Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 1 of 46 PageID #: 9681
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`v.
`
`
`AMGEN INC.,
`
`Defendant and Counterclaim Plaintiff.
`
`
`GENENTECH, INC. and CITY OF HOPE, )
`)
`Plaintiffs and Counterclaim Defendants, )
`)
`)
`)
`)
`)
`)
`)
`
`GENENTECH, INC. and CITY OF HOPE, )
`)
`Plaintiffs and Counterclaim Defendants, )
`)
`)
`)
`)
`)
`)
`)
`
`v.
`
`SAMSUNG BIOEPIS CO., LTD,
`
`Defendant and Counterclaim Plaintiff.
`
`
`
`C.A. No. 18-924-CFC
`
`C.A. No. 18-1363-CFC
`
`
`
`
`
`
`
`DECLARATION OF DR. HANSJÖRG HAUSER IN SUPPORT OF
`PLAINTIFFS’ OPENING CLAIM CONSTRUCTION BRIEF
`
`
`
`
`
`ActiveUS 171281095v.1
`
`
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`v.
`
`
`AMGEN INC.,
`
`Defendant and Counterclaim Plaintiff.
`
`
`GENENTECH, INC. and CITY OF HOPE, )
`)
`Plaintiffs and Counterclaim Defendants, )
`)
`)
`)
`)
`)
`)
`)
`
`GENENTECH, INC. and CITY OF HOPE, )
`)
`Plaintiffs and Counterclaim Defendants, )
`)
`)
`)
`)
`)
`)
`)
`
`v.
`
`SAMSUNG BIOEPIS CO., LTD,
`
`Defendant and Counterclaim Plaintiff.
`
`
`
`C.A. No. 18-924-CFC
`
`C.A. No. 18-1363-CFC
`
`
`
`
`
`
`
`DECLARATION OF DR. HANSJÖRG HAUSER IN SUPPORT OF
`PLAINTIFFS’ OPENING CLAIM CONSTRUCTION BRIEF
`
`
`
`
`
`ActiveUS 171281095v.1
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 2 of 46 PageID #: 9682
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`I, Dr. Hansjörg Hauser, declare as follows:
`
`I.
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`Professional Experience and Qualifications
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`1.
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`I am an expert in cell culture technology, which is the science of
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`isolating cells from their natural environment and growing them in a controlled,
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`artificial environment. In particular, I have expertise in cell culture processes used
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`to manufacture biotherapeutics, such as therapeutic antibodies. I have over forty
`
`years of experience in molecular biology and have conducted significant research
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`concerning the development of cell lines for protein expression. For the past two
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`decades, I have served as editor of one of the leading textbooks in the field of cell
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`culture technology for protein production: the “Mammalian Cell Biotechnology in
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`Protein Production” textbook series (later retitled “Animal Cell Biotechnology: In
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`Biologics Production”).
`
`2.
`
`I obtained a degree in Food Science from the Universität Stuttgart-
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`Hohenheim, Germany in 1973, and a Ph.D. in Biology from the University of
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`Konstanz, Konstanz, Germany in 1978.
`
`3.
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`After earning my Ph.D., I received postdoctoral training at Max
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`Planck Institute for Molecular Genetics in Berlin, Germany from 1978 to 1980,
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`and from the German Cancer Research Centre in Heidelberg, Germany in 1980.
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`The Max Planck Institute is a leading research center that concentrates on
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`understanding the function and regulation of the human genome. The German
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`
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`2
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`
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 3 of 46 PageID #: 9683
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`Cancer Research Centre is one of the largest biomedical research institutes in
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`Germany. I completed a European Molecular Biology Organization (“EMBO”)
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`fellowship at the Medical Research Council National Institute for Medical
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`Research at Mill Hill (“NIMR”) in the United Kingdom in 1982. During my
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`postdoctoral training and fellowship, my research focused on the molecular
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`biology of mammalian cells with an emphasis on gene regulation. This work
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`formed the basis for expression of individual genes in mammalian cells for
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`production of biopharmaceuticals.
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`4.
`
`In 1981, I became a Staff Scientist at Helmholtz Centre for Infection
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`Research (formerly Gesellschaft f. Biotechnologische Forschung (GBF)) in
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`Braunschweig, Germany, and have worked there since. In 1986, I was promoted to
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`Head of Research Group for Genetics of Eukaryotes. In 1994, I was promoted to
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`Head of the Department of Gene Regulation and Differentiation. In 1995, I
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`became Head of the Division of Molecular Biotechnology. In these positions, I
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`conducted research and published extensively in the field of cell culture
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`technology.
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`5.
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`For example, I was the first investigator worldwide to express
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`interferon-ß in mammalian cells and to make production cells lines in BHK-21 and
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`CHO cells. In further activities I collaborated with in-house researchers for the
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`construction of cells expressing IL-2. Further work included the expression of
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`
`
`3
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 4 of 46 PageID #: 9684
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`potential biopharmaceuticals like antithrombin III, PDGF and various antibodies.
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`Over the years, I have collaborated on issues related to cell culture with several of
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`the world’s leading biotechnology companies, including Merck KgaA, Ciba-Geigy
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`(now known as Novartis), Boehringer Ingelheim, Roche and Bayer.
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`6.
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`I have served as the chairman of the European Society of Animal Cell
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`Technology (ESACT). ESACT was founded in 1976 to create a forum for the
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`exchange of ideas on biological and engineering techniques to promote knowledge
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`and the use of human and animal cells, e.g., for the manufacturing of products.
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`Members include scientists and engineers in academic, medical and industrial
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`R&D and production at applied science institutions and universities, in the medical
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`services, in industry, and in the political and regulatory bodies. I have also been
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`involved with ACTIP (Animal Cell Culture Technology Industrial Platform) as an
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`academic advisor from 1995 through 2017. I am also a guest professor at the
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`University of Lisbon and a reviewer for scientific journals and research
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`foundations in Germany, Europe, Israel, and the United States.
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`7. My curriculum vitae describes in greater detail my professional
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`experience and qualifications, and includes a list of my numerous publications in
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`the field. I have attached it as Exhibit 1.1
`
`
`1 All exhibits cited herein are Exhibits to the Declaration of Nancy Lynn
`Schroeder, as described in the Exhibit List at the end of this declaration.
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`
`
`4
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 5 of 46 PageID #: 9685
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`8.
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`During the preceding five years, I have testified at deposition on
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`behalf of Genentech in Case No. 18-cv-00574-RMB before the United States
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`District Court for the District of New Jersey.
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`II. Legal Standards and Instructions
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`9.
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`I have been asked by counsel for Genentech to provide my opinion as
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`to the construction of the claim language “following fermentation” and “pre-
`
`harvest [culture fluid]” in U.S. Patent No. 8,574,869 (the “Kao patent”)
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`(JA00000152-246). The purpose of this section of my declaration is to summarize
`
`the instructions I received from counsel in connection with preparing this opinion.
`
`A.
`
`Instructions Regarding Legal Concepts
`
`1.
`
`The Person of Ordinary Skill
`
`10.
`
`I have been asked to provide an opinion as to the person of ordinary
`
`skill in the art (or “POSA”) to whom the invention disclosed and claimed in the
`
`Kao patent was directed. I understand that the POSA is a hypothetical person and
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`can possess the skills and experience of multiple individuals working together as a
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`team. I have been informed that factors that may be considered in determining the
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`level of ordinary skill in the art may include: (1) the educational level of the
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`inventors; (2) the types of problems encountered in the art; (3) prior art solutions to
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`those problems; (4) rapidity with which innovations are made; (5) sophistication of
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`the technology; and (6) the educational level of active workers in the field.
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`
`
`5
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 6 of 46 PageID #: 9686
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`11.
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`I have been instructed that this assessment is performed as of the time
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`of the invention. I have been asked to assume that the time of the invention is July
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`9, 2007, the filing date of the provisional application No. 60/948,677. My opinion
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`concerning the person of ordinary skill in the art would not change if a date a few
`
`years earlier or later were used instead. References to the person of ordinary skill
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`in this declaration refer to such a hypothetical person as of the relevant date.
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`12. Based upon my experience working in the field and my interactions
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`with others, the person of ordinary skill would have had a Ph.D. in chemical
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`engineering, molecular biology, or a related discipline and experience in the
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`manufacture of antibodies for therapeutic use. The person of ordinary skill could
`
`also have less formal education in these fields but more direct experience in the
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`manufacture of antibodies for therapeutic use.
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`2.
`
`Claim Construction
`
`13.
`
`I have been instructed that claim language should generally be given
`
`its “ordinary and customary” meaning to the person of ordinary skill in the art in
`
`the context of the patent.
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`14.
`
`In ascertaining that meaning, I have been instructed that the words of
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`the patent’s claims and the context in which the term is used in the claims can be
`
`highly instructive. I further understand that the terms of a claim are to be
`
`interpreted in the context of the entire patent, including the patent’s claims, its
`
`
`
`6
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`
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 7 of 46 PageID #: 9687
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`“written description,” and its figures (which together I have been told are called the
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`“specification”).
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`15. Further, I have been instructed that a patent’s “prosecution history”
`
`may often provide helpful evidence about how the Patent Office and the inventor
`
`understood the patent and its claims. Consequently, I have been instructed that
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`claim terms should, in addition to the claims themselves and the remainder of the
`
`specification, also be interpreted in light of the patent’s prosecution history.
`
`16.
`
`I have been instructed that these sources—the claims, the written
`
`description, the figures, and the prosecution history—are referred to as “intrinsic
`
`evidence.”
`
`17.
`
`In addition to the “intrinsic evidence,” I have been instructed that
`
`certain “extrinsic evidence” such as the testimony of individuals working in the
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`field and scientific or technical references may also shed useful light on the way in
`
`which the person of ordinary skill in the art might understand the claim term. I
`
`have been instructed that such extrinsic evidence must always be considered in the
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`context of the intrinsic evidence.
`
`18.
`
`I have been retained on behalf of Plaintiff Genentech, Inc. to perform
`
`this analysis, but the opinions set forth in this declaration are my own. I am being
`
`paid my normal, hourly rate of $350.00 for my time. My compensation does not
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`depend in any way on the outcome of this matter.
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`
`
`7
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 8 of 46 PageID #: 9688
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`B. Materials Considered
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`19.
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`I have reviewed the Kao patent and its prosecution history. I also
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`have reviewed the portion of the “Joint Claim Construction Chart” relating to the
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`Kao patent, and in particular, the proposals concerning the terms “following
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`fermentation” and “pre-harvest [culture fluid]” included at pages 24-28. I
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`understand that both Plaintiffs and Defendants have cited in this Chart the
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`“Intrinsic Evidence” that they contend to be relevant to the interpretation of these
`
`terms, and I have paid particular attention to those cited portions of the Kao patent
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`and its prosecution history, as well as the prosecution histories of the other patent
`
`applications and the scientific literature listed in the Chart.
`
`20.
`
`I also have considered the various articles and books cited throughout
`
`this declaration in forming my opinion. I have also relied on my decades of
`
`experience in the cell culture field.
`
`III. Technical Background
`
`21. The purpose of this section of my declaration is to provide
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`background information regarding some of the technical concepts implicated by
`
`the Kao patent. These concepts would be uncontroversial and well known to the
`
`person of ordinary skill.
`
`A. Antibodies
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`22. Proteins are a class of molecules critical to life. A protein is formed
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`from a linear sequence of smaller subunits known as “amino acids.” There are
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`8
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 9 of 46 PageID #: 9689
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`twenty different amino acids typically used by living things to make proteins, each
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`of which has different chemical properties. Different sequences of these different
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`amino acids give proteins a vast array of chemical properties and functions. The
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`interactions between the different amino acids in a protein will cause the protein to
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`“fold” into a particular structure. The structure of a protein, in turn, plays a key
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`role in determining its properties and biological activity.2
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`23. Antibodies are a class of proteins. Antibodies are produced by the
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`immune system, where their natural function is to recognize and specifically bind
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`to a molecule, such as a virus, toxin or other chemical species. (The molecule to
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`which an antibody binds is sometimes referred to as an “antigen.”) Over the past
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`several decades, scientists have exploited the natural ability of an antibody to bind
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`specifically to a particular target and have, through modifying the sequences of
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`antibodies, generated many new antibodies capable of binding to targets that have
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`a therapeutic benefit. For example, trastuzumab (the antibody in Herceptin) binds
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`to the HER2 receptor, a protein involved in breast cancer.
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`24. An antibody like trastuzumab consists of four different protein chains:
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`two identical light chains, and two identical heavy chains. The heavy and light
`
`
`2 These concepts are explained in further detail in the attached excerpt from
`“Molecular Biology of the Cell,” a leading textbook on molecular biology. See
`Exhibit 2.
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`
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`9
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 10 of 46 PageID #: 9690
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`chains are so named because the heavy chain has a longer amino acid sequence and
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`has a correspondingly higher molecular weight than the light chain. The four
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`chains that comprise a typical antibody are frequently depicted, in a simplified
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`format, as having a “Y”- structure, as shown below. The two light chains are
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`shown in gold and the two identical heavy chains are shown in blue.
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`
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`25. These four chains are held together by “disulfide bonds.” A disulfide
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`bond is sometimes referred to as an “S-S bond.” A disulfide bond is a bond
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`between two sulfur (“S”) atoms that forms from the interaction between two
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`sulfur- containing “thiol groups.” A thiol group consists of a hydrogen atom that is
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`bound to a sulfur atom (“H-S”), which is attached in turn to a carbon atom.
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`26.
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`“Cysteine” is one of the twenty amino acids that make up most
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`proteins. Cysteine has one thiol group. It is the only one of the twenty amino
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`acids that has a thiol group, and thus it is the only one of the twenty amino acids
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`that has the ability to form a disulfide bond.
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`
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`10
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 11 of 46 PageID #: 9691
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`27. Disulfide bonds are critical to antibodies. As mentioned above, the
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`four chains that comprise a typical antibody are held together by disulfide bonds.
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`In an antibody like trastuzumab, two disulfide bonds connect the heavy chains to
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`each other, and two additional disulfide bonds connect the heavy chains to the light
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`chains. These disulfide bonds are called inter-chain bonds.3 The figure below
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`depicts the inter-chain disulfide bonds (red lines) that hold together an antibody
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`like trastuzumab:
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`28. As discussed in more detail below, disulfide bonds can break. The
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`breaking of a disulfide bond is referred to as “reduction;” an antibody with a
`
`
`
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`3 Additional disulfide bonds form between cysteines within the same chain, so-
`called intra-chain bonds. These intra-chain bonds also are important to an
`antibody’s structure.
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`11
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 12 of 46 PageID #: 9692
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`broken disulfide bond has been “reduced.” Disulfide bond reduction is a problem
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`for antibodies because such broken bonds change its structure substantially.
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`29.
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`In order to perform their biological functions, proteins, including
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`antibodies, must properly fold into the correct spatial conformations. This
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`complex folding process is driven by numerous interactions between the amino
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`acids that comprise the protein, including the formation of any disulfide bonds
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`between cysteines.
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`30. The structure of an antibody determines its biological activity,
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`including its specificity for binding a particular antigen (the purpose for which a
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`therapeutic antibody is used). See Ex. 2 (Molecular Biology of the Cell) at 129
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`(“the precise shape of each protein molecule determines its function in a cell”).
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`Without the proper structure, an antibody would not recognize its antigen and
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`perform its immune functions. As the patent notes, and the POSA would
`
`understand, even small changes in shape can have substantial impacts on activity.
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`See, e.g., JA00000193 (Kao patent at 1:33-37) (“For a protein to remain
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`biologically active, the conformation of the protein, including its tertiary structure,
`
`must be maintained during its purification and isolation, and the protein’s multiple
`
`functional groups must be protected from degradation.”); Ex. 2 (Molecular Biology
`
`of the Cell) at 142 (“Proteins are so precisely built that the change of even a few
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`
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`12
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 13 of 46 PageID #: 9693
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`atoms in one amino acid can sometimes disrupt the structure of the whole molecule
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`so severely that all function is lost.”).
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`31. Because disulfide bonds impact the shape of an antibody, the
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`reduction of disulfide bonds in an antibody can change the shape of the antibody,
`
`resulting in loss of activity due to structural deformity. See Ex. 3 (Mullan 2011) at
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`1 (“Disulphide bonding is critical to maintaining immunoglobulin (IgG) . . .
`
`structure for therapeutic monoclonal antibodies.”).
`
`32. As the inventors of the Kao patent observed, “during the recombinant
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`production of polypeptides comprising disulfide bonds, especially multi-chain
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`polypeptides comprising inter-chain disulfide bonds such as antibodies, it is
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`essential to protect and retain the disulfide bonds throughout the manufacturing,
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`recovery and purification process, in order to produce properly folded polypeptides
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`with the requisite biological activity.” JA00000193 (Kao patent at 2:13-20).
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`B. Overview of Antibody Manufacturing
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`33. Antibodies have become prevalent in the treatment of many diseases
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`over the last 20 years. This is due, in part, to advances in molecular biology that
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`allow for antibodies to be made by genetically engineered cells in sophisticated
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`cell culture processes. Mammalian cells, and especially Chinese Hamster Ovary or
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`“CHO” cells, are most frequently used for the production of therapeutic antibodies.
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`
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`13
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 14 of 46 PageID #: 9694
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`See JA00000193 (Kao patent at 1:38-42); Ex. 4 (Kao 2010) at 622; Ex. 5 (Trexler-
`
`Schmidt 2010) at 452.
`
`34. A review article published in 2001 by Genentech scientists describes
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`the process of antibody manufacturing as follows:
`
`Large-scale production of antibodies as pharmaceutical
`products is a complex endeavour, including a
`manufacturing process with multiple steps and significant
`analytical support. Antibody manufacturing includes cell
`banking and cell culture, recovery, filling (possibly
`including lyophilization), finishing, and packaging.
`Product recovery includes harvest, which is removal of
`cells and cell debris by tangential flow filtration or
`centrifugation (van Reis et al., 1991), chromatography
`for antibody purification, and formulation . . . .
`
`Ex. 6 (Fahrner 2001) at 301-02. This review article is cited in the Kao patent at
`
`JA00000206 (27:26-29) and incorporated into the disclosure of the Kao patent.
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`35. The Kao patent provides a similar overview of the typical antibody
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`manufacturing process at JA0000205-206 (Kao patent at 25:40-27:49), which
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`begins “[a] protocol for the production, recovery and purification of recombinant
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`antibodies in mammalian, such as CHO, cells may include the following steps . . .
`
`.”
`
`36.
`
`I provide further background information regarding the production,
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`recovery, and purification of antibodies in the following sections.
`
`1.
`
`Production/Fermentation
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`
`
`14
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 15 of 46 PageID #: 9695
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`37. The cell growth and protein production process is referred to in the
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`Kao patent and in the field as “fermentation.” JA00000205 (Kao patent at 25:43-
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`26:41); Ex. 7 (Birch 2006) at 681. Growth and production parameters are
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`controlled during this process to target optimal growth and production conditions.
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`JA00000193 (Kao patent at 1:60-63).
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`38. During the “growth phase” of fermentation, cells are cultured under
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`controlled conditions based on parameters “such as temperature, pH, and the like,”
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`to enhance cell division and viability. JA00000205 (Kao patent at 25:36-39;
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`25:64-26:24). When cell division and viability are enhanced, the number of viable
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`cells, i.e., cells that are alive in the culture, will increase. During the growth phase,
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`the cells also produce the desired protein, but because the bioreactor has not yet
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`reached maximum cell density, the production is at a lower scale than when
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`maximum cell density is reached.
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`39. During the “production phase” of fermentation, conditions (such as
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`temperature, pH, and nutrients) may be changed or optimized to enhance
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`production of the desired protein. JA00000205 (Kao patent at 26:34-37) (“In a
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`preferred aspect, the production phase of the cell culture process is preceded by a
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`transition phase of the cell culture in which parameters for the production phase of
`
`the cell culture are engaged.”). In a typical production phase, cells will continue to
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`15
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 16 of 46 PageID #: 9696
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`divide, but the total number of viable cells may not increase (or could even
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`decrease) because the rate of cell division may no longer outpace cell death.
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`40. A diagram of a typical culture process is shown in Figure 23 of the
`
`Kao patent, JA00000174. The cylindrical figures represent bioreactors. They
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`increase in size from left to right, which conveys that the total volume of cells is
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`increasing and the cells are being moved to larger and larger bioreactors. The
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`production bioreactor is the figure on the far right.
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`41. Antibodies like trastuzumab are made inside of cells and then secreted
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`by host cells into the culture fluid during production. The culture fluid can also
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`contain a variety of other cellular proteins and components as a result of the
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`16
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 17 of 46 PageID #: 9697
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`“natural death of cells and release of intracellular host cell proteins and
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`components in the course of the protein production run.” JA00000205 (Kao patent
`
`at 26:54-56). As the inventors discovered, this can result in the culture fluid
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`becoming contaminated with proteins that cause the reduction of an antibody’s
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`disulfide bonds.
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`2.
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`Recovery/Harvest
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`42. As shown in Figure 23 of the Kao patent, JA00000174, reproduced
`
`above, the antibodies generated during the cell culture process are then
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`“harvest[ed].” The Kao patent explains that, “[t]ypically, harvesting includes
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`centrifugation and filtration to produce a Harvested Cell Culture Fluid (HCCF).”
`
`JA00000193 (Kao patent at 2:3-4). Elsewhere, the Kao patent repeats this concept,
`
`explaining that “the harvested cell culture fluid (HCCF)” is “obtained after
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`harvesting by centrifugation, filtration, or similar separation methods.”
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`JA00000203 (Kao patent at 22:3-5).
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`43. The purpose of this process is to remove the cells from the culture
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`fluid to produce a “clarified” solution. JA00000193, JA00000203, JA00000205
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`(Kao patent at 2:1-5; 22:3-7; 26:52-60). As the Kao patent explains, “[t]he HCCF
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`lacks intact host cells but typically contains host cell proteins and other
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`contaminants, including DNA, which are removed in subsequent purification
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`
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`17
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 18 of 46 PageID #: 9698
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`steps.” JA00000203 (Kao patent at 22:5-7). (I discuss the subsequent purification
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`process in more detail in the next section.)
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`44. Figure 3 of the Birch 2006 review paper is a diagram of a typical
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`antibody manufacturing process that provides more detail than Figure 23 of the
`
`Kao patent as to the typical harvest steps referred to in the Kao patent. I have
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`reproduced it below; the bioreactors circled in green correspond to the final
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`production bioreactor on the right of Figure 23 of the Kao patent, JA00000174.
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`
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`18
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`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 19 of 46 PageID #: 9699
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`45.
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`In this diagram, the culture fluid moves from the bioreactor to a
`
`centrifuge (right side of the diagram, middle) and then pumped through various
`
`filters to the “harvest tank” (shown in gray, left side of the diagram, middle).
`
`3.
`
`Purification
`
`46. The Kao patent discusses purification techniques at 26:57-27:29,
`
`JA00000205-206. It states that “[o]nce a clarified solution containing the protein
`
`of interest has been obtained, its separation from the other proteins produced by the
`
`cell is usually attempted using a combination of different chromatography
`
`techniques.” JA00000205 (Kao patent at 26:57-60). The 2001 Genentech review
`
`article incorporated into the Kao patent at 27:26-29, JA00000206 discusses some
`
`of these purification techniques in additional detail. It describes a three-step
`
`process comprising “protein A affinity chromatography, followed by cation
`
`exchange chromatography, followed by anion exchange chromatography.” Ex. 6
`
`(Fahrner 2001) at 305.
`
`47. Referring back to Figure 3 from the Birch 2006 paper, steps like these
`
`are indicated in the “third row” of the figure. From the harvest tank, culture fluid
`
`is pumped to the “1st column step,” which refers to a chromatography process used
`
`to separate components from the culture fluid and thus purify the antibody. Ex. 6
`
`(Birch 2006) at 680 (“[A]t the end of the batch cycle, the contents of the reactor are
`
`clarified through a centrifuge and through filters prior to purification in a series of
`
`
`
`19
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 20 of 46 PageID #: 9700
`
`chromatography steps.”). The culture fluid proceeds through multiple column
`
`steps to purify the antibodies.
`
`C. Reduction of Disulfide Bonds and the Kao patent
`
`48. Protecting and retaining disulfide bonds of therapeutic antibodies
`
`during the manufacturing, recovery and purification process is critical. As the Kao
`
`patent explains, “during the recombinant production of polypeptides comprising
`
`disulfide bonds, especially multi-chain polypeptides comprising inter-chain
`
`disulfide bonds such as antibodies, it is essential to protect and retain the disulfide
`
`bonds throughout the manufacturing, recovery and purification process, in order to
`
`produce properly folded polypeptides with the requisite biological activity.”
`
`JA00000193 (Kao patent at 2:13-20).
`
`49. Reduction of one or more disulfide bonds in an antibody can cause
`
`major structural deformations. Breaking the inter-chain bonds holding the heavy
`
`chains together, for example, would result in the fragmentation of the antibody to
`
`produce molecules of only one heavy chain with one light chain, as illustrated
`
`below:
`
`
`
`20
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 21 of 46 PageID #: 9701
`
`
`
`50. The antibody fragments that result from reduction of an antibody’s
`
`disulfide bonds are impurities. They represent a loss in production yield that, if
`
`large enough, could result in an entire batch being rejected.4
`
`51. The inventors of the Kao patent observed that, in certain large-scale
`
`productions of therapeutic antibodies, some batches of antibodies would be
`
`discarded, i.e., found to be unusable, due to disulfide bond reduction. See Ex. 5
`
`(Trexler-Schmidt 2010) at 452-53. The inventors discovered that “the root cause
`
`of this reduction is an active thioredoxin (Trx) or thioredoxin-like system” that
`
`accumulates in the cell culture fluid as a result of cell lysis during the fermentation
`
`process, as well as from cell lysis due to the mechanical forces applied during
`
`harvesting. JA00000202 (Kao patent at 20:33-35).
`
`
`4 A “batch” of drug substance is refers to a quantity of drug that is intended to have
`uniform character and quality because it was produced during the same cycle of
`production.
`
`
`
`21
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 22 of 46 PageID #: 9702
`
`52. The “thioredoxin system” refers to an enzyme called thioredoxin and
`
`other enzymes that together cause reduction of disulfide bonds in proteins,
`
`including antibodies.
`
`53. After recognizing how the release of thioredoxin into the cell culture
`
`fluid was the root cause of disulfide bond reduction in the manufacturing process
`
`for certain antibodies, JA00000202 (Kao patent at 20:33-35), the inventors
`
`developed ways of addressing this problem, JA00000194 (Kao patent at 3:22-27).
`
`54. The solution claimed in the Kao patent is to supply dissolved oxygen
`
`following fermentation in the pre-harvest or harvested cell culture fluid by
`
`sparging (i.e., bubbling) air into the culture fluid. JA00000246 (Kao patent at
`
`107:44-49 (Claim 1)). The oxygen, as explained by the patent, interferes with
`
`thioredoxin and thioredoxin-like systems and prevents the resulting damage to the
`
`disulfide bonds of the antibody. JA00000203-204 (Kao patent at 22:38-39; 23:22-
`
`42).
`
`55.
`
`In addition to obtaining the Kao patent, the inventors published their
`
`research in three peer-reviewed articles. See Ex. 5 (Trexler-Schmidt 2010); Ex. 4
`
`(Kao 2010); Ex. 8 (Mun 2014). The Kao patent inventors’ work has also been
`
`cited in several publications written by others in industry, including scientists
`
`associated with Amgen. See, e.g., Ex. 3 (Mullan 2011); Ex. 9 (Hutterer 2013); Ex.
`
`10 (Chung 2017).
`
`
`
`22
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 23 of 46 PageID #: 9703
`
`IV. “Following Fermentation”
`
`56.
`
`I have been asked to provide my opinion as to how the person of
`
`ordinary skill in this field would have understood the “following fermentation”
`
`language in the methods claimed in the Kao patent. For reference, I have included
`
`below the language of claim 1, with the “following fermentation” language
`
`highlighted:
`
`
`
`A. Ordinary Meaning in the Field
`
`57.
`
`In the context of the Kao patent, the POSA would have understood the
`
`phrase “following fermentation” to mean “after the end of the cell growth and
`
`antibody production phases.” In my experience, “fermentation” is understood in
`
`the field to refer to growing cells to produce a product of interest, hence the term
`
`encompasses both the cell growth and antibody production processes.
`
`58. This ordinary understanding is reflected in Birch 2006, a review paper
`
`from Lonza Biologics, an industry leader in cell culture processes. The Birch 2006
`
`paper (Ex. 7) at 678 refers to the “fermentation process” as encompassing the times
`
`when the culture receives feeds, which the POSA would understand can occur
`
`during both the growth and production phases of cell culture. The Birch 2006
`
`
`
`23
`
`
`
`Case 1:18-cv-01363-CFC Document 81 Filed 03/22/19 Page 24 of 46 PageID #: 9704
`
`paper (Ex. 7) at 681 emphasizes that improvements in the “fermentation processes”
`
`have come from improvements in both cell growth and productivity, further
`
`reinforcing that the ordinary meaning of “fermentation” encompasses both cell
`
`growth and antibody production.
`
`B. Written Description
`
`59. The Kao patent discusses fermentation consistent with this ordinary
`
`meaning. In the “Compositions and Methods of the Invention” section of the
`
`specification, the patent describes “the growth phase of the cell culture” and “the
`
`production phase of the cell culture”:
`
`In the growth phase cells are grown under conditions and
`for a period of time that is maximized for growth….
`
`At a particular stage the cells may be used to inoculate a
`production phase or step of the cell culture.… The cell
`culture environment during the production phase of the
`cell culture is typically controlled. ….
`
`Following fermentation proteins
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