Control No. 90/007,542
`
`Attorney Docket No. 22338-10230
`
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`Group An Unit:
`
`3991
`
`Examiner:
`
`Bennett Celsa
`
`Confirmation No.:
`
`7585
`
`) ) ) ) ) ) ) ) ) %
`
`)
`
`Reexamination of Patent No. 6,331,415
`
`Shmuel CABILLY et al.
`
`Control No. 90/007,542
`
`Filed: May 13, 2005
`
`For: METHODS OF PRODUCING
`
`IMMUNOGLOBULINS, VECTORS
`AND TRANSFORMED HOST CELLS
`
`FOR USE THEREIN
`
`DECLARATION OF DR. TIMOTHY JOHN ROY HARRIS UNDER 37 C.F.R. § 1.132
`
`1, Timothy John Roy Harris, do hereby declare and state:
`
`1.
`
`2.
`
`3.
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`4.
`
`I am a citizen of the United Kingdom, and reside in San Diego, California. My c.v. is
`attached as Exhibit A.
`
`I am presently Chief Executive Officer of Novasite Pharmaceuticals. Prior to this
`position, I served in a variety of research and management positions in the biotechnology
`industry.
`
`In early 1983, I was head of Molecular Biology at Celltech, Ltd., now part of UCB
`Pharma. Recombinant antibody production was a key research focus for the company,
`and its scientific advisors were experts in that field. Celltech is the same corporate entity
`that was involved in a protracted interference contest in the'Patent and Trademark Office
`(PTO) with Genentech and City of Hope concerning recombinant antibody production.
`
`I have been retained by Genentech and City of Hope to provide my views on certain
`issues that have arisen in connection with the reexamination proceeding of U.S. Patent
`No. 6,331,415 (the ’415 patent)
`‘
`
`5.
`
`I have reviewed the following patents and publications:
`
`-
`-
`
`-
`
`-
`
`-
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`Cabilly, U.S. Patent No. 4,816,567 (the ’567 patent)
`Cabilly, U.S. Patent No. 6,331,415;
`'
`
`Axel, U.S. Patent No. 4,399,216 (Axel)?
`
`Rice, PNAS 79: 7862, 1982 (Rice)
`
`Kaplan, European Patent No. 0 044 722 (Kaplan)
`
`-1-
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`Sanofi/Regeneron Ex. 1028, pg 894
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`Mylan Ex. 1028, pg 894
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`

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`Control No. 90/007.542
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`Attorney Docket No. 22338-10230
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`-
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`-
`
`_.
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`Accolla, PNAS 77: 536, 1980 (Accolla)
`
`Builder, U.S. Patent No. 4,511,502 (Builder)
`
`6.
`
`I have also reviewed certain documents associated with the reexamination proceeding of
`the ‘415 patent, including:
`
`-
`
`-
`
`-
`
`A PTO Office Action in reexamination no. 90/007,542 dated September
`13, 2005 (“Office Action”);
`
`A PTO Order granting ex parte reexamination of the ’4l5 patent, dated
`July 7, 2005 (“Reexamination Order”); and
`
`A Request for Ex Parte Reexamination dated May 13, 2005 (“Request for
`Reexamination”).
`
`7.
`
`8.
`
`9.
`
`10.
`
`In addition, in preparing this declaration, I reviewed literature I found relevant from the
`same general time period as the ’567 and ’415 patents.
`
`In this declaration, I provide my opinions on the scientific observations found in the PTO
`Office Action concerning Axel, Rice, Kaplan, Accolla and Builder from the perspective
`of a person of ordinary skill in this art on or before the filing date of the ’415 patent (i.e.,
`April 8, 1983).
`
`’
`
`I understand that the ’567 patent claims are directed to processes, vectors and host cells
`for producing chimeric immunoglobulin heavy or light chain polypeptides, and to a
`composition containing a chimeric immunoglobulin heavy or light chain polypeptide.
`The ’567 patent method claims cover situations where only one chimeric
`immunoglobulin heavy or light chain polypeptide is produced in a single host cell.
`
`The ’415 patent claims differ from the ’567 patent claims. One difference is that the
`method claims in the ’415 patent require that DNA sequences encoding the heavy an_d the
`light immunoglobulin chain polypeptides be independently expressed by a single host
`cell. Another difference is that the method claims in the ’415 patent require assembly of
`the heavy and light chain polypeptides into an immunoglobulin molecule or an ,
`immunologically functional fiagment that comprises at least the variable domains of the
`heavy and light chain polypeptides.
`
`Meaning of “Having Specificityfor a Particular Known Antigen” in the ‘56 7 Patent Claims
`
`11.
`
`12.
`
`The ’567 patent claims use the phrase “having specificity for a particular known
`antigen...
`I have been asked to explain what that phrase would have meant to a person
`of ordinary skill in the art in view of the ’567 patent disclosure in early April of 1983.
`
`By this time, the physical structure and biological functions of immunoglobulins were
`fairly well known. The description of immunoglobulin structure in the ’567 and ’41 5
`patents (e.g., ’4l5 patent, col. 3, line 17 to col. 4, line 5) is consistent with what was
`generally understood about immunoglobulin structure and function. By this time, it also
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`Sanofi/Regeneron Ex. 1028, pg 895
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`Mylan Ex. 1028, pg 895
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`Control No. 90/007,542
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`T
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`Attorney Docket No. 22338-10230
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`13.
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`14.
`
`was accepted that the antigen binding function of immunoglobulins was associated with
`the variable domains of the heavy and light chain polypeptides, and that an individual
`heavy or light chain polypeptide ordinarily would not bind to antigen very well, if at all.
`
`I would rely on this general understanding of immunoglobulin structure and function to
`answer the question of what the phrase “having specificity for a particular known
`antigen” means as it is used in the claims of the ’567 patent.
`I view that phrase as it is
`used in the claims of the ’567 patent as referring to amino acid sequences within the
`variable domain of the individual chimeric heavy chain or light chain polypeptide that
`confer antigen binding specificity. In such a chimeric polypeptide, these sequences
`would be derived from the variable domains of an antibody or an antibody fragment
`exhibiting an antigen binding function.
`
`I do not read this phrase as it is used in the ’567 patent claims as requiring that the
`individual chimeric heavy chain or light chain polypeptide be assembled into a molecule
`that actually exhibits antigen-binding function, such as an immunoglobulin molecule or
`an immunologically functional fiagment that includes the variable domains of the heavy
`and light chain polypeptides.
`
`General Observations on State ofthe Art in 1983
`
`15.
`
`16.
`
`17.
`
`I understand that the PTO has suggested that the inventions claimed in the ’4l5 patent
`would have been considered obvious to a scientist working in this field in April of 1983.
`-I also understand that this is based on their opinion of what the claims of the ’567 patent
`would have suggested to a scientist at the time in view of Axel, Rice, Kaplan, Builder and
`Accolla.
`I do not agree with the conclusions or rationale offered by the PTO.
`
`By early April of 1983, I was aware that a number of groups had successfully expressed
`polypeptides using recombinant techniques. These experiments generally involved
`expression of genes encoding relatively small polypeptides with simple tertiary structures
`(e.g., monomeric or dimeric proteins). The state of the art in this time frame is reflected
`in a review paper I authored (Harris, “Expression of Eukaryotic Genes in E. coli,”
`Genetic Engineering 4: 127-85 (1983), attached as Exhibit B). In early April of 1983, I
`was not aware of any publications reporting the production of an active multimeric
`protein with a complexity comparable to an immunoglobulin by independent expression
`of the genes encoding the distinct constituent polypeptides of the protein in a single host
`cell.
`
`Immunoglobulin molecules are large (approx. 150 kD) and complex tetrameric proteins.
`By early April of 1983, it was believed that the functional properties of immunoglobulins
`— particularly antigen binding — were dependent on specific covalent and non-covalent‘
`interactions within and between the heavy and light chains. For example, each pair of
`heavy and light chain polypeptides in an immunoglobulin is joined by several inter— and
`intra-chain cystine bonds. The immunoglobulin tetramer also has several inter-chain
`cystine linkages. These interactions between the heavy and light chain polypeptides were
`known to be important to antigen binding and other functions associated with
`
`Sanofi/Regeneron Ex. 1028, pg 896
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`Mylan Ex. 1028, pg 896
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`

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`C0I1t1’01 N0. 90/007,542
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`Attorney Docket No. 22338-10230
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`immunoglobulins. See, e.g., Edelman, G. M., Ann. N. Y. Acad. Sci. 190: 5-25 (1971),
`referenced in col. 3, lines 18-19 of the ‘4l5 patent and provided as Exhibit C.
`
`18.
`
`19.
`
`Scientists working in this field at the time understood that mature B cells are able to
`assemble immunoglobulin tetramers out of the endogenous light and heavy immuno-
`globulin chain polypeptides naturally produced by those cells. However, I do not believe
`a scientist in this field, in early April of 1983, would equate this general understanding of
`B cell fiinction as providing any particular insights into the challenge of recombinant
`production of an immunoglobulin molecule or immunologically functional fragment
`through expression of exogenous heavy and light chain genes in a single host cell.
`
`I therefore do not agree with the suggestion of the PTO that, by early April of 1983, the
`patents and publications they identify demonstrate that the expression using recombinant
`DNA techniques of genes encoding complex multimeric proteins such as
`immunoglobulins had become routine.
`
`The Axel Patent
`
`20.
`
`The first publication the PTO identifies is U.S. Patent No. 4,399,216, to Axel, Wigler,
`and Silverstein (“Axel patent”). The PTO describes the relevance of the Axel patent as
`follows:
`
`Axel et al teaches a process for inserting foreign DNA into eukaryotic cells
`by co-transforming the cells with this foreign DNA and an unlinked DNA
`that codes for a selectable phenotype not otherwise expressed by the cell
`(see colurrm 3, lines 21-27). Axel describes the process as particularly
`suited for the transformation of DNA into eukaryotic cells for making
`immunoglobulins (see column 3, lines 31 to 36). Axel thus demonstrates
`the predictability of expression of multiple heterologous proteins in a single
`host cell. Axel also suggests the desirability of expressing immunoglobulins
`in mammalian host cells, and as intact (assembled) proteins. Office Action,
`page 5.
`
`21.
`
`22.
`
`The Axel patent describes a process for inserting a single heterologous gene (“DNA I”)
`into a host cell co-transformed with a “selectable marker” gene (“DNA II"). Figure 1 in
`the patent provides an overview of the Axel process. In the Axel patent terminology,
`“DNA I” encodes a desired “proteinaceous material not associated with a selectable
`phenotype” that is to be isolated from the transformed host cell. See, col. 3, lines 31 to
`36. The selectable marker is introduced by DNA II.
`
`Two elements are essential to the process described in the Axel patent. First, the host cell
`.must be co-transformed to contain DNA I and DNA II. Second, DNA II must impart into
`the transformed host cell a selectable marker associated with expression of DNA 11 by the
`cell. This enables a scientist to select transformed cells that are expressing DNA 11 from
`cells that are not expressing DNA H. This is done, according to the Axel patent, by
`introducing into the mediumin which the cells are growing an agent that facilitates the
`selective removal of those cells that are not expressing DNA II.
`
`'
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`Sanofi/Regeneron Ex. 1028, pg 897
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`Mylan Ex. 1028, pg 897
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`

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`Control No. 90/007,542
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`Attorney Docket No. 22338-10230
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`23.
`
`The choices in Axel for DNA II are limited to genes that introduce selectable markers.
`As Axel explains at col. 5, lines 58-67:
`
`Although any DNA II coding for a selectable phenotype would be usefiilin
`the cotransforrnation process of the present invention, the experimental
`details set forthparticularly concern the use of a gene for thyrnidine kinase
`obtained from herpes simplex virus and the use of a gene for adenine
`phosphoribosyl transferase.
`In addition, a DNA II which includes a gene
`coding for a selectable phenotype associated with drug resistance, e.g., a
`mutant dihydrofolate reductase gene which renders cells resistant to
`methotrexate, greatly extends the applicability of the process.
`
`24.
`
`25.
`
`26.
`
`27.
`
`28.
`
`For the process described in the Axel patent to work, DNA II must encode a polypeptide
`that introduces a selectable phenotype not normally exhibited by the cell. A gene
`encoding an immunoglobulin heavy or light chain polypeptide cannot function in the role
`described in the Axelpatent for DNA II, because its expression in a cell would not have
`introduced a “selectable marker” into the cell.
`
`I do not find a description in the Axel patent for procedures where cells are transformed
`to express more than two distinct DNA sequences. Instead, the patent consistently states
`that one DNA (DNAI) encodes the polypeptide to be expressed by and isolated from the
`cell, and a second DNA (DNA II) encodes an introduced selectable marker.
`I, also see
`nothing in the Axel patent describing or suggesting procedures where host cells are
`transformed with an additional, different DNA (a “DNA III”) which would be necessary
`to use the Axel patent method to express genes encoding immunoglobulin heavy and
`light chain polypeptides in a single transformed host cell.
`
`I also do not read the brief references to “antibodies” in the Axel patent as suggesting that
`genes encoding both heavy and light chain polypeptides can or should be expressed in a
`single host cell. These references are simply suggesting that antibody polypgptides might
`be a type of “proteinaceous material” that could be produced using the method described
`in the Axel patent.
`
`I also do not find in the Axel patent any description of methods for producing a complex
`multimeric protein, such as an immunoglobulin, by independently expressing the genes
`encoding the individual polypeptide constituents of the multimeric protein in a single host
`cell.
`I note that the only examples in Axel concern small monomeric polypeptides (e.g.,
`the rabbit B-globin polypeptide). In addition, none of the experiments described in the
`Axel patent actually show isolation of the polypeptides that were produced by the
`transformed host cells.
`.
`
`I do not agree with the Examiner that the Axel patent suggests the desirability of
`producing immunoglobulins as “intact (assembled) proteins.” I am unable to find any
`mention in Axel of the desirability of producing “intact (assembled)" immunoglobulins,
`and nothing in the Axel patent provides any guidance on how to assemble “intact”
`immunoglobulins.
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`Sanofi/Regeneron Ex. 1028, pg 898
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`Mylan Ex. 1028, pg 898
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`

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`Control No. 90/007,542
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`Attorney Docket No. 22338-10230
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`29.
`
`30.
`
`The Axel patent does theorize that eukaryotic cells might process proteinaceous materials
`encoded by a DNA I to form complete, biologically active material (col. 7, lines 57 to
`67). However, what the Axel patent is discussing at this point is the idea that eukaryotic
`cells will add non-protein elements (particularly carbohydrate side chains) to the
`produced polypeptide. Since the Axel patent does not envision that two distinct
`polypeptides will be produced by and isolated from the transformed host cell or that the
`expression products of DNA I and DNA II will form a protein complex, this passage
`cannot be read as addressing the idea that an immunoglobulin molecule might be
`produced by the transformed cell and assembled into an intact tetramer.
`
`I do not disagree with the Examiner’s observation that Axel describes a process where a
`host cell is co-transformed to contain two foreign genes (a foreign DNA of interest and
`an unlinked foreign DNA that codes for a selectable marker). However, I do not agree
`that Axel can be read as establishing, to a scientist working in this field in early April of
`1983, that producing two or more complex polypeptides, in addition to the required
`selectable marker, in a single host cell would be predictable.
`I also do not agree with the
`Examiner’s statement that Axel suggests the desirability of producing immunoglobulins
`as “intact (assembled) proteins,” or that doing so would be predictable based on the
`contents of the Axel patent in early April of 1983. As I explain above, there is simply no
`discussion in the Axel patent regarding production of intact immunoglobulins.
`
`The Rice Publication
`
`31.
`
`The PTO cites a paper by Rice and Baltimore (Rice) as showing that “it was known in the
`art that host cells could express ‘heavy and light chains,’ and that expression of both
`chains was routine, resulting in assembly into immunoglobulins.” Office Action, page 6.
`I do not agree that this is what the Rice paper actually describes or suggests.
`
`32. While it was known by early April of 1983 that B cells express endogenous DNA
`corresponding to heavy and light immunoglobulin chain polypeptides and assemble these
`chains into immunoglobulin tetramers, the Rice paper does not address whether
`exogenous recombinant DNA sequences corresponding to heavy and light chain
`polypeptides could be independently expressed in a single host cell or whether those
`polypeptides could be assembled into immunoglobulin molecules or immunologically
`functional fragments.
`
`33.
`
`34.
`
`The Rice paper reports on experiments designed to explore the mechanisms that regulate
`immunoglobulin gene expression in immunoglobulin-producing cells. As Rice
`acknowledges at page 7862, col. 1, “although much is now known about Ig gene
`structure, relatively little is lcnown about the molecular mechanisms that control lg gene
`expression.”
`
`The experiments described in Rice involved insertion of a rearranged kappa (K) light
`chain gene into an Abelson murine leukemia virus-transformed lymphoid cell line
`designated 81A-2. Rice reports that the 81A-2 subclone expresses an endogenous
`immunoglobulin heavy chain gene, but does not express an endogenous K light chain
`gene.
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`Sanofi/Regeneron Ex. 1028, pg 899
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`Mylan Ex. 1028, pg 899
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`Control No. 90/007,542
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`Attorney Docket No. 22338-10230
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`35.
`
`. 36.
`
`37.
`
`38.
`
`39.
`
`Rice indicates that the transfected cells expressed the introduced murine K light chain
`gene based on their detection of mRNA corresponding to the introduced gene. Rice
`reports that they detected three classes of mRNA, two of which were “aberrant" and
`appeared to contain an intervening sequence that is not present in correctly processed
`mRNA for the murine K light chain gene, which suggests that the transfected cells may
`not have been consistently or correctly transcribing the exogenous immunoglobulin light
`chain gene.
`
`I do not believe a scientist, in early April of 1983, would view the Rice publication as
`establishing that expression of recombinant DNAS encoding exogenous heavy and light
`immunoglobulin chain polypeptides in one host cell was a routine matter.
`In my view,
`the Rice paper does not address the question of whether exogenous light and heavy chain
`polypeptides, if expressed by a transformed host cell, will be assembled into an “intact”
`immunoglobulin molecule. Instead, what Rice shows is that it is possible to express an
`exogenous light chain polypeptide in a particular mature B cell subclone that was already
`expressing an endogenous heavy chain and had lost its previous ability to produce
`endogenous light chain.
`"
`
`I also note that the particular lymphoid subclone used in Rice would not be suitable for
`processes that are the focus of the ’4l5 patent. This is because that subclone was already
`expressing an endogenous heavy chain.
`
`Rice does not explain how to selectively deactivate or control immunoglobulin chain
`expression in the 81A-2 cell line used in their experiments. The paper only reports that
`the line has lost functional K constant region genes and that the line continued to express
`its endogenous heavy chain gene. Rice does not describe any other transformed host
`cells in the paper.
`
`I therefore disagree with the suggestions of the PTO that Rice shows that “it was known
`in the art that host cells could express ‘heavy and light chains, and that expression of both
`chains was routine, resulting in assembly into immunoglobulins.”
`
`Kaplan, Accolla and Builder
`
`40.
`
`4].
`
`In the Office Action,.the PTO also addresses a number of other publications, including a
`published European Patent application filed by Kaplan, a paper published by Accolla, and
`a U.S. patent issued to Builder.
`I do not believe any of these publications suggests the
`idea of producing bothheavy and light immunoglobulin chain polypeptides in a single
`host cell.
`
`Kaplan, in my opinion, does nothing more than illustrate a general hypothetical approach
`that one might try to express an individual immunoglobulin light chain or heavy chain
`polypeptide. There are no examples provided in Kaplan of successful expression of
`immunoglobulin heavy or light chain polypeptides. Most significantly, nothing in
`Kaplan suggests that a heavy chain polypeptide and a light chain polypeptide should be
`produced in a single cell. Instead, as I read Kaplan, it suggests that a scientist could
`attempt to produce individual immunoglobulin chain polypeptides in separate host cell
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`Sanofi/Regeneron Ex. 1028, pg 900
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`Mylan Ex. 1028, pg 900
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`Control No. 90/007,542
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`Attorney Docket No. 22338-10230
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`42.
`
`43.
`
`cultures. As such, I do not believe a scientist working in this field in early April of 1983
`would have viewed Kaplan as suggesting the production of heavy and light
`immunoglobulin chain polypeptides in a single transformed host cell.
`
`Accolla describes a source for antibodies that bind to carcinoembryonic antigen (CEA).
`It does not describe or suggest any manipulations of the genes encoding the antibodies. It
`provides no suggestion that one should produce both heavy and light immunoglobulin
`chains in a single host cell.
`
`The Builder patent describes methods for refolding proteins produced by bacterial
`expression systems in which the proteins have formed insoluble “refiactile” bodies. It
`does not describe any approaches for modulating or selecting the conditions for
`expression of genes encoding immtmoglobulin chains. In my view, the Builder patent
`does not suggest the idea of expressing multiple polypeptides, particularly
`immunoglobulin heavy and light chain polypeptides, in a single host cell.
`
`'
`
`*¢###¥¢##¢$
`
`I declare that all statements made herein of my own knowledge are true and that all statements
`made on information and belief are believed to be true; and further tlmt these statements were
`made with the knowledge that willful false statements and the like so made are punishable by
`fine or imprisonment, or both, under Section 1001 of Title 18 of the United States Code and that
`such willful false statements may jeopardize the validity ofthe patent subject to this
`reexamination proceeding.
`
`Timo
`
`hn Roy Harris
`
`Date
`
`Mvedd MA 'w>s/
`
`-2-
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`Sanofi/Regeneron Ex. 1028, pg 901
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`Mylan Ex. 1028, pg 901