ViaCyte, Inc v Mount Sinai School of Medicine of New York University
[2011] APO 104
•22 December 2011
IP AUSTRALIA
AUSTRALIAN PATENT OFFICE
ViaCyte, Inc v Mount Sinai School of Medicine of New York University [2011] APO 104
Patent Application: 2003304106
Title: Mesoderm and definitive endoderm cell populations
Patent Applicant: Mount Sinai School of Medicine of New York University
Opponent: ViaCyte, Inc.
Delegate: Dr. B. Akhurst
Decision Date: 22 December 2011
Hearing Date: 28 September 2011, in Canberra
Catchwords: PATENTS - section 59 - opposition to the grant of a patent - manner of manufacture – whether a broad method claim is a manner of manufacture - utility – the claims do not encompass an embodiment that the skilled addressee understands would lead to an unworkable result - lack of utility not established - full description - enabling disclosure where principles provided but the claimed method is not exemplified - insufficiency not established - definition of the invention - claims are present and unambiguously define the monopoly - fair basis - whether claimed method is fairly based where it has not been demonstrated to work in the specification - the claims are fairly based - opposition is unsuccessful on all grounds
Representation: Patent applicant: Mr John Slattery of Davies Collison Cave, Melbourne.
Opponent: Written submissions were filed by Freehills, Melbourne.
IP AUSTRALIA
AUSTRALIAN PATENT OFFICE
Patent Application: 2003304106
Title:Mesoderm and definitive endoderm cell populations
Patent Applicant: Mount Sinai School of Medicine of New York University
Date of Decision: 22 December 2011
DECISION
The opposition is unsuccessful on all grounds. Costs are awarded according to Schedule 8 against ViaCyte, Inc.
REASONS FOR DECISION
Background
1. Patent application 2003304106 was filed by Mount Sinai School of Medicine of New York University (‘MSSM’) on 19 May 2003 under the provisions of the PCT, claiming priority from US basic applications 60/381,617 and 60/444,851 dated 17 May 2002 and 4 February 2003, respectively. After examination, acceptance of the application was advertised on 25 June 2009.
2. Cythera, Inc. filed a notice of opposition to grant of the patent on 25 September 2009, followed by a statement of grounds and particulars on 24 December 2009. On 8 March 2011, Cythera, Inc. advised it had changed its name to ViaCyte, Inc (‘ViaCyte’) and the Notice of Opposition was amended accordingly.
3. On 22 March 2010, MSSM filed a request under section 104 to amend the accepted specification which amendment was advertised allowed on 28 October 2010.
4. Evidence in support was served on 22 March 2010, consisting of a statutory declaration by
·Dr. Kevin D’Amour dated 16 March 2010 with Exhibits A to I.
5. Evidence in answer was completed on 17 November 2010, consisting of statutory declarations by
·Dr. Kathleen P. Mullinix dated 9 November 2010
·Dr. Alan Colman dated 1 November 2010 with Exhibits A to I
6. Evidence in reply, which was limited to correction of an inadvertent entitlement claim in the evidence in support, was completed on 11 February 2011 and consisted of a statutory declaration by
·Dr. Kevin D’Amour dated 7 February 2011 with Exhibit J.
7. ViaCyte chose not to attend the hearing and instead filed written submissions. Attached was a 2009 journal article[1] co-authored by the applicant’s expert declarant. This document was not in evidence and ViaCyte had made no request for leave to file further evidence. At the hearing, Mr Slattery objected to the document being admitted as evidence. I have reviewed the article and the only potentially relevant statement is in Table 1. In the context of the generation of disease-specific ES cells, the article states that appropriate genetic modification of normal human ES cells, particularly homologous recombination, is very difficult. However, the matter already in evidence establishes this level of difficulty in the process. The additional document is of little additional significance and it would not change my conclusions in this opposition. Consequently, I see no reason to invoke regulation 5.11.
[1] Colman, A and Dreesen, O. ‘Pluripotent stem cells and disease modelling’ (2009) Cell Stem Cell 5: 244-247
Standard of proof
8. The onus of proof in opposition proceedings lies with the opponent, who must establish that it is clear that a valid patent cannot be granted (F.Hoffman-La Roche AG v New England Biolabs Inc [2000] FCA 283 at [29], [67]; (2001) 50 IPR 305 at 311 [29], 319 [67]; Commissioner of Patents v Sherman [2008] FCAFC 182 at [18], [22]; (2009) 79 IPR 426 at 430 [18], 432 [22]).
Grounds of Opposition
9. The grounds for opposing the grant of a patent under section 59 of the Patents Act 1990 are identified in the statement of grounds and particulars as manner of manufacture, utility, full description, definition of the invention, clarity and fair basis. However, in its written submissions, ViaCyte did not include clarity in the grounds and made no submissions in this respect. Therefore, my interpretation of the written submissions is that ViaCyte did not press lack of clarity as a ground of opposition.
The specification and claims
10. The application is entitled “Mesoderm and definitive endoderm cell populations”. On pages 1-2, the description teaches that the tissues of the body are formed from the primary germ cell layers, ectoderm, mesoderm and definitive endoderm. Each of these layers generates a specific set of cell populations and tissues. While the segregation of developmental fates is well accepted, prior to the application there were no methods available to isolate mesoderm and endoderm cells prior to commitment to tissue-specific lineages. The invention addresses this by providing a method for isolating mesoderm and definitive endoderm cell populations. The isolated cell populations are said to be useful for identifying agents that affect cell growth and differentiation; for identifying the genes involved in tissue development; and to generate differentiated cells and tissues for cell replacement therapies.
11. The description teaches that brachyury is a conserved gene and the sequences of human and mouse brachyury are known in the art. Expression of the brachyury gene is described as one of the best markers of early mesoderm and had previously been used to track the development of this lineage. An embodiment of the invention relates to the recombinant targeting of the brachyury locus with a selectable marker gene. As embryonic stem (ES) cells differentiate, the selectable marker is expressed in a pattern that reflects brachyury expression and allows cells expressing brachyury to be isolated from embryoid bodies.[2] Enhanced green fluorescent protein (GFP) is the preferred marker; however other known selectable markers that will facilitate cell sorting may be used[3].
[2] Description page 6 line 31 to page 7, line 30
[3] Description at page 7, lines 20-23
12. The present invention is also said to relate to the discovery of a mesendoderm cell population that gives rise to mesoderm and endoderm cells and their corresponding lineages. The inventors have also discovered that the presence or absence of serum may be used to dictate which lineage is generated from mesendoderm cells cultured in vitro. [4] Mesoderm and mesendoderm cells are brachyury-positive (brach+). Mesendoderm is capable of generating endoderm cells, which are brachyury-negative (brachˉ) and capable of differentiating into lung, liver and pancreatic cells[5].
[4] Description page 9, lines 19 to page 10, line 2
[5] Description page 2, lines 19-22
13. The specification ends with 18 claims as follows:
“1. A method of isolating a cell population enriched for mesendoderm cells and mesoderm cells comprising culturing embryonic stem cells in the presence of serum for a time sufficient to obtain cells that express brachyury, and isolating said cells that express brachyury wherein a selectable marker gene is inserted into the brachyury locus of said embryonic stem cells, and cells that express brachyury are isolated by selecting for cells that express the selectable marker.”
Claim 2 specifies the selectable marker as enhanced GFP. Claim 3 defines a cell population enriched for mesendoderm and mesoderm cells obtained by the method of claim 1 or 2. Claims 4-6 limit the cell population of claim 3 to comprising at least about 50%, 75% or 90% mesendoderm and mesoderm cells, respectively.
“7. A cell population obtained by culturing human embryonic stem cells in the presence of serum for about two to about ten days, isolating cells that express brachyury, and culturing said cells that express brachyury in the absence of serum for about one to about fifteen days.”
Resort to the description[6] makes it clear that the cell populations of claim 7 are enriched for endoderm cells. This conclusion is consistent with the subject matter of dependent claims 13 and 16.
[6] Description at paragraph bridging pages 9-10
Claim 8, dependent on claim 7, specifies that the human ES cells contain a selectable marker gene inserted into the brachyury locus, and that the isolation step is carried out by selecting for cells that express the selectable marker. Claim 9 specifies the selectable marker as enhanced GFP.
“10. A method of identifying endodermal cells capable of functioning as mature hepatocytes comprising transplanting a subpopulation of the cell population of any one of Claims 7 to 9, into an animal exhibiting a disorder associated with hepatocyte destruction or dysfunction, and assaying for liver function, wherein an improvement in liver function in said animal is indicative of the identification of endodermal cells capable of functioning as mature hepatocytes.”
Claim 11 specifies the animal of claim 10 as a fumarylacetoacetate-deficient mouse.
“12. A method of identifying an agent that affects the proliferation, differentiation or survival of mesendoderm and mesoderm cells comprising culturing the cell population of Claim 3 in the presence of an agent to be tested and comparing the proliferation, differentiation or survival of said cells in the presence and absence of said agent, wherein a difference in the presence of said agent is indicative of the identification of an agent that affects the proliferation, differentiation or survival of said cells.”
Claim 13 defines a method in identical terms as claim 12, except that the cells are endoderm and the cell population is that of any one of claims 7-9.
“14. A method of identifying genes involved in cell differentiation comprising incubating embryonic stem cells under conditions to obtain cells that express brachyury, isolating two populations of cells that express brachyury after two different amounts of time in culture, comparing gene expression profiles in said two populations, and identifying genes that are uniquely expressed in a population, wherein identification of a gene that is uniquely expressed in a population is indicative of identification of a gene involved in cell differentiation.
15. A method for generating mammalian cells comprising culturing the cell population of Claim 3 under conditions effective for the differentiation of mesoderm into cardiac muscle, vascular smooth muscle, endothelium or hematopoietic cells.
16. A method for generating mammalian cells comprising culturing the cell population of any one of Claims 7 to 9 under conditions effective for the differentiation of endoderm into liver cells or pancreatic cells.
17.A transgenic non-human mammal having a genome comprising a transgene in which DNA encoding a selectable marker is present in the brachyury locus and the selectable marker is expressed in cells that express brachyury.
18.A method according to any one of Claims 1, 2 and 10-16 or a cell population according to any one of Claims 3-9 or a transgene of Claim 17 substantially as herein described with reference to the Figures and/or Examples.”
Claim 18 has no scope insofar as it defines a cell population according to claims 7-9 by way of reference to the Figures and/or Examples. Claims 7-9 define a cell population enriched for endoderm cells derived from human ES cells. The Figures and Examples refer to cell populations derived from mouse ES cells. The Figures and Examples teach nothing within claims 7-9 and consequently, insofar as it is dependent on claims 7-9, claim 18 is of no effect.
Insofar as it is dependent on claim 17, claim 18 defines a transgene at the brachyury locus in a non-human mammalian cell. In effect therefore, it defines the transgenic non-human mammal of claim 17, by reference to the Figures and/or Examples.
Section 40(2)(a): Sufficiency of description
14. Section 40(2)(a) requires that a complete specification must describe the invention fully, including the best method known to the applicant of performing the invention. The “invention” in section 40 is “the embodiment which is described, and around which the claims are drawn”[7].
[7] Kimberly-Clark Australia Pty Ltd v Arico Trading International Pty Ltd [2001] HCA 8 at [19], [21]; (2001) 207 CLR 1 at 14 [19], 15 [21]
15. The High Court in Kimberly-Clark Australia Pty Ltd v Arico Trading International Pty Ltd [2001] HCA 8 at [25]; (2001) 207 CLR 1 at 17 [25] provided the test for full description:
“The question is, will the disclosure enable the addressee of the specification to produce something within each claim without new inventions or additions or prolonged study of matters presenting initial difficulty?”
In Kimberly-Clark at [25], the High Court cited Romer LJ in No-Fume Ltd v Frank Pitchford & Co Ltd (1935) 52 RPC 231 at 243:
“It is not necessary that [the applicant] should describe in his specification the manner in which the invention is to be performed, with that wealth of detail with which the specification of the manufacturer of something is usually put before the workman who is engaged to manufacture it.”
The question of sufficiency is one of fact which is best determined by the evidence of the person skilled in the art[8]. The complete specification must be read as a whole, through the eyes of a skilled addressee, and construed in light of the common general knowledge and the art before the priority date[9]. However, for the purposes of determining sufficiency, the relevant date is, at the earliest, the date of grant[10] and the addressee of the specification can take into account the common general knowledge and prior art as at the date that sufficiency is determined[11].
[8] Universal Oil Products Co v Monsanto Co [1973] RPC 212 at 218
[9] Kimberly-Clark v Arico [2001] HCA 8 at [16], [24]; (2001) 207 CLR 1 at 13 [16], 16 [24]
[10] Pfizer Overseas Pharmaceuticals v Eli Lilly & Co [2005] FCAFC 224 at [337], [347]; (2006) 68 IPR 1 at 71 [337], 73 [347]
[11] Eli Lilly & Co v Pfizer Overseas Pharmaceuticals [2005] FCA 67 at [184]; (2005) 64 IPR 506 at 538 [183]
16. It was not in dispute that the parties’ expert declarants were persons skilled in the art at the priority date of the application. Mr Slattery noted that Dr D’Amour is not an independent witness, being an employee of the opponent. However, this does not mean his evidence is not capable of being given weight by a hearing officer. Both Dr D’Amour and Dr Colman and have extensive experience in stem cell research, including with human ES cells. As a consequence, I believe that the conclusions of both experts may be given weight in this opposition.
17. ViaCyte has opposed claim 7 and dependent claims 8-11, 13, 16 and 18 on the basis of insufficiency. However, as I have found above that claim 18 is of no effect insofar as it is dependent on claims 7-9, I will not consider this claim further.
ViaCyte’s submissions are essentially that the specification does not provide an enabling disclosure of a method for producing recombinant human ES cells with a selectable marker at the brachyury locus. ViaCyte contended that without this, brach+ cells cannot be isolated and the claimed human cell populations could not be produced.
18. Claim 7 defines a cell population in terms of the process by which it is obtained from human ES cells. MSSM submitted that it is not an essential feature of claim 7 that this step be carried out using recombinant ES cells carrying a selectable marker, because the description teaches that antibodies can be used to isolate cells expressing brachyury.
The use of antibodies to isolate brach+ ES cells
19. An embodiment of the invention is described as the provision of antibodies that specifically recognise brach+ cells[12].
The description teaches that it had not been possible to isolate early mesoderm cell populations by cell sorting because suitable antibodies were not well defined[13]. The application addresses this problem by providing methods for making antibodies that recognise brach+ cells but not brachˉ cells[14]. Such antibodies may be made by injecting an animal with the cells of the invention in an immunogenic form, or by identifying cell surface markers that are present in GFP+ but not GFPˉ cells[15].
[12] Description page 2, lines 29-31
[13] Description page 6, lines 28-30
[14] Description page 11, lines 10-13
[15] Description page 11, lines 10-18
20. The first option, the production of specific antibodies using brach+ cells as an immunogen, would require isolated brach+ cells. As to the second option, the specification does not identify any suitable cell surface markers, and does not suggest that brachyury is such a marker. I do not believe that the brachyury protein itself could be considered a suitable target for antibody-based cell sorting because it is a transcription factor[16] and proteins with this function are highly unlikely to be exposed on the cell surface. Therefore, in order to produce antibodies specific for brach+ cell surface markers, the skilled addressee would require isolated brach+ cells in order to identify a suitable marker for use as an immunogen. In either case, since a method for isolating brach+ cells is required in order to raise specific antibodies, the antibody-based methods taught by the specification would not be enabled in the absence of an alternative method for isolating brach+ cells.
[16] Description page 6, lines 31-33
21. The specification teaches that brach+ ES cells may be isolated by targeting a selectable marker to the brachyury locus. In order to satisfy the requirements of section 40(2)(a), it is the description of this method that must be sufficient to enable the addressee of the specification to produce something within each claim without new inventions or additions or prolonged study of matters presenting initial difficulty.
Isolation of brach+ ES cells by insertion of a selectable marker into a brachyury locus
22. The principles involved in gene targeting at the time of filing the application were explained by Dr Colman in his evidence at [13] - [14], and include the following:
· Electroporation methods were commonly used to transfect (get DNA into) a cell in order that the exogenous DNA can be incorporated into a chromosome by the process of homologous recombination.
· Targeted homologous recombination into mammalian cells, including ES cells, requires a DNA construct (targeting vector) comprising 5’ and 3’ sequences that are substantially identical in sequence to the target site in the chromosomal DNA, and an intervening exogenous sequence that is to be inserted into the chromosome at the target site. The homologous ‘arm’ regions facilitate substitution of the exogenous DNA sequence for the endogenous DNA at the target site.
· Homologous recombination at the target site occurs in only a small fraction of cells. Therefore, in order to detect the rare recombination events, selectable marker genes can be incorporated into the targeting construct to simplify the process of identifying cells that have correctly integrated the exogenous DNA into the target site on the chromosome.
23. ViaCyte submitted that given the complexity involved in the steps of transfecting human ES cells by electroporation and homologous recombination of non-expressed loci in human ES cells; transferring the methods for mouse ES cells to an application in human ES cells is uncertain and fraught with difficulty. I will address each of these steps in turn.
Transfection of human ES cells by electroporation
24. Dr D’Amour, at [5(b)] and [7] states that successful transfection of human ES cells was not possible at the filing date of the application because (i) electroporation methods developed for mouse ES cells did not work for human ES cells; and (ii) methods for electroporating human ES cells were undeveloped at the filing date of the application. In support of his statements, Dr D’Amour referred to an article published in March 2003 by Zwaka and Thomson[17]. I note however, that the passage relied on by Dr D’Amour describes the state of the art prior to the author’s work. Zwaka and Thomson describe a modified electroporation protocol for use in human ES cells.
[17] Zwaka T. P. and Thomson J. A. ‘Homologous recombination in human embryonic stem cells’ (March 2003) Nature Biotechnology 21: 319-321 Published online 10 February 2003
25. Zwaka and Thomson reported that, in their hands, electroporation of human ES cells using a typical mouse ES cell protocol achieved a stable transfection rate of approximately 10-7, which they describe as “too low to be practical for identifying rare homologous recombination events”[18]. However, their modified electroporation protocol achieved a transfection rate in human ES cells 100-fold or more higher than that achieved using the standard mouse protocols[19]. Using the modified protocol, Zwaka and Thomson successfully electroporated human ES cells to target two expressed genes[20].
[18] Zwaka and Thomson, page 319, right column, first full paragraph
[19] Zwaka and Thomson, page 319, right column, para 2
[20] Zwaka and Thomson, last sentence of the Abstract
26. At the hearing, Mr Slattery accepted that the transfection efficiency of standard mouse electroporation protocols in human ES cells was too low for practical purposes. However, he argued that the specification on page 8 referred to the use of “methods known in the art” to introduce the targeting vectors into ES cells. He submitted that using the methods taught by the specification, supplemented by the electroporation protocol taught by Zwaka and Thomson, the person skilled in the art would have been able to transfect human ES cells.
27. Both Dr D’Amour at [3] and Dr Colman at [5] refer to the worldwide communication in regard to advances in this art. Dr D’Amour states that “knowledge in this field was rapidly disseminated by journals published … by scientists from around the world”. The Zwaka and Thomson article was published in a prestigious journal and is described by Dr Colman at [8] as “known at the time of filing the application”. Therefore, I accept that a person skilled in the art, wishing to apply the principles taught by the opposed application to human ES cells would, at the relevant date for sufficiency, have had knowledge of the Zwaka and Thompson publication. Even if I am wrong, if the skilled addressee had needed to consult the literature for suitable transfection methods, the article would have been readily available for reference and I believe it would have been quickly identified.
28. Although Dr D’Amour in his supporting evidence at [9] states that electroporation methods for human ES cells remain difficult now, he does not acknowledge the modified protocol for human ES cells taught by Zwaka and Thomson, or comment on the potential effectiveness or otherwise of this method. Dr Colman at [8] and [10], describes the Zwaka and Thomson electroporation protocol for human ES cells as successful and efficient. ViaCyte provided no relevant evidence in reply that might qualify Dr Colman’s conclusion.
29. I can only conclude that, prima facie, the disclosure of the specification, supplemented by the modified electroporation protocol for human ES cells taught by Zwaka and Thomson, is sufficient to enable the skilled addressee to transfect human ES cells with exogenous DNA, without the need for new inventions or additions or prolonged study of matters presenting initial difficulty.
Homologous recombination in human ES cells
30. In respect to the process of homologous recombination in human ES cells, ViaCyte submitted that even as late as 2009, there was no known general approach to manipulating the human ES cell genome, making gene targeting in these cells difficult.
31. Dr D’Amour at [5(a)] states that, prior to May 2003, there was only one reported instance of homologous recombination in human ES cells[21] and this was into an expressed gene. He notes at [6] that a second, similar report followed in 2004[22], and at [10] that homologous recombination into an unexpressed locus was not reported until 2008[23]. On the basis that, at the filing date of the application, homologous recombination in human ES cells was nowhere near being a “standard” technique as it was for mouse ES cells; and the fact that there were no reports of successful homologous recombination into a non-expressed gene before the filing date of the application; Dr D’Amour concludes that homologous recombination of brachyury, a gene which is not endogenously expressed in undifferentiated ES cells could not be accomplished in May 2003 using the methods taught in the opposed application[24].
[21] Zwaka and Thomson Nature Biotechnology (March 2003) 21: 319-321.
[22] Urbach, A. et al. ‘Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells’ (2004) Stem Cells 22: 635-641
[23] Davis R. P. et al ‘Targeting a GFP reporter gene to the MIXL1 locus of human embryonic stem cells identifies human primitive streak-like cells and enables isolation of primitive hematopoietic precursors’ (2008) Blood 111(4): 1876-1884
[24] Dr D’Amour at [5], [6], [8]-[12]
32. The effect of Dr D’Amour’s reasoning is that the specification would only provide an enabling disclosure for homologous recombination of a non-expressed gene in human ES cells, if this result had been previously reported. However, patent specifications by nature relate to advances in an art. That a process had not been previously reported does not necessarily establish that the specification is not enabling for that process. Nevertheless, I accept as fact that there were no reports of successful homologous recombination into a non-expressed genetic locus before the filing date of the specification, and few since that date. I also accept Dr D’Amour’s evidence in general, that successful gene targeting by homologous recombination in human ES cells has proven difficult and that a general approach to manipulate the human ES cell genome was still lacking as late as 2009. However, the fact that the task is a difficult one does not, of itself, mean that the claimed subject matter could not be worked without further invention[25].
[25] Eli Lilly and Company v Pfizer Overseas Pharmaceuticals [2005] FCA 67 at [194]; (2005) 64 IPR 506 at 540 [193], affirmed by Pfizer Overseas Pharmaceuticals v Eli Lilly and Company [2006] FCAFC 224 at [336]; (2005) 68 IPR 1 at [336]
33. Apart from his statements that homologous recombination into non-expressed genetic loci had not been previously reported and his belief that it could not have been performed; Dr D’Amour gives little in the way of reasons as to why the targeting strategy for mouse ES cells taught by the opposed specification could not be adapted by the skilled addressee for use in human ES cells without new inventions or prolonged study. At [11], Dr D’Amour refers to “missing information” in the opposed specification, but he does not elaborate on exactly what information is missing.
34. Turning to Dr Colman’s evidence, at [11] Dr Colman says the method for targeting the brachyury locus at Example 2 of the opposed application involves technology that does not rely on the activity of the targeted gene, due to the presence of a selectable marker gene under the control of its own promoter between the homology arms of the targeting construct. Dr Colman at [14] describes alternative targeting strategies for expressed and non-expressed genes, summarised below:
· Where a targeted gene is expressed in a cell, a selectable marker gene inserted in-frame downstream of the endogenous gene’s active promoter will be expressed, allowing direct identification of cells in which homologous recombination has occurred at the target site.
· Where the target gene is not expressed, cells in which homologous recombination has occurred may be identified if the targeting vector includes a constitutively active promoter controlling expression of the selectable marker gene. Screening for cells expressing the marker gene (i.e. cells in which the exogenous DNA has been incorporated anywhere in the chromosomal DNA) is then followed by molecular screening, to identify cells in which the endogenous DNA has been incorporated into the chromosomal DNA at the target site.
35. The Zwaka and Thompson article exemplifies both targeting strategies. Dr Colman notes at [18] that although the promoterless construct was more efficient, both strategies were successful for homologous recombination of expressed genes. Dr Colman at [20] believes that there is no reason why the approach in which expression of a selectable marker is driven by a promoter in the targeting construct would not work for targeting genes that are not expressed in human ES cells. He notes at [21] that this strategy was used in 2008[26] to successfully target a non-expressed gene in human ES cells.
[26] Davis R. P. et al. (2008) Blood 111(4): 1876-1884
The targeting strategy taught by the specification
36. On pages 7-8, the specification describes recombinant targeting of the brachyury locus with a selectable marker gene. In a preferred embodiment, the targeting vector is designed to replace approximately two-thirds of the first exon of the brachyury gene with a GFP expression cassette. Following successful targeting the brachyury start codon becomes the start codon of GFP, and the recombinant brachyury allele is inactivated.
37. Example 2 of the opposed specification describes a targeting strategy for generating recombinant mouse ES cells with the coding sequence for GFP inserted into the brachyury locus. The targeting vector is depicted in Figure 1. Inside the homology arms, the vector contains, among other things, the GFP coding sequence and a loxP-flanked neo cassette, i.e. two selectable marker genes for insertion into the brachyury locus. The first encodes GFP which, in the recombinant cell, will be expressed under the control of the brachyury promoter and will facilitate later identification of brach+ cells. A second selectable marker is present in the form of a neo cassette containing a neomycin resistance gene which, when expressed, will confer antibiotic resistance on the recombinant cell.
38. The specification does not explicitly state that the neo cassette includes a promoter. However, the neo cassette is described in Example 2 as a XhoI/SaII fragment derived from plasmid pL2-Neo2[27]. Dr Colman at [23] believes that this fragment contains the MC1 (HSV-thymidine kinase) promoter controlling expression of the neomycin resistance gene. Consistent with an active promoter in the transfected cells, Example 2 describes positive selection of the cells using the antibiotic G418[28] (recombinant cells expressing the neomycin resistance gene will be resistant to the bactericidal activity of G418). After successful targeting, the LoxP-flanked neo cassette is removed from the transgene using Cre recombinase[29], leaving the GFP coding sequence as the only marker gene in place. Cells that had undergone homologous recombination at the target site were identified by PCR and confirmed by Southern blotting[30]. The targeting efficiency of this strategy in mouse ES cells was increased by the additional step of negative selection of recombinant clones using Gancylovir[31], facilitated by the thymidine kinase gene at the 3’ end of the targeting construct, to select against random integration[32]. The critical question is whether this strategy could be put into practice to generate recombinant human ES cells.
[27] Description page 16, lines 11-12
[28] Description page 16, lines 30-31
[29] Description page 17, lines 10-13, Figure 1
[30] Description page 16, line 32 to page 17, line 8
[31] Description page 16, lines 30-32 and page 17, lines 8-10
[32] Description page 15, lines 22-25
39. There is nothing in the evidence to suggest that an equivalent vector construct suitable for targeting the brachyury locus in human ES cells could not be prepared in accordance with the principles taught in the specification. The description on page 7 teaches that the human brachyury gene is known in the art, and that the targeting vectors may be constructed by methods known in the art. Therefore, what must now be answered is whether the brachyury locus in human ES cells could be successfully targeted using an equivalent, human brachyury-specific, targeting vector.
40. The targeting strategy of Example 2 for mouse cells is prima facie that identified by Dr Colman (see [34] above), as suitable for targeting non-expressed genetic loci. The strategy successfully achieves this goal in mouse ES cells[33]. Dr Colman at [21]-[23] states that the same strategy was used in 2008[34] to successfully generate several human ES cell lines in which sequences encoding a fluorescent protein were targeted to non-expressed loci. Dr Colman concludes at [25] that:
“by following the teachings of the Application and using methods known in the art at the time of filing the Application, one of ordinary skill in the art could generate human ES cells having a selectable marker gene inserted into the brachyury locus.”
[33] Description page 17, lines 18-31 and Figure 2
[34] Davis R. P. et al (2008) Blood 111(4): 1876-1884
41. As indicated above at [15], the addressee of the specification can take into account the common general knowledge and prior art as at the date that sufficiency is determined. If in 2011, the skilled addressee wishing to perform the claimed invention had needed to consult the literature for additional guidance, the article by Davis et al in 2008 is relevant prior art which has been freely available to the skilled addressee since its publication. Davis et al describes a method for targeting a non-expressed genetic locus in a human ES cell with a selectable marker as presently claimed.
42. Given the evidence before me, I can only conclude that prima facie, following the principles described by the present application, with or without the teaching of Davis et al, the non-inventive skilled addressee could have successfully inserted a selectable marker into the brachyury gene without new inventions or additions or prolonged study of matters presenting initial difficulty.
43. In its written submissions, ViaCyte argued that non-expressed genes are not readily accessible for homologous recombination because they are tightly packaged around histones. However, neither Dr D’Amour nor Dr Colman, both experts in the field, raised this point in their evidence. ViaCyte’s submission is not expressly supported by their expert’s evidence and is in conflict with Dr Colman’s evidence. Therefore, this submission carries little weight.
44. At [11], the balance of Dr D’Amour’s evidence on homologous recombination is that “skilled people in the field have not generated a cell population enriched for mesendoderm cells and mesoderm cells from human ES cells by following the teaching of the application”. However, fatally for this line of argument, ViaCyte has adduced no evidence to establish that anyone has attempted to produce something within claim 7 at least, and failed.
45. ViaCyte submitted that claim 7 is not enabled over its full scope, because it encompasses isolation of brach+ ES cells by means other than the insertion of a selectable marker gene into the brachyury locus. However, section 40(2)(a) does not require that a claim is enabled over its full scope; all that is required is that the disclosure of the specification enable the addressee of the specification to produce something within each claim[35]. One embodiment is sufficient[36].
[35] Kimberly-Clark v Arico [2001] HCA 8 at [25]; (2001) 207 CLR 1 at 17 [25]
[36] Eli Lilly and Company v Pfizer Overseas Pharmaceuticals [2005] FCA 67 at [185]; (2005) 64 IPR 506 at 540 [184]
46. I am sympathetic to the opponent’s concerns with the level of information provided by the opposed specification in relation to the generation of recombinant human ES cells. However, ViaCyte has not established that the specification does not provide sufficient information for the skilled addressee to produce recombinant human ES cells having a selectable marker at a brachyury locus, in order to isolate cells that express brachyury, as required by claims 7-11, 13 and 16. It follows that I find the specification to meet the requirement of section 40(2)(a).
Section 40(2)(b): Claims defining the invention
47. Section 40(2)(b) requires that a complete specification end with a claim or claims defining the invention. ViaCyte’s particulars under this ground are to the effect that insofar as the claims are not limited to methods involving a selectable marker inserted into the brachyury locus of a cell, claims 1-18 do not define the invention.
48. The requirement of section 40(2)(b) that a complete specification for a standard patent shall end with a claim or claims defining the invention is simply that there must be a claim or claims that clearly and distinctly define the monopoly for which the application has been made. Invalidity will only arise if the claim is “incapable of resolution by a skilled addressee by the application of common sense and common knowledge”. [37]
[37] AMP Inc v UtiluxPty Ltd [1971] 45 ALJR 123 at 128, PhotoCure ASA v Queen’s University at Kingston [2005] FCA 344 at [117]; (2005) 64 IPR 314 at 347 [117]
49. ViaCyte provided no submissions under this ground nor has it argued that the claims are ambiguous. I consider that the claims are capable of resolution and clearly define the monopoly sought by the applicant. Consequently, the claims define the invention as required by section 40(2)(b).
Section 40(3): Fair basis
50. Section 40(3) relevantly requires that the claim or claims in a patent specification must be fairly based on the matter described in the specification.
51. As the test for fair basis, the High Court in Lockwood Security Products Pty Ltd v Doric Products Pty Ltd [2004] HCA 58 at [69]; (2004) 217 CLR 274 at 300 [69] approved the words of Gummow J in Rehm Pty Ltd v Websters Security Systems (International) Pty Ltd (1988) 81 ALR 79 at 95:
“… the question is whether there is a real and reasonably clear disclosure in the body of the specification of what is then claimed, so that the alleged invention as claimed is broadly, that is to say in a general sense, described in the body of the specification.”
52. In their reasoning[38] the High Court approved the principle provided by Barwick CJ in Olin Corporation v Super Cartridge Co Pty Ltd [1977] HCA 23 at [6]; (1994) 180 CLR 236 at 240:
“The question whether the claim is fairly based is not to be resolved, in my opinion, by considering whether a monopoly in the product would be an undue reward for the disclosure. Rather, the question is a narrow one, namely whether the claim to the product … as expressed, travels beyond the matter disclosed in the specification”.
[38] Kimberly-Clark v Arico [2001] HCA 8 at [15]; (2001) 207 CLR 1 at 12 [15]; Lockwood v Doric [2004] HCA 58 at [57]; (2004) 217 CLR 274 at 300 [57]
53. ViaCyte’s submissions were in effect, that there was no real and reasonably clear disclosure where there was, in its view, no enabling disclosure. ViaCyte submitted that the gene targeting methods of the application were only demonstrated to work in mouse ES cells and consequently claims to methods other than for mouse cells travel beyond the methods taught in the specification. However, the decisions of the High Court[39] establish that consideration of section 40(3) requires only a comparison between the matter described in the specification and the claims which define the monopoly. It does not call for any inquiry into, among other things, the technical contribution to the art.
[39] Kimberly-Clark v Arico [2001] HCA 8 at [15]; (2001) 207 CLR 1 at 12 [15]; Lockwood v Doric [2004] HCA 58 at [54]; (2004) 217 CLR 274 at 300 [54]
54. Under this ground, ViaCyte opposed claims 7-11, 13, 16 and 18. As above, I will not further consider claim 18 which is of no effect. The balance of these claims are drawn to cell populations, and the use of cell populations, obtained by following a method comprising at least the steps provided by independent claim 7. For the method, claim 7 specifies minimal culture conditions and includes the step of isolating brach+ human ES cells.
Claims 7-9
55. The specification teaches a method for generating cell populations enriched for endoderm cells from recombinant human ES cells containing a selectable marker at the brachyury locus. The method involves culturing the cells in the presence of serum for about 2-10 days and then sorting and isolating GFP+ cells (i.e. cell populations relevantly enriched for mesendoderm cells), followed by culturing the GFP+ cells in the absence of serum for from about 1-15 days[40].
[40] Description page 9, line 31 to page 10, line 2
56. ViaCyte relevantly submitted that claims encompassing methods for isolating brach+ cells other than through homologous recombination of GFP into the brachyury locus were not fairly based. However, one embodiment of the invention is said to be the provision of antibodies that specifically recognise brach+ cells[41], which antibodies are useful for isolating mesendoderm cell populations[42]. Clearly, the disclosure of the description is consistent with the subject matter of claims 7-9.
[41] Description page 2, lines 29-31
[42] Description page 2, lines 29-31; page 11, line 17-18
Claims 10-11 and 16
57. On pages 11-12 of the description, encompassed within the invention is a method of culturing a cell population enriched in endoderm cells under conditions that are known in the art to be effective for the differentiation of endoderm into liver cells (which would be understood by the skilled addressee to include hepatocytes)[43]. The description teaches that such cells are useful for cell replacement therapy for the treatment of, among other things, liver failure[44]. The suitability of the cell populations for cell replacement therapy can be tested in animal models such as the fumarylacetoacetate-deficient mouse which suffer from progressive liver failure unless treated, for example, by cell transplantation with hepatocytes[45]. This disclosure is consistent with the subject matter of claims 10-11 and 16.
[43] Description page 11, lines 24-27 and page 26, lines 26 to page 27, line 12
[44] Description page 12, lines 9-10
[45] Description page 12, lines 10-24
Claim 13
58. The invention is said to provide a method for identifying agents that affect the proliferation, differentiation, or survival of the cell populations of the invention[46]. The method includes culturing cells from the enriched cell population in the presence and absence of an agent to be tested, and determining, by standard techniques, whether the agent has an effect on proliferation, differentiation or survival of the cell population. This method is consistent with the method of claim 13.
[46] Description page 10, line 23 to page 11, line 2
59. In summary, the subject matter of the description is consistent with that of claims 7-11, 13 and 16, and provides a real and reasonable clear disclosure of the subject matter of these claims which is consequently fairly based.
Section 18(1)(a): Manner of Manufacture
60. Section 18(1)(a) requires that an invention must be a manner of manufacture within the meaning of section 6 of the Statute of Monopolies. Whether an invention is a manner of manufacture is determined by asking whether the claimed invention lacks the necessary quality of inventiveness on the face of the specification[47].
[47] NV Philips Gloeilampenfabrieken v Mirabella International Pty Ltd [1995] HCA 15 at [9]; (1995) 183 CLR 655 at 663-664
61. ViaCyte submitted that the subject matter of claim 7 and dependent claims is not a manner of manufacture, as follows:
“Claim 7 purports to define a monopoly for ‘[a] cell population obtained by culturing human embryonic stem cells in the presence of serum for about two to ten days, isolating cells that express brachyury, and culturing said cells that express brachyury in the absence of serum for about one to fifteen days.’
This claim does not provide a manner of manufacture - there is no indication of what ‘isolating cells that express brachyury’ requires in relation to a method for manufacturing the cell population claimed. The very point of the invention was to find a means of identifying such cells as they are not easily identifiable. The fact that additional information is required in order to make this a manner of manufacture is illustrated by the fact that Claim 8 does amount to a manner of manufacture by reason of the inclusion of the means of identifying such cells - i.e. through insertion of a selectable marker gene into the brachyury locus.
As it stands, the cell population claimed in Claim 7 does not amount to a manner of manufacture but rather describes only a desired result of isolating cells that express brachyury.” (Emphasis in original)
62. ViaCyte’s argument appears to be that a claimed invention will not be a manner of manufacture if the claim defines an invention in terms of the result to be achieved. Notwithstanding that a “claim by result” may be allowable in Australia[48]; this argument does not establish that the claimed invention is not a manner of manufacture.
[48] Lockwood v Doric [2004] HCA 58 at [59]; (2004) 217 CLR 274 at 292 [59], referring to the principle stated in Shave v H V McKay Massey Harris Pty Ltd (1935) 52 CLR 701 at 709
63. ViaCyte has made no submissions to the effect that the cell population of claim 7 and the additional matter in the dependent claims lacks inventiveness on the face of the specification. Therefore, its opposition under this ground fails.
Section 18(1)(c): Utility
64. The requirements for utility in a claimed invention under section 18(1)(c) were summarised by the Full Court of the Federal Court in as follows:
“If the claimed invention does what it is intended by the patentee to do and the end result obtained is itself useful, the invention is useful within the meaning of s 18(1)(c) … As to the first aspect, the invention as claimed must attain the result promised by the patentee”[49]
“A claim is bad if it covers means that will not produce the desired result, even if a skilled person would know which means to avoid. That is to say, everything that is within the scope of a claim must be useful, otherwise the claim will fail for inutility.”[50]
[49] Ranbaxy Australia Pty Ltd v Warner-Lambert Co LLC [2008] FCAFC 82 at [141]; (2008) 77 IPR 449 at 479 [141]
[50] H Lundbeck A/S v Alphapharm Pty Ltd [2009] FCAFC 70 at 247 [81], 272 [217]; (2009) 81 IPR 228 at [81], [217]
However, in construing the claims for the purposes of utility, the claims must be construed from the perspective of a skilled addressee in a commonsense way, and not in such a way that any such addressee would appreciate would lead to an unworkable result[51].
[51] SNF (Australia) Pty Ltd v Ciba Speciality Chemicals Water Treatments Limited and Others [2011] FCA 452 at [293]; (2011) 92 IPR 46 at 212 [293]; Inverness Medical Switzerland GmbH v MDS Diagnostics Pty Limited [2010] FCA 108 at [117]; (2010) 85 IPR 525 at 551 [117]
65. ViaCyte opposed claims 1-10, 12-13 and 15-16 on the basis of utility, submitting that the specification does not teach the skilled addressee how to perform the invention for cells other than mouse cells. Specifically, homologous recombination into non-expressed genes in human ES cells could not be achieved at the filing date of the application.
In addition, based on Dr D’Amour’s observation at [13] that the claims encompass homozygous brachyury knockouts that would not differentiate into the claimed cell populations, ViaCyte submitted that the claims encompass matter that would render the invention inutile.
Homologous recombination of human ES cells
66. I have found above that ViaCyte have not established that the principles taught by the specification and exemplified in mouse ES cells could not be successfully applied to human ES cells. The specification teaches the utility of the claimed invention in generating differentiated cells for cell replacement therapies[52]. Prima facie the claimed invention is useful.
[52] Description page 12, lines 9-10
Homozygous brachyury knockouts
67. I agree that a claimed invention would lack utility if, on a proper construction, it encompassed the use of ES cells in which the selectable marker gene is incorporated into, and consequently inactivates (knocks out), both brachyury loci.
68. The specification teaches that mice heterozygous for a mutant brachyury gene are viable. However, homozygous mutants are not viable and display defects in the development of posterior mesodermal tissues[53]. Consistent with the viability of the heterozygous animals, recombinant ES cells in which one brachyury allele is inactivated are viable and develop and differentiate normally[54]. The specification explicitly defines the successfully targeted ES cell as “ES cells in which one brachyury allele is inactivated and GFP is expressed under the control of the brachyury regulatory elements”[55] (Emphasis added).
[53] Description page 6, line 33 to page 7, line 2
[54] Description page 8, lines 11-13
[55] Description page 8, lines 8-10
69. Dr D’Amour at [13], having explained the deleterious consequences of a homozygous knockout of the brachyury genes in an ES cell, states:
“From my understanding of embryonic stem cell differentiation and what I am taught in the Application, I would not expect these homozygous mutant cells to exhibit the in vitro developmental potential as required by the claims.”
70. Dr Colman at [26] states:
“… I understand claim 1 to refer to a cell in which a selectable marker is inserted into a single brachyury locus.”
71. It is clear that, in the context of the specification, both experts understand that a homozygous brachyury knockout would lead to an unworkable result. Therefore, the claims, construed in the context of the specification and from the perspective of a skilled addressee in a commonsense way, do not encompass the use of homozygous brachyury knockout ES cells. It follows that the claims do not lack utility on this basis.
72. Prima facie, the methods of the claimed invention do what was intended and claimed by the patentee. ViaCyte have not established that the opposed claims lack utility.
Conclusion
73. The opposition fails on all grounds.
74. Under the rules of the Federal Court, parties will have 21 days from the date of this decision to file a notice of appeal with the Court. Unless the Commissioner is served with a notice of appeal within 28 days of the date of this decision, I direct that the application proceed to sealing.
Costs
75. MSSM submitted that costs should follow the event, while ViaCyte made no submissions on costs. I see no reason to vary the usual practice. The opponent has been unsuccessful in its opposition and consequently I award costs according to Schedule 8 against ViaCyte, Inc.
Dr B. Akhurst
Delegate of the Commissioner of Patents
0
16
0