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`C.A. No. 17-1407-CFC
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`GENENTECH, INC. and CITY OF HOPE, )
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`AMGEN INC.,
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`Defendant.
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`GENENTECH, INC.,
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`Plaintiff and
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`AMGEN INC.,
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`Defendant and
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`C.A. No. 18-924-CFC
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`DECLARATION OF DR. HANSJÖRG HAUSER IN SUPPORT OF
`GENENTECH’S LETTER-BRIEF CONCERNING CONSTRUCTION OF
`“FOLLOWING FERMENTATION”
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`PUBLIC VERSION FILED:
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`October 14, 2019
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`C.A. No. 17-1407-CFC
`(CONSOLIDATED)
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`GENENTECH, INC. and CITY OF HOPE, )
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`Plaintiffs,
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`AMGEN INC.,
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`Defendant.
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`____________________________________)
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`GENENTECH, INC.,
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`Plaintiff and
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`Counterclaim Defendant,
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`AMGEN INC.,
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`Defendant and
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`Counterclaim Plaintiff.
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`____________________________________)
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`C.A. No. 18-924-CFC
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`DECLARATION OF DR. HANSJÖRG HAUSER IN SUPPORT OF
`GENENTECH’S LETTER-BRIEF CONCERNING CONSTRUCTION OF
`“FOLLOWING FERMENTATION”
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`PUBLIC VERSION FILED:
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`October 14, 2019
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 2 of 75 PageID #: 31463
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`I, Dr. Hansjörg Hauser, declare as follows:
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`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
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`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”).
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`2.
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`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.
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`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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`2
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 3 of 75 PageID #: 31464
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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.
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`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 cell 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-00924-CFC Document 417 Filed 10/14/19 Page 4 of 75 PageID #: 31465
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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, 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 publications in the field. It
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`is attached as Exhibit A.
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`8.
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`During the preceding five years, I have testified on behalf of
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`Genentech in these cases and in Genentech vs. Celltrion, Case No. 18-cv-00574-
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`4
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 5 of 75 PageID #: 31466
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`RMB, before the United States District Court for the District of New Jersey,
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`another case concerning the Kao patent.
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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, Inc. to analyze U.S.
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`Patent No. 8,574,869 (the “Kao patent,” Appx1). I have been asked to provide
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`technical background regarding the Kao patent’s field and its claimed methods. I
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`have been asked to explain how the “person of ordinary skill in the art” (or
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`“POSA”) would have understood aspects of the Kao patent, particularly the
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`claimed methods’ requirement that sparging occur “following fermentation.” I
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`have also been asked to consider whether the person of ordinary skill in the art
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`would have understood the scope of the claimed methods with “reasonable
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`certainty.”
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`10.
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`I have been retained by Genentech to perform this analysis, but the
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`opinions set forth in this declaration are my own. I am being paid my normal,
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`hourly rate of €310 for my time. My compensation does not depend in any way on
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`the outcome of this matter.
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`A.
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`11.
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`Instructions Regarding the Person of Ordinary Skill in the Art
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`I have been instructed that various patent issues must be assessed
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`from the perspective of the person of ordinary skill in the art to whom the
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`invention disclosed and claimed in the Kao patent was directed. I understand that
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`5
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 6 of 75 PageID #: 31467
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`the POSA is a hypothetical person and can possess the skills and experience of
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`multiple individuals working together as a team. I have been informed that factors
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`that may be considered in determining the level of ordinary skill in the art may
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`include: (1) the educational level of the inventors; (2) the types of problems
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`encountered in the art; (3) prior art solutions to those problems; (4) rapidity with
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`which innovations are made; (5) sophistication of the technology; and (6) the
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`educational level of active workers in the field.
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`12.
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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
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`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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`13. The Kao patent is directed to the manufacture of antibodies. This is a
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`technical field that combines engineering disciplines (like chemical engineering)
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`with biological disciplines (like molecular and cellular biology). Based upon my
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`experience working in the field and my interactions with others, the person of
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`ordinary skill would have had a Ph.D. in chemical engineering, molecular biology,
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`or a related discipline, and experience in the manufacture of antibodies for
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`therapeutic use. In my experience, this is the typical educational background of
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`6
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 7 of 75 PageID #: 31468
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`individuals involved in designing and implementing antibody manufacturing
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`processes. The person of ordinary skill could also have less formal education in
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`these fields but more direct experience in the manufacture of antibodies for
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`therapeutic use.1
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`B.
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`14.
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`Instructions Regarding “Ordinary Meaning”
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`I have been instructed that claim language should generally be given
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`its “ordinary and customary” meaning to the person of ordinary skill in the art in
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`the context of the patent.
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`15.
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`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
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`highly instructive. I further understand that the terms of a claim are to be
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`interpreted in the context of the entire patent, including the patent’s claims, its
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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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`1 I have also considered the definition of a POSA adopted by Amgen’s expert Dr.
`Glacken. I understand that Dr. Glacken has opined that the POSA “would have
`had a Ph.D. or Sc.D. in chemical engineering, molecular biology, or a closely
`related field, and at least 2-3 years of experience related to protein and/or antibody
`production.” In general, those qualifications are consistent with the skills of the
`POSA I have described above. As such, my opinion would not change if Dr.
`Glacken’s definition of the POSA were used instead.
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`7
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 8 of 75 PageID #: 31469
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`16. Further, I have been instructed that a patent’s “prosecution history”
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`may often provide helpful evidence about how the Patent Office and the inventor
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`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
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`specification, also be interpreted in light of the patent’s prosecution history.
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`17.
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`I have been instructed that these sources—the claims, the written
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`description, the figures, and the prosecution history—are referred to as “intrinsic
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`evidence.”
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`18.
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`In addition to the “intrinsic evidence,” I have been instructed that
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`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
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`which the person of ordinary skill in the art might understand the claim term. I
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`have been instructed that such extrinsic evidence must always be considered in the
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`context of the intrinsic evidence.
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`C.
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`19.
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`Instructions Regarding “Definiteness”
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`I have been instructed that a patent’s claims, when read in light of the
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`patent’s specification and file history, must inform those of ordinary skill in the art
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`of the scope of the invention with “reasonable certainty,” or the claims will be
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`invalid as “indefinite.”
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`8
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 9 of 75 PageID #: 31470
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`20.
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`I understand that, although the claim must describe the scope of the
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`invention with reasonable clarity, the definiteness requirement takes into account
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`the inherent limitations of language, and some degree of uncertainty is acceptable.
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`I further understand that the definiteness requirement is not addressed to lawyers or
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`to laypersons. Rather, I understand the definiteness requirement is directed to the
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`POSA, and for that reason, a patent is not required to include technical subject
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`matter that is known in field.
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`21.
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`I understand that when a patent refers to a particular parameter, a
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`claim involving that parameter is not indefinite simply because there may be
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`multiple ways to measure the parameter, so long as the POSA would understand
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`how to perform such measurements, and those measurements, if performed
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`correctly, would produce consistent results.
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`III. Technical Background
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`22. 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
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`the Kao patent. These concepts would be uncontroversial and well-known to the
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`person of ordinary skill.
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`A. Antibodies
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`23. 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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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 10 of 75 PageID #: 31471
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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.
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`24. 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, bevacizumab (the antibody in Avastin) binds
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`to human vascular endothelial growth factor (“VEGF”), a protein involved in
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`tumor growth, and trastuzumab (the antibody in Herceptin) binds to human
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`epidermal growth factor receptor 2 (“HER2”).
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`25. An antibody like bevacizumab or trastuzumab consists of four
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`different protein chains: two identical light chains, and two identical heavy chains.
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`The heavy and light chains are so named because the heavy chain has a longer
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 11 of 75 PageID #: 31472
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`amino acid sequence and has a correspondingly higher molecular weight than the
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`light chain. The four chains that comprise a typical antibody are frequently
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`depicted, in a simplified format, as having a “Y”- structure, as shown below. The
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`two light chains are shown in gold and the two identical heavy chains are shown in
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`blue.
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`26. 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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`27.
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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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`28. 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 bevacizumab or trastuzumab, two disulfide bonds connect the
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`heavy chains to each other, and two additional disulfide bonds connect the heavy
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`chains to the light chains. These disulfide bonds are called inter-chain bonds.2
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`The figure below depicts the inter-chain disulfide bonds (red lines) that hold
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`together an antibody like bevacizumab or trastuzumab:
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`29. 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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`2 Additional disulfide bonds form between cysteines within the same chain, so-
`called intra-chain bonds. These intra-chain bonds are also important to an
`antibody’s structure.
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`12
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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 the antibody’s structure
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`substantially.
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`30.
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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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`31. 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 Appx98 (Molecular Biology of the Cell) (“[T]he
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`precise shape of each protein molecule determines its function in a cell.”). Without
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`the proper structure, an antibody would not recognize its antigen and perform its
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`immune functions. As the patent notes, and the POSA would understand, even
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`small changes in shape can have substantial impacts on activity. See, e.g., Appx42
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`at 1:33-37 (Kao patent) (“For a protein to remain biologically active, the
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`conformation of the protein, including its tertiary structure, must be maintained
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`during its purification and isolation, and the protein’s multiple functional groups
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`must be protected from degradation.”); Appx111 (Molecular Biology of the Cell)
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`(“Proteins are so precisely built that the change of even a few atoms in one amino
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`acid can sometimes disrupt the structure of the whole molecule so severely that all
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`function is lost.”).
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`32. 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,
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`resulting in loss of activity due to structural deformity. See Appx127 (Mullan
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`2011) (“Disulphide bonding is critical to maintaining immunoglobulin (IgG) . . .
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`structure for therapeutic monoclonal antibodies.”).
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`33. 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.” Appx42 at 2:13-20 (Kao patent).
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`34. The inventors of the Kao patent observed that, in certain large-scale
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`productions of therapeutic antibodies, some batches of antibodies would have to be
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`discarded because they were unusable as a result of disulfide bond reduction. See
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`Appx130 (Trexler-Schmidt 2010). The inventors discovered that “the root cause
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`of this reduction is an active thioredoxin (Trx) or thioredoxin-like system” that
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`accumulates in the cell culture fluid as a result of cell lysis. Appx51 at 20:33-35
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`(Kao patent). The “thioredoxin system” refers to an enzyme called thioredoxin and
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`14
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`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 15 of 75 PageID #: 31476
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`other enzymes that together cause reduction of disulfide bonds in proteins,
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`including antibodies.
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`35. After recognizing how the release of thioredoxin into the cell culture
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`fluid was the root cause of disulfide bond reduction in the manufacturing process
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`for certain antibodies, Appx51 at 20:33-35 (Kao patent), the inventors developed
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`ways of addressing this problem, Appx43 at 3:22-27. The solution claimed in the
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`Kao patent is to supply dissolved oxygen following fermentation in the pre-harvest
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`or harvested cell culture fluid by sparging (i.e., bubbling) air into the culture fluid.
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`Appx95 at 107:44-49 (Kao patent, Claim 1). The oxygen, as explained by the
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`patent, interferes with thioredoxin and thioredoxin-like systems and prevents the
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`resulting damage to the disulfide bonds of the antibody. Appx21 at 22:38-39;
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`Appx22 at 23:22-42.
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`36.
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`In addition to obtaining the Kao patent, the inventors published their
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`research. In my experience, scientists are fortunate if their research results in a
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`single peer-review publication. The research disclosed in the Kao patent, however,
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`was so significant it produced a series of peer-reviewed articles. See Appx130
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`(Trexler-Schmidt 2010); Appx140 (Kao 2010); Appx151 (Mun 2014). These
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`papers have been cited in several publications written by others in industry,
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`including scientists associated with Amgen. See, e.g., Appx127 (Mullan 2011);
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`Appx160 (Hutterer 2013); Appx166 (Chung 2017).
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`15
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`B. Overview of Antibody Manufacturing
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`37. 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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`See Appx42 at 1:38-42 (Kao patent); Appx140 (Kao 2010); Appx130 (Trexler-
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`Schmidt 2010).
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`38. A review article published in 2001 by Genentech scientists describes
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`the process of antibody manufacturing as follows:
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`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 . . . .
`
`Appx178-179 (Fahrner 2001). This review article is cited in the Kao patent at
`
`27:26-29 and incorporated into the disclosure of the Kao patent.
`
`39. The Kao patent provides a similar overview of the typical antibody
`
`manufacturing process at 25:40-27:49, which begins “[a] protocol for the
`
`
`
`16
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 17 of 75 PageID #: 31478
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`
`
`production, recovery and purification of recombinant antibodies in mammalian,
`
`such as CHO, cells may include the following steps . . . .” Appx 54.
`
`40.
`
`In the following sections, I provide further background information
`
`regarding the manufacturing of antibodies in the context of the Kao patent.
`
`1.
`
`Fermentation
`
`41. The cell growth and protein production process is referred to in the
`
`Kao patent as “fermentation.” Appx54 at 25:43-26:41 (Kao patent). Growth and
`
`production parameters are controlled during this process to target optimal growth
`
`and production conditions. Appx42 at 1:60-63 (Kao patent).
`
`42. During the “growth phase” of fermentation, cells are cultured under
`
`controlled conditions based on parameters “such as temperature, pH, and the like,”
`
`to enhance cell division and viability. Appx54 at 25:36-39, 25:64-26:24 (Kao
`
`patent). When cell division and viability are enhanced, the number of viable cells,
`
`i.e., cells that are alive in the culture, will increase. During the growth phase, the
`
`cells also produce the desired protein, but because the bioreactor has not yet
`
`reached maximum cell density, the production is at a lower scale than when
`
`maximum cell density is reached.
`
`43. During the “production phase” of fermentation, conditions (such as
`
`temperature, pH, and nutrients) may be changed or optimized to enhance
`
`production of the desired protein. Appx54 at 26:34-37 (Kao patent). In a typical
`
`
`
`17
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 18 of 75 PageID #: 31479
`
`
`
`production phase, cells will continue to divide, but the total number of viable cells
`
`may not increase (or could even decrease) because the rate of cell division may no
`
`longer outpace cell death.
`
`44. A diagram of a typical process is shown in Figure 23 of the Kao
`
`patent. The cylindrical figures represent bioreactors. They increase in size from
`
`left to right, which conveys that the total volume of cells is increasing and the cells
`
`are being moved to larger and larger bioreactors. The production bioreactor is the
`
`cylindrical figure on the far right.
`
`45. Antibodies like bevacizumab and trastuzumab are made inside of cells
`
`and then secreted by host cells into the culture fluid during production. The culture
`
`
`
`
`
`18
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 19 of 75 PageID #: 31480
`
`
`
`fluid can also contain a variety of other cellular proteins and components as a
`
`result of the “natural death of cells and release of intracellular host cell proteins
`
`and components in the course of the protein production run.” Kao patent at 26:54-
`
`56. As the inventors discovered, this can result in the culture fluid becoming
`
`contaminated with proteins that cause the reduction of an antibody’s disulfide
`
`bonds.
`
`2.
`
`Recovery/Harvest
`
`46. As shown in Figure 23 of the Kao patent, reproduced above, the
`
`antibodies generated during the cell culture process are then “harvest[ed].” The
`
`Kao patent explains that, “[t]ypically, harvesting includes centrifugation and
`
`filtration to produce a Harvested Cell Culture Fluid (HCCF).” Appx42 at 2:3-4
`
`(Kao patent). Elsewhere, the Kao patent repeats this concept, explaining that “the
`
`harvested cell culture fluid (HCCF)” is “obtained after harvesting by
`
`centrifugation, filtration, or similar separation methods.” Appx52 at 22:3-5 (Kao
`
`patent).
`
`47. The purpose of this process is to remove the cells from the culture
`
`fluid to produce a “clarified” solution. Appx42 at 2:1-5, Appx52 at 22:3-7 (Kao
`
`patent). As the Kao patent explains, “[t]he HCCF lacks intact host cells but
`
`typically contains host cell proteins and other contaminants, including DNA, which
`
`
`
`19
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 20 of 75 PageID #: 31481
`
`
`
`are removed in subsequent purification steps.” Appx52 at 22:5-7 (Kao patent). (I
`
`discuss the subsequent purification process in more detail in the next section.)
`
`48. A diagram of a typical 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 can be found in a review paper from Lonza Biologics, an
`
`industry leader in cell culture processes. Appx205 (Birch 2006). I have
`
`reproduced that diagram (Figure 3 of Birch 2006, Appx213) below; the bioreactors
`
`circled in green (to be clear, I have added these circles to the original figure for
`
`illustrative purposes) correspond to the final production bioreactor on the right of
`
`Figure 23 of the Kao patent.
`
`
`
`20
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 21 of 75 PageID #: 31482
`
`
`
`
`
`49.
`
`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
`
`50. The Kao patent discusses purification techniques at 26:57-27:29. 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.” Appx54
`
`at 26:57-60 (Kao patent). The 2001 Genentech review article incorporated into the
`
`
`
`21
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 22 of 75 PageID #: 31483
`
`
`
`Kao patent (Appx55 at 27:26-29) 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.” Appx182 (Fahrner 2001).
`
`51. 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.
`
`Appx214 (Birch 2006) (“[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 chromatography steps.”). The culture fluid proceeds through multiple column
`
`steps to purify the antibodies.
`
`IV.
`
` “Following Fermentation”
`
`52. The Kao patent’s claimed methods relate to sparging culture fluid
`
`“following fermentation.” I understand that the Court has asked about the meaning
`
`to the POSA of the technical term, “fermentation,” and that the Court has asked
`
`whether the POSA would understand with reasonable certainty when
`
`“fermentation” has ended. I have attempted to address the Court’s questions in the
`
`following sections.
`
`
`
`22
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 23 of 75 PageID #: 31484
`
`
`
`A. The Ordinary Meaning of “Fermentation” to the POSA
`
`53.
`
`“Fermentation” is a technical term used in my field to refer to a
`
`biological process, the growing of cells to manufacture a product of interest. This
`
`understanding of “fermentation” is reflected in many sources, including
`
`dictionaries, regulatory documents, and scientific literature, and the POSA would
`
`understand this ordinary meaning to apply in the antibody manufacturing context
`
`of the Kao patent.
`
`1.
`
`“Fermentation”
`
`54. The word “fermentation” arises from some of the earliest efforts to
`
`use biology to make products. This history is captured in the definitions of
`
`“fermentation” provided in the Webster’s Dictionary, Appx220. The first
`
`definition relates to processes for using yeast to make bread rise. The second
`
`definition relates to processes of using organisms like yeast in brewing to make
`
`alcohol. The third definition in the Webster’s dictionary is the one pertinent to my
`
`and the Kao patent’s field of making biological products. It defines “fermentation”
`
`as “any of various controlled aerobic or anaerobic processes used for the
`
`manufacture of certain products (as alcohols, acids, vitamins of the B complex, or
`
`antibiotics) by the action usu. of yeasts, molds, or bacteria.” This definition
`
`conveys that fermentation is a controlled process involving growing cells to make
`
`products.
`
`
`
`23
`
`
`
`Case 1:18-cv-00924-CFC Document 417 Filed 10/14/19 Page 24 of 75 PageID #: 31485
`
`
`
`55. This general understanding from a non-technical dictionary is refined
`
`in technical materials relating to antibody manufacture prepared by the United
`
`States Food & Drug Administration for training its personnel. The FDA published
`
`in November 1991 a “Biotechnology Inspection Guide” to educate its staff. It
`
`includes a glossary that defines fermentation as follows:
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