knockout mutant following the methods described in Baba et al., Construction of E. coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol. 21, p. 1-10 (2006) which is hereby incorporated by reference.
  • the menE gene was targeted for mutagenesis with PCR products containing a resistance cassette (such as kanamycin) flanked by FLP recognition target sites and a 50 base pair homologies to the adjacent chromosomal sequences.
  • the mutagenesis yielded approximately 10-1000 kanamycin resistance colonies when the host cells were incubated aerobically at 37° C. on Luria-Bertani broth (LB) agar containing 30 g/mL kanamycin.
  • menE gene-deleted E. coli host cells were transformed with plasmid constructs that encoded for two recombinant proteins, PROT 1 and PROT 2, and two recombinant antibodies, AB 1 and AB2, per standard techniques well-known to those of skill in the art (see for example, Simmons et al., Expression of full-length immunoglobulins in E. coli : rapid and efficient production of aglycosylated antibodies, J of Immunol Methods 263 p. 133-147 (2002)). Fermentation of the four recombinant proteins/antibodies proceeded as described herein (see also U.S. Pat. No. 6,979,556 which is hereby incorporated by reference).
  • the filtered bulk recombinant product for all four recombinant protein/antibodies were tested for DHNA-protein adduct formation by IEC assay at 310 nm and showed no detectable DHNA-protein adduct formation (see FIG. 11 for exemplary results for PROT 1).

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