Regeneron Pharmaceuticals, Inc. v Merus N.V

[2017] APO 19

IP AUSTRALIA

AUSTRALIAN PATENT OFFICE

Regeneron Pharmaceuticals, Inc. v Merus N.V. [2017] APO 19

Patent:2009263082

Title:Antibody producing non-human mammals

Patent Applicant:                   Merus N.V.

Opponent:  Regeneron Pharmaceuticals, Inc.

Delegate:  Dr B. Akhurst

Decision Date:  5 May 2017

Hearing Date:  13 & 14 September 2016 in Melbourne, with additional evidence and submissions filed by the parties on 5 and 19 October 2016

Catchwords:  PATENTS – section 59 opposition to grant of a patent – grounds of novelty, inventive step, utility, fair basis, clarity, and definition of the invention – novelty – a prior disclosure of a transgenic mouse model provides a clear description of a transgenic mouse that in fact falls within the scope of opposed claims – other grounds unsuccessful – costs awarded – opportunity to amend.  

Representation:  Counsel for the applicant:  Christian Dimitriadis.

Patent attorneys for the applicant:  James Cherry and Adam Denley of Freehills Patent Attorneys.

Counsel for the opponent:  Ben Fitzpatrick.

Patent attorneys for the opponent:  Mark Wickham and David Longmuir of Phillips Ormonde Fitzpatrick.

IP AUSTRALIA

AUSTRALIAN PATENT OFFICE

Patent Application:                2009263082

Title:Antibody producing non-human mammals

Applicant:  Merus N.V.

Date of Decision:                   5 May 2017

DECISION

The opposition succeeds.  Claims 1-3, 5-7, 9-13 and 24-26 lack novelty.

Merus N.V has 2 months from the date of this decision to propose amendments to the claims.

Costs are awarded according to Schedule 8 against Merus N.V.

REASONS FOR DECISION

Background

1. Merus N. V. (the applicant) filed patent application 2009263082 on 29 June 2009, via the PCT, claiming priority from application PCT/NL2008/050430 filed on 27 June 2008.  Following examination, application 2009263082 was advertised as accepted on 20 March 2014. 

2. Regeneron Pharmaceuticals, Inc. (the opponent) filed a notice of opposition on 20 June 2014 and a statement of grounds and particulars (SGP) on 22 September 2014.  Evidence in support, answer and reply was completed on 22 December 2014, 2 June 2015 and 19 October 2015, respectively.  The matter was heard on 13 and 14 September 2016 at IP Australia’s Melbourne Patent Examination Centre. 

3. At the hearing, I gave the parties a period of time in which to file evidence and responding evidence on a particular point in relation to a document I had admitted into the hearing under reg 5.23.  This evidence was filed on 5 October 2016 and 19 October 2016, respectively.

   The Evidence

4. Evidence in support of the opposition consisted of declarations by:

   ·David Tarlinton dated 21 December 2014 (Tarlinton#1) with Exhibits DT-1 and DT-2;

   ·Anthony L. De Franco dated 21 December 2014 (DeFranco#1) with Exhibits ALD-1 to ALD-4; and

   ·Andrew Murphy dated 21 December 2014 (Murphy#1) and Annexure 1.

5. Evidence in answer consisted of declarations by:

   ·Robert Brink dated 30 April 2015 (Brink#1) with Exhibits RB-1 and RB-2;

   ·Robert Brink dated 2 June 2015 (Brink#2) with Exhibits RB-3 to RB-6;

   ·Peter Hudson dated 1 May 2015 (Hudson#1) with Exhibits PH-1 to PH-3;

   ·Peter Hudson dated 2 June 2015 (Hudson#2) with Exhibit PH-4; and

   ·Adam Denley dated 1 May 2015 (Denley) with Exhibits AD-1 to AD-7.

6. Evidence in reply consisted of declarations by:

   ·David Tarlinton dated 15 October 2015 (Tarlinton#2);

   ·Anthony L. DeFranco dated 18 October 2015 (DeFranco#2) with Exhibit ALD-5; and

   ·Christopher C. Goodnow dated 16 October 2015 (Goodnow#1) with Exhibits CCG-1 to CCG-2.

7. After the hearing, both parties filed evidence and responding evidence on 5 October 2016 and 19 October 2016, respectively on a particular point in relation to the journal article Sirac, C. et al. (2006) Blood 108: 536-543.  The opponent’s evidence and responding evidence in this regard consisted of declarations by:

   ·Christopher C. Goodnow dated 4 October 2016 (Goodnow#2) with Exhibit CCG-3;

   ·Anthony L. DeFranco dated 4 October 2016 (DeFranco#3) with Exhibits ALD-6 to ALD‑8; and

   ·Anthony L. DeFranco dated 18 October 2016 (DeFranco#4) with Exhibit ALD-9.

8. The applicant’s evidence and responding evidence consisted of declarations by:

   ·Robert Brink dated 4 October 2016 (Brink#3) with Exhibits RB-6 (second occurrence) to RB-9; and

   ·Robert Brink dated 19 October 2016 (Brink#4) with Exhibit RB-10.

9. During the evidentiary stages the applicant argued that Sirac, C. et al. (2011) Contrib. Nephrol. 169: 247-261 (Exhibit ALD-5) was part of evidence that was not properly in reply to the evidence in answer.  However, Prof DeFranco clearly relies on this document in responding to the applicant’s evidence where it challenges aspects of his evidence in support[1].  As such, I am satisfied that Prof DeFranco’s evidence relying on Exhibit ALD-5 is properly in reply to the evidence in answer.

   [1] DeFranco#2 at [70]-[73].

10. Attached to this decision as Annexure B is an extract from Exhibit ALD-3 to DeFranco#1, which is a technical primer that provides a basic summary of antibody structure and the processes involved in generating antibody diversity in an animal during B cell development.  I have corrected an error identified by Prof DeFranco[2] on page 3 of the document.  Regarding the statement on page 5 that in vivo antibody specificity will largely be a function of just rearrangement, Dr Hudson adds that where an antibody exhibits cross-reactivity with multiple antigens, then somatic hypermutation may also contribute to increased specificity[3].  In other respects, the information reproduced in Annexure B was not contentious and where I rely on it in this decision I have called it ‘the Primer’.

    [2] DeFranco#1 [55], [146].

    [3] Hudson#1 [23].

11. In his reply evidence, Prof Goodnow refers to a publication Phan et al. (2006) J Exp Medicine 203: 2419-2424 originating in Prof Brink’s lab[4].  However, Phan et al. is not in evidence, and in any event relates to a mouse model enabling laboratory-based investigations of the processes involved in B cell affinity maturation and differentiation, rather than antibody discovery, and is therefore of little relevance in the present context.  Consequently, I accord little weight this aspect of Prof Goodnow’s evidence.

    [4] Goodnow#1 [55], [105].

    Grounds of opposition

12. The grounds of opposition pressed by the opponent at the hearing were utility, novelty, inventive step and section 40 issues.

    Onus of Proof

13. The request for examination in relation to the patent application was filed on 12 November 2012.  As a consequence, the substantive amendments of the Patents Act (the Act) brought about by the Intellectual Property Laws Amendment (Raising the Bar) Act 2012 do not apply to the present patent application.  This includes the amendment to subsection 60(3A) that allows the Commissioner to refuse a patent application if satisfied on the balance of probabilities that a ground of opposition has been made out.  Instead, the onus of proof in this opposition proceeding lies with the opponent, who must establish that it is clear that a valid patent cannot be granted[5].

    [5] F.Hoffman-La Roche AG v New England Biolabs Inc [2000] FCA 283; 50 IPR 305 at [29], [67] and Commissioner of Patents v Sherman [2008] FCAFC 182 at [18], [22]; 79 IPR 426).

    The specification

14. The specification relates to antibody-producing non-human mammals[6].  The accepted specification ends with 11 Tables, 27 Figures and 31 claims.  These claims are reproduced at Annexure A to this decision. 

    [6] Opposed specification page 1, Title and para 1.

    Principles of construction

15. The principles for the construction of specifications are well established and were summarised by Middleton J in Eli Lilly and Company Limited v Apotex Pty Ltd[7]:

    “… the Court should, from the outset, approach the task of patent construction with a generous measure of common sense.  The Court must place itself in the position of a person skilled in the relevant art, being the subject matter of the patent.  From this perspective, the patent is to be read as a whole, in the context of the specification and in light of the prevailing common general knowledge and state of the relevant art at the priority date.”

    [7] [2013] FCA 214; 100 IPR 451 [139].

    The field of the invention

16. The technical field of the invention is identified on page 1 of the specification, as follows:

    “The invention relates to the production and use of non-human animals capable of producing antibodies or derivatives thereof, which are expressed from at least partially exogenous nucleic acids (transgenes).  Transgenes to produce such transgenic animals and methods to produce such heterologous antibodies; methods and vectors for producing such transgenic animals are disclosed.”[8]

    [8] Specification page 1.

17. Antibodies are proteins produced by B cells that identify and neutralize pathogens such as bacteria and viruses[9]. 

    [9] Consistent with the Primer page 4, para 3.

    The person skilled in the art

18. It is well established that many of the issues in an opposition are answered by reference to the person skilled in the art:

    “He is the person to whom the patent is addressed and who must construe it.  He is the person whose knowledge will determine whether a patent is novel.  He is the person who will judge whether a patent is obvious.”[10]

    [10] Root Quality Pty Ltd v Root Control Technologies Pty Ltd [2000] FCA 980; 49 IPR 225 at 241 [70].

19. The notional person skilled in the art is an artificial construct that is used as a tool of analysis which guides the court in determining, by reference to expert and other evidence, whether an invention as claimed does not involve an inventive step[11].  In general, the skilled person or addressee is the person who works in the art or science with which the invention is connected.  He or she is a person, or team, likely to have a practical interest in the subject matter of the invention, and while the skilled person may be assumed to be well-versed in the relevant art, such a person must be taken to be non-inventive.[12]

    [11] AstraZeneca AB v Apotex Pty Ltd [2015] HCA 30; (2015) 89 ALJR 798 at [23].

    [12] Root Quality Pty Ltd v Root Control Technologies Pty Ltd [2000] FCA 980; 49 IPR 225 at [71]-[72] referring to Catnic Components Ltd v Hill & Smith Ltd [1982] RPC 183 at 242 and General Tire [1972] RPC 457 at 485; Minnesota Mining [1980] HCA 9; 144 CLR 253 at 293 [119].

20. There was no dispute, and I agree, that each of the declarants in this opposition has experience and expertise relevant to establishing the knowledge of the relevant person skilled in the art.

    The description of the invention

21. As background to the invention, the specification summarises the role of B cells in the immune system and the structural features of the antibodies.   Briefly, B cells mediate humoral immunity by producing specific antibodies.  It is convenient to note here that the ‘specificity’ of an antibody refers to its selectivity for a particular antigen[13], whereas ‘affinity’ refers to the strength of the interaction between the antibody’s antigen binding site and the epitope it binds[14].

    [13] The Primer page 5, section (e) first para.

    [14] The Primer page 5, section (e) first para.

22. A mammalian antibody (Ab), also known as an immunoglobulin (Ig), consists of a complex of two identical heavy chain polypeptides and two identical light chains (LC) polypeptides, these last being of either kappa (k) or lambda (l) type.  A variable (V) region (domain) appears at the amino terminus of each of the heavy and light chains (abbreviated to V_H and V_L, respectively), within which three ‘complementarity determining regions’ (CDRs) have the greatest amino acid sequence variability.  The amino acid sequence of the remaining part of the heavy and light chains is relatively constant and is named the constant (C) region, accordingly.  In the antibody, the heavy and light chain variable regions (or variable domains) are juxtaposed and their CDRs interact to form the potential antigen-binding site.

23. Diversity in antibody structure is achieved cumulatively by several mechanisms, including gene rearrangement and somatic hypermutation[15].  The gene rearrangement process during pre-B cell differentiation involves recombination of immunoglobulin gene segments (V, D and J gene segments for the heavy chain and V and J gene segments for the light chain), which generates combinatorial diversity in the antibodies produced by B cells[16].  Additional diversity may be derived from pairing of different heavy and light chain variable regions[17].  Collectively this yields a primary repertoire of antibodies encoded by germline gene segments and expressed by newly-formed B cells[18].  Subsequently, when a B cell first encounters an antigen to which it binds, it may be activated and go on to secrete the cognate antibody[19].  These activated B cells can then target the somatic hypermutation process to the rearranged gene segments in the heavy and light chain genes, allowing the production of daughter cells making variant antibodies, facilitating affinity maturation – the production and selection of high affinity antibodies for an antigen [20].

    [15] Specification page 1, and page 2, lines 9-10 (which is consistent with the Primer, page 1 part (b)).

    [16] Specification para bridging pages 1-2.

    [17] Specification page 2, para 1.

    [18] Specification page 2, para 1.

    [19] Specification page 2, para 2.

    [20] Specification page 2, para 2, lines 22-24.

24. The specification notes there were high expectations for monoclonal antibodies (mAbs) as targeted therapeutics for human disease[21].  However, a major impediment to using non-human antibodies is their immunogenicity in humans[22].  This had been decreased, but not prevented, by humanisation or de-immunisation strategies, some of which have adversely affected binding affinity[23].  Phage display technology, using libraries of human antibody heavy and light chain variable regions, had complemented and extended the ‘humanisation’ approaches to developing less immunogenic therapeutic antibodies[24].  Transgenic mouse strains producing human antibodies in the absence of mouse antibodies provided another platform for generating specific and high affinity human antibodies[25].  However, the immunogenicity data for two ‘fully human’ mAbs produced by transgenic mice had not established this class as any less immunogenic than humanised mAbs[26]. 

    [21] Specification page 2.

    [22] Specification pages 2-3.

    [23] Specification pages 3-5.

    [24] Specification page 5, para 1. 

    [25] Specification page 5, para 2.

    [26] Specification page 5, para 2 and page 6, paras 1-2.

25. The specification goes on to identify a remaining need in the art for “a method and means for producing antibodies that are specific for their targets, but are less immunogenic” [27]. According to the invention the reduction of immunogenicity is at least partially achieved by providing a transgenic non-human mammal comprising, at least in its B cell lineage, a nucleic acid encoding at least an immunoglobulin light chain or heavy chain, wherein the heavy- or light chain encoding sequence is provided with a means that renders it resistant to DNA rearrangements and/or somatic hypermutations, preferably such a non-human animal is a rodent, more specifically a mouse. The nucleic acid preferably encodes a human, human-like or humanized immunoglobulin chain.”[28]  The specification identifies the ‘ultimate goal’ of the invention as the production antibodies to be used in human therapeutics[29].  To this end, methods are disclosed for producing a desired antibody from an immunised transgenic murine mammal[30].     

    [27] Specification page 6, para 3.

    [28] Specification page 6, para 3.

    [29] Specification page 15, para 4.

    [30] Specification pages 15-16.

26. The specification contains 22 examples.  Examples 1-16 describe the protocols and materials used to generate transgenic mice, and Examples 17-22 describe their characterisation and potential applications[31].  Most relevant to this opposition are Examples 18 and 22.

    [31] Brink#1 [19]; DeFranco#1 [37]-[40].

27. Example 18 discloses a mouse heterozygous for a transgene comprising the human light chain kappa V1-39 gene segment and a rat kappa constant region (together ‘IGKVl-39/rat Ckappa’)[32].  B cell-specific transgene expression is achieved using a Cre-lox system activated by the CD19 promoter[33].  Evaluating transgene expression during B cell development, Example 18 concludes that the IGKVl-39/rat Ckappa transgene expressed from the mouse’s Rosa locus facilitates timely, B cell-specific expression of a transgenic light chain which is capable of pairing with a normal repertoire of murine heavy chains[34].  The expert evidence confirms that Example 18 demonstrates B cell-specific expression of the transgene and that the transgenic light chain is displayed on the B cell surface paired with an endogenous heavy chain[35].

    [32] Brink#1 [22].

    [33] Specification page 60, lines 26-28.

    [34] Specification page 63, para 1.

    [35] DeFranco#1 [42]; Hudson#1 [33]-[35]; Brink#1 [77].

28. Example 22 is titled “Isolation, characterization, Oligoclonics formatting and production of antibodies targeting human IL6 for treatment of chronic inflammatory diseases such as rheumatoid arthritis”.  It describes the use of the transgenic mice immunised against IL-6 antigen, as the source of a repertoire of heavy chain variable regions which are paired back to the original human IGKVl-39/rat Ckappa light chain.  After an analysis of binding specificity, mixtures of monoclonal and bispecific antibodies are produced each of which include the pre-rearranged transgenic light chain and various mouse heavy chains that were selected as pairing with the transgenic rearranged light chain to form antibodies that bind epitopes of human IL-6[36].  Example 22 also refers to humanising the heavy chains of lead antibodies[37].

    [36] DeFranco#1 [44]; Hudson#1 [42]; and consistent with Brink#1 [26].

    [37] Specification page 73, lines 5-12; Brink#1 [26].

    The claimed invention

29. The principles to be applied in construing the claims are well settled in law and were summarised by Bennett J in H Lundbeck A/S v Alphapharm Pty Ltd[38].  Most relevantly, the words in a claim should be read through the eyes of the skilled addressee in the context in which they appear.  Words used in a specification, including the claims, are to be given the meaning which the person skilled in the art would attach to them, having regard to his or her own general knowledge and to what is disclosed in the body of the specification.   While the claims define the monopoly claimed in the words of the patentee’s choosing, the specification should be read as a whole.  It is not permissible to read into a claim an additional integer or limitation to vary or qualify the claim by reference to the body of the specification.  However, terms in the claims that are unclear may be defined or clarified by reference to the body of the specification.  The construction of a specification, including the claims, is ultimately a question of law for the decision maker.

    [38] [2009] FCAFC 70; 81 IPR 228 at [118]-[120].

30. Where the construction of a claim was in dispute I have addressed this below.  Claim 1 is the only independent claim.  

    Claim 1

    A transgenic murine mammal comprising, integrated in its genome, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region, wherein said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, murine mammal, such that variety in specificity of antibodies is retained through rearrangements and hypermutations in the heavy chains, and wherein said light chain further comprises a murine light chain constant region.

    A transgenic murine mammal …

31. The term ‘murine’ relates to the rodent family Muridae, which includes mice and rats[39].  Thus, the murine mammal of claim 1 encompasses a mouse, rat or any other murid mammal.  

    [39] Murphy#1 [7]; and consistent with the experts statements at DeFranco#1 [49], Hudson#1 [77], Goodnow#1 [56].

1. A ‘transgenic’ animal is produced by the artificial insertion of genetic material not normally present in (i.e. exogenous to) that animal[40].  The exogenous genetic material in claim 1 is the “nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region”.  Dependent claims 5-8 and 13-19 further characterise the nucleic acid molecule in terms of its structure and additional regulatory elements.  For convenience in this decision, I will refer to any one of these exogenous nucleic acid molecules as ‘the transgene’.  This term encompasses the nucleic acid molecules specified in claims 1 and 13-15 which encode the rearranged human immunoglobulin light chain variable region, together with any associated regulatory elements, leader sequences and/or constant regions such as those explicitly identified in claims 7-8, 16-19.  It also encompasses the associated expression cassettes and constructs disclosed in the specification. 

   … comprising, integrated into its genome, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region … and wherein said light chain further comprises a murine light chain constant region.

   [40] Consistent with the specification page 1, para 1.

2. This phrase was not contentious.  Above, I have summarised the immunoglobulin gene rearrangement process and its contribution to achieving antibody diversity in an organism and in determining the specificity of any given antibody.  Consistent with the expert evidence[41], the requirement in claim 1 that the nucleic acid molecule encodes “a rearranged human immunoglobulin light chain variable region” means that it comprises a nucleotide sequence the same as that of a human immunoglobulin light chain gene that has undergone V-J recombination.

   [41] Dr Hudson describes the nucleic acid molecule as having “a sequence of human immunoglobulin light chain V and J gene segments stitched together” (#2 [15]). Prof DeFranco refers to the human light chain gene sequence as “pre-rearranged” or “pre-selected rearranged” (#1 [27] [91]). Prof Tarlinton views claim 1 as referring to a mouse “in which there is an existing human rearranged light chain variable region that is used in the generation of the animal”.(#2 [18]).

3. The light chain further comprises “a murine light chain constant region”, which phrase encompasses an endogenous murine constant region or, as in the exemplified transgenic mouse, a light chain constant region from another murid mammal such as a rat[42]. 

   … wherein said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, murine mammal …

   [42] DeFranco#1 [49]; Goodnow#1 [56] and consistent with Tarlinton#2 [18].

4. A light chain variable region ‘capable of’ pairing, means it ‘has the ability to’ or ‘is suitable for’ pairing[43]. 

   [43] Hudson#2 [13]; DeFranco#1 [121]; and consistent with Brink#1 [59] and the plain meaning of the term.

5. The limitation imposed by the word ‘pairing’ was contentious at the hearing.  The applicant distinguished an ‘association’ of light and heavy chain variable regions to form a basic structure that may or may not be functional, from the ‘pairing’ of these polypeptides to form functional antigen binding sites.  The applicant argued that the reference in claim 1 to ‘pairing’ of light and heavy chain variable regions, requires the rearranged light chain variable region to ‘productively’ pair with at least two different heavy chain variable regions from the transgenic murine mammal such that a functional antigen binding site is formed.  The opponent responded that there was no basis in the evidence for this distinction.    

6. It is convenient at this point to provide some background regarding the antibody-producing B cells.  The life of a B cell can be divided into two distinct stages - B cell maturation is followed by B cell differentiation.  The information in the Primer and Prof Tarlinton’s evidence[44] regarding the B cell maturation process is not disputed by the applicant’s experts.  B cell maturation takes place in the bone marrow and generates naïve B cells (i.e. B cells that have not been exposed to antigen) from haematopoietic stem cells.  Relevantly, ‘productive’ rearrangements of the heavy and light chain V(D)J gene segments give rise to the B cell receptor, which has essentially the same structure as the antibody a B cell is capable of producing[45].  Cell surface expression of a B cell receptor allows an immature B cell to progress to the next stage of development[46].  In contrast, ‘non-productive’ rearrangements lead to a non-functional B cell receptor, which renders the B cell unable to survive[47].  The B cell maturation process takes place in the absence of antigen and generates the primary B cell repertoire which, once purged of auto(self)-reactive B cells, exit the bone marrow and enter the peripheral lymphocyte pool where they are available to respond to exogenous antigen[48].

   [44] Tarlinton#1 [24]-[27].

   [45] Tarlinton#1 [26]; the Primer page 3, paras 1-2.

   [46] Tarlinton#1 [26]; the Primer page 3, paras 2.

   [47] Tarlinton#1 [26]; the Primer page 3, para 2.

   [48] Tarlinton#1 [25]-[26]; the Primer page 3, para 2.

7. Claim 1 explicitly requires that variety in antibody specificity is retained in the transgenic mouse, albeit as a function of the heavy chains.  It follows that the antibody repertoire produced by the transgenic murine mammal of claim 1 potentially binds to a variety of different antigens[49].  However, until it is challenged with a cognate antigen, it cannot be definitively established that any naïve B cell expresses a B cell receptor (and thus is capable of producing an antibody) that will in fact bind an antigen[50].  Consequently, I prefer Dr Hudson’s construction of claim 1, reproduced below, which is not challenged by the opponent’s experts:

   “… in the context of claim 1, the rearranged light chain variable region must have the ability to form a functional antigen binding site with different heavy chain variable regions encoded by the transgenic animal.  In other words, the rearranged human variable light chain region can pair with at least two heavy chain variable regions encoded by the animal and the resulting light chain / heavy chain pairs can bind to an antigen under appropriate conditions.” [51] (Emphasis added.)

   Logically, the ‘appropriate conditions’ to which Dr Hudson refers must include the presence of a cognate antigen. 

   [49] Hudson#2 [14].

   [50] Hudson#1 at [50] “The primary selection for affinity is a random chance event that the [antibody] repertoire contains an antibody surface with sufficient amino acids compatible with binding to and not repelling the cognate antigen surface”; the Primer in the sentence bridging pages 3-4; and consistent with Brink#1 [29] first sentence “It cannot be reliably predicted whether the light chain or heavy chain variable regions or both, will contribute to binding an antigen until the interaction between an antibody and an epitope on an antigen is interrogated.”

   [51] Hudson#2 [13].

8. In the absence of any express reference to a cognate antigen, the Primer confirms that ‘productive’ immunoglobulin light chain gene rearrangements resulting in a functional light chain are confirmed in the body by the presence of a B cell receptor on the surface of a B cell[52].  The expert evidence is consistent with cell surface expression of a B cell receptor on a B cell being prima facie evidence that the heavy and light chains making up that B cell receptor are ‘paired’[53].  Accordingly, the opposed specification identifies surface expression of the transgenic light chain on a B cell as an indication that the transgenic light chain is capable of pairing with endogenous heavy chains in that cell[54].  

   [52] The Primer page 3 para 2.

   [53] Hudson#1 [35], referring to the results in Fig 27 of the opposed specification which “show that the rearranged human light chain variable region is expressed on the cell surface in the correct way by pairing with a heavy chain …”; Tarlinton#1 [58] “… only those B cells whose light chains pair with a heavy chain would make it out of the bone marrow.”; and consistent with DeFranco#1 [42] “It is important to note that for a light chain to be detected on the surface of a B cell, it must be paired with a heavy chain”; Brink#1 [23] - in the context of Example 18 of the opposed specification, Prof Brink notes the presence of the transgenic light chain on the B cell surface (as evidenced by detection of the rat kappa light chain constant region) and concludes that “the light chain containing the human light chain variable region is pairing with the endogenous mouse heavy chains”.

   [54] Specification Example 18, and in particular page 62, line 29 to page 63, line 6 - Prof DeFranco confirms same logic is used (#1 [112]).

9. Since the function of the B cell receptor and the antibodies the B cell produces depends largely on the antigen-specificity and affinity conferred by the light and heavy chain variable regions[55], I see no reason to distinguish the reference in claim 1 to pairing of light and heavy chain variable regions in particular, from references in the description and evidence to ‘productive’ or ‘functional’ pairing of light and heavy chains.  Accordingly, in the absence of clear evidence to the contrary, I consider it reasonable to proceed on the basis that the presence of a transgenic light chain on the surface of a B cell outside the bone marrow is sufficient to satisfy the requirement in claim 1 that the light chain variable region is capable of pairing with a heavy chain variable region in that cell.  It follows that determining whether a light chain variable region is capable of pairing with a heavy chain variable region does not require it to be established as a matter of fact that a B cell receptor expressed by a B cell, or an antibody produced by that B cell, would specifically bind to any particular antigen.

   [55] Consistent the Primer, page 1 section (a) para 2, and with Hudson#1 [77].

10. Insofar as the applicant characterised the invention as a “common light chain” mouse, the transgenic light chain in the murine mammal of claim 1 is only required to be common to “at least two” different heavy chains encoded by that mammal.

    … such that variety in specificity of antibodies is retained through rearrangements and hypermutations in the heavy chains …

11. This feature requires the murine heavy chain genes to be capable of rearrangement and hypermutation, which leads to diversity (variety) in antibody specificity (its selectivity for an antigen)[56].  Nevertheless, the terms of claim 1 do not preclude the possibility of further (secondary) rearrangements and/or somatic hypermutations in the light chain-encoding nucleic acid molecule[57].

    [56] Consistent with Hudson#2 [14].

    [57] Murphy#1 [9]; DeFranco#1 [48], #2 [40]; Hudson#2 [14]; Tarlinton#2 [67], [73]; Brink#4 [45].

    Claim 4

    A transgenic murine mammal according to any one of claim 3, wherein the integration is in the Rosa-locus.

12. A transgene inserted into the Rosa-locus will be ubiquitously and constitutively expressed in all cells of the transgenic murine mammal[58].

    [58] DeFranco #1 [34], [95]; Tarlinton#2 [29]; Goodnow#1 [62] and consistent with Brink #1 [60].

    Claim 5

    A transgenic murine mammal according to any one of claims 1-4, wherein the human immunoglobulin light chain variable region encoding nucleic acid molecule is provided with a means that allows expression of said nucleic acid molecule essentially limited to cells of B cell lineage.

13. The specification provides a dictionary for “essentially limited expression” [59] which accords with the expert’s understanding of the term[60].  Accordingly, claim 5 requires ‘the means’ to limit transgene expression predominantly to cells of the B cell lineage, but that lower levels of expression in other cells, as compared to the level of expression in B-cells, is possible[61]. 

    [59] Specification at page 8, lines 16-19.

    [60] Prof DeFranco (#1 [57]) and Prof Tarlinton (#2 [31]).

    [61] Specification page 8, lines 16-19.

    Claim 6

    A transgenic murine mammal according to claim 5, wherein the human immunoglobulin light chain variable region encoding nucleic acid molecule is provided with a means that allows expression of the light chain encoding nucleic acid molecule predominantly during a certain stage of the development of B cells.

14. The ‘means’ in claim 6 imposes a temporal limitation on transgene expression.  The opponent construed claim 6 as requiring a means that turns transgene expression on, and then off again, in order that expression occurs only during the certain stage of B cell development.  However, I am not satisfied that such a narrow construction is appropriate.  Insofar as the claim is ambiguous in this regard, references can be found in the specification to embodiments in which transgene expression is confined to a ‘certain period’ in the development of a cell[62].  However, the specification also refers to embodiments in which the transgene includes a means that either prevents it being silenced (i.e. once expression is turned on it stays on), or renders it resistant to silencing[63].   

    [62] Specification page 12, para 2 to page 13, para 2.

    [63] Specification page 11, paras 1 and 3; para bridging pages 14-15.

15. In construing claim 6, Prof Tarlinton equates ‘allowing’ transgene expression with ‘turning on’ its expression predominantly during a certain stage[64].  Likewise, both Dr Hudson and Prof Brink understand claim 6 to mean that transgene expression is turned on at a certain stage, rather than it necessarily defining a window during which expression occurs[65].  In contrast, and without reference to the word ‘allows’, Prof DeFranco construes claim 6 as requiring B cell-specific expression to occur predominantly during a certain stage of B cell development, and by inference not, or less, at other stages[66].  However, Prof DeFranco acknowledges that such a construction is confusing and inconsistent with what the inventors have done[67].  

    [64] Tarlinton#2 [33].

    [65] Hudson#1 [80]; Brink#1 [61]-[62].

    [66] DeFranco#1 [62].

    [67] DeFranco#1 [62], [65].

16. Balancing the evidence, a reasonable construction of claim 6 is that in addition to defining a window during which expression occurs it also encompasses a means that that simply allows transgene expression to commence predominantly during a certain stage of the development of B cells.  This latter construction is consistent with dependent claim 8, which specifies the means as a cre-lox system, which can switch on gene expression but cannot switch it off[68]. 

    [68] DeFranco#1 [69]; Hudson#1 [80]; Brink#1 [64].

17. B cell development is a continuum, and the maturation process involves pro-B cell, pre-B cell, immature B cell and mature/naïve-B cell stages[69].  In this context, the reference in claim 6 to ‘a certain stage’ of B cell development is ambiguous in that it does not explicitly identify any one or more stage(s) during which transgene expression should occur.  Where the claims are ambiguous, it is permissible to resort to the body of the specification to define or clarify the meaning of words used in the claims[70].  Assistance is provided on pages 12-13 of the specification which refer to embodiments in which the means is an expression cassette and the developmental period is chosen such that expression of (relevantly) a light chain polypeptide from the transgene:

    “… does not significantly interfere with the normal differentiation and/or maturation of the cell and when applicable, allows for pairing of the light chain with its heavy chain counterpart”[71].

    [69] Brink#1 [61]; Hudson#1 [80]; Tarlinton#1 [27].

    [70] Interlego AG v Toltoys Pty Ltd [1973] HCA 1; (1973) 130 CLR 461 at 479 [14].

    [71] Specification page 12 para 2, and para bridging pages 12-13.

18. Consistent with these requirements, in the context of promoter-driven transgene expression, the specification identifies a stage at which expression commences:

    “… said certain stage starts at a stage immediately preceding or coinciding with the onset of the expression of light chain molecules by said cells at a certain stage of development into a mature B cell.”[72]

    [72] Specification page 13 para 1.

19. Accordingly, I construe the “certain stage of the development of B cells” in claim 6 to be a stage during which transgene expression will not significantly interfere with the normal differentiation and/or maturation of the B cell and which would allow for pairing of the expressed light chain with a heavy chain counterpart.  The expert evidence establishes that these requirements will be met if transgene expression commences during the pro-B cell or pre-B cell stages of B cell development, and no later than the pre-B cell to immature B cell transition[73]. 

    [73] DeFranco#1 [63]-[64]; Hudson#1 [81]; Goodnow#1 [67]-[68]; Tarlinton#2 [33].

20. Thus, in its broadest embodiment, claim 6 simply requires the ‘means’ of claim 5 to turn on transgene expression predominantly during the pro-B cell or pre-B cell stages of B cell development and no later than the pre-B cell to immature B cell transition. 

    Claims 14 and 15

21. Claims 14 and 15 are both ultimately dependent on claim 1 via claim 13.  Claims 13-15 are reproduced below:

    13.  A transgenic murine mammal according to any one of claims 1-12, wherein the sequence of the light chain encoding sequence is a human vk sequence.

    14.  A transgenic murine mammal according to claim 13, wherein the light chain encoding sequence is a germline sequence.

    15. A transgenic murine mammal according to claim 14, wherein the germline sequence is based on O12.

22. Claim 13 specifies that the nucleic acid sequence of the transgenic light chain encodes a human kappa light chain variable region[74]. 

    [74] DeFranco#1 [39]; Tarlinton#2 [44]; Goodnow#1 [90].

23. Claim 14 is construed by the experts as defining a nucleic acid molecule encoding a rearranged human immunoglobulin kappa light chain variable region (in accordance with claims 1 and 13) in which there are no somatic mutations[75] and as a consequence it encodes the same amino acid sequence as a germline gene sequence [76].

    [75] DeFranco#1 [86]; Tarlinton#2 [44]; Goodnow#1 [93].

    [76] DeFranco#1 [86].

24. Claim 15 narrows the germline sequence to one based on O12.  ‘O12’ refers to a specific immunoglobulin gene rearrangement where the immunoglobulin kappa V1-39 segment is combined with the immunoglobulin Jk1 segment[77].

    [77] Specification page 14, lines 12-15; DeFranco#1 [87], which is consistent with Tarlinton#2 [45] and Hudson#1 [83].

    Utility

25. Paragraph 18(1)(c) of the Act provides that an invention, so far as claimed in any claim, must be useful.  In Artcraft Urban Group Pty Ltd v Streetworx Pty Ltd[78], the Full Court of the Federal Court distilled the basic principles of inutility down to two questions, which are:

    1.   What is the promise of the invention derived from the whole of the specification?

    2.   By following the teaching of the specification, does the invention, as claimed in the patent, attain the result promised for it by the patentee?

    [78] [2016] FCAFC 29 at [121].

26. There was no dispute that the invention disclosed and claimed in the specification is directed to a transgenic murine mammal that serves as a platform for antibody discovery.  This is consistent with the technical field of the invention which is described on page 1 of the specification as relating to the production and use of transgenic non-human animals capable of producing antibodies or antibody derivatives[79].

    [79] Specification page 1, lines 3-7.

    The promise of the invention

27. The opponent considered the principal promise of the invention to be decreased immunogenicity in the antibodies produced by the transgenic murine mammal, in accordance with the need in the art identified in the specification for specific but less immunogenic antibodies[80].  The opponent argued that where the claims encompass a human light chain variable region that may be subject to further rearrangement and somatic hypermutation, the claimed invention will not be useful for producing antibodies that are less immunogenic.

    [80] Specification page 6, lines 16-17.

1. The applicant submitted that therapeutic antibodies are not claimed as such, nor the additional steps necessary to arrive at an antibody that is suitable for administration to a human.  The applicant distinguished the production of antibodies (making large numbers of the same antibody), from the generation of antibodies (making a range of different antibodies with varying specificities from which a new antibody can be found), submitting that the opposed specification relates to the latter, and it is the end result that must be suitable for administration to humans, not necessarily the antibody achieved from the transgenic mouse.  

2. For the reasons that follow, the promise of the claimed transgenic murine mammal is that, once immunised, it is capable of generating specific and high affinity hybrid murid-human lead antibodies for a target antigen.  The specification does not promise that this mammal will necessarily produce an antibody product with a sufficiently low immunogenicity that it is suitable for administration to a human, without further engineering.

3. Most relevant to the features of claim 1, the specification states:

   “The present invention provides a transgenic non-human mammal comprising, at least in its B cell lineage, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region, wherein said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, non-human mammal.”[81]

   [81] Specification page 16, para 3.

4. This is immediately followed by:

   “The present invention provides transgenic non-human mammals, preferably mice, capable of generating specific and high affinity hybrid mouse-human antibodies with preferably human immunoglobulin light chain variable (VL) regions in or near germline configuration and preferably murine immunoglobulin heavy chain variable (VH) regions that may have accumulated somatic mutations during the process of antigen driven affinity maturation.  It is envisaged that the murine VH regions of the hybrid antibodies may be subjected to humanization procedures to yield mAbs that have reduced immunogenicity when applied in humans based on germline or near-germline VL regions and murine VH regions that have been humanized.” [82]

   [82] Specification page 16, para 4.

5. Properly construed, this last paragraph indicates that the transgenic mammals must be capable of generating specific and high affinity antibodies that are a hybrid of murine and human parts.  Less immunogenic germline or near-germline light chain variable regions are no more than a preferred embodiment, and humanisation of the heavy chains to reduce immunogenicity is optional.  This conclusion is supported by the applicant’s evidence reproduced below, which is not directly challenged by the opponent’s experts, that the antibodies produced by the transgenic mammal can be used a starting point from which to develop humanised (and therefore less immunogenic) antibodies:

   “While the antibodies generated from the transgenic animal may be used for direct clinical application it is highly likely that they will be subject to further modification such as a process of humanisation.”[83]

   “The antibody generated from the mouse could be exactly what is cloned from a B cell isolated from the animal or an antibody that has been further modified whether that be by a process for humanisation or formatting into a different antibody structure.”[84]

   [83] Hudson#1 [39].

   [84] Brink#1 [49].

6. Other parts of the specification also support a conclusion that the transgenic murine mammal need not necessarily produce an antibody product with all the characteristics required to make it suitable for therapeutic administration.  In particular, Example 22 discloses the use of the transgenic mammal as a source of a repertoire of heavy chain variable regions which are then assembled into antibodies with the original rearranged IGKV1-39 human light chain variable region[85].  This strategy, which requires additional work ex-vivo, ensures that any mutations introduced into the transgenic light chain by secondary rearrangement and/or somatic hypermutation during B cell differentiation in the immunised mammal, are not present in the antibody selected for therapy[86].  Example 22 also refers to humanising the heavy chains in a selected lead antibody[87].  Commenting on Example 22, Dr Hudson confirms that for antibody production purposes there are many different re-formatting options that could be taken[88]. 

   [85] Hudson#1 [42]-[43], [72]; Brink#1 [26]; DeFranco#1 [44].

   [86] Hudson#1 [43]; Brink#1 [26]; DeFranco#2 [16].

   [87] Specification page 73, lines 5-12; Brink#1 [26].

   [88] Hudson#1 [42].

7. Construed as a whole, the specification does not promise that the transgenic murine mammal will necessarily, without further intervention, produce an antibody with sufficiently low immunogenicity to be administered to a human.  This renders moot the opponent’s submissions for lack of utility based on a promise of antibodies with reduced immunogenicity. 

8. Relevant to the promise of the invention is the statement reproduced above, that the invention provides transgenic non-human mammals capable of generating specific and high affinity hybrid mouse-human antibodies[89].  Pages 26 and 28 of the opposed specification carry similar statements emphasising that the invention provides a platform for the generation of specific and high affinity antibodies[90].  In my view, this is the promise made for the transgenic non-human mammal - it must be capable of generating antigen-specific and high affinity murid-human lead antibodies in response to antigen.  

   By following the teaching of the specification, is the claimed transgenic murine mammal capable of generating specific and high affinity hybrid mouse-human lead antibodies against the antigen?

   [89] Specification page 16, lines 17-19.

   [90] Specification page 26, lines 9-11 & page 28, lines 19-21.

   Claims 1-10 - Silencing the endogenous light chain

9. The opponent submitted that without a requirement for silencing (i.e. preventing expression of[91]) the endogenous light chain loci, claims 1-10 encompass mice that are not useful for producing antibodies comprising the transgenic rearranged human light chain.  The applicant responded that while it would be useful to silence the endogenous light chain, it is not essential, and the expert evidence suggests it is not a problem for generating high affinity, antigen-specific antibodies.

   [91] DeFranco#1 [53].

10. What must be determined is whether a transgenic murine mammal in accordance with the invention is capable of generating specific and high affinity hybrid mouse-human lead antibodies in response to antigen, where it expresses both the transgenic and endogenous light chains. 

11. Many of the parties’ submissions on this point were based on the transgenic mouse disclosed in Example 18 of the specification that falls within the scope of claim 1[92], and the use it is put to in Example 22.  The cells of this mouse contain one copy of a transgene comprising a rearranged human kappa light chain variable region and a rat kappa constant region[93], and the majority of its B cells co-express the endogenous and transgenic light chains[94], resulting in a mixture of antigen-specific antibodies based on the endogenous light chain repertoire and the transgenic light chain[95].   

    [92] Specification page 60, lines 26-28.

    [93] Brink#1 [22].

    [94] DeFranco#1 [42]-[43], #2 [7]; Hudson#1 [84]; Brink#1 [22]; Goodnow#1 [39]-[41]; and consistent with Tarlinton#2 [10]-[11], [15], [42].

    [95] Example 18 and Figure 27; DeFranco#1 [36], [80]-[82]; Tarlinton#2 [42]; Goodnow [39].

12. Prof DeFranco provides a cogent argument that where both the endogenous and transgenic light chains are expressed in the mouse, the much greater diversity in the endogenous light chain repertoire and the antibodies they produce would provide them with “a large competitive advantage during the immune response to an antigen of interest, making it difficult to obtain high affinity antibodies comprising the transgenic light chain”[96].  Notwithstanding, in the context of Example 22, Prof DeFranco appears to accept that in vitro screening of the heavy chain repertoire would facilitate isolation of mouse heavy chains that pair with the original transgenic light chain and specifically bind the immunizing antigen[97].

    [96] DeFranco#1 [81], #2 [10]-[13].

    [97] De Franco#2 [16].

13. The applicant’s experts consider the claimed transgenic murine mammal useful in that, once immunised with an antigen, it can provide a repertoire of heavy chain variable regions for use in antibody engineering[98].  In this context, Prof Brink considers the strategy used in Example 22 a good approach to generating a bispecific antibody using the transgenic mice[99], and notes that once the repertoire of heavy chain sequences are obtained from the transgenic mouse, other options such as humanisation or antibody formatting could be applied.[100] Dr Hudson does not consider the presence of an endogenous light chain detrimental and he sees nothing in the results that suggest the mice are not useful for “immunization to generate high affinity leads” [101].

    [98] Hudson#1 [28]; Brink#1 [51].

    [99] Brink#1 [26].

    [100] Brink#1 [51].

    [101] Hudson#1 [76], [84].

14. Of the opponent’s experts, Prof DeFranco agrees that using the fixed rearranged light chain variable region has benefits in the context of generating oligoclonal or bispecific antibodies[102], and Prof Tarlinton appears of the same view with respect to oligoclonics[103].  I accord less weight to Prof Goodnow’s comments on the utility of the claimed transgenic mouse since he views it as the potential production system for therapeutic antibodies [104] which is inconsistent with the Example 22 disclosure.

    [102] DeFranco#2 [24].

    [103] Tarlinton#2 [73].

    [104] Goodnow#1 [81], [131].

15. Balancing the evidence, I am not satisfied that it is necessary to silence the endogenous light chain in order for the heterozygous transgenic mouse disclosed in the specification to be capable of generating antigen-specific high affinity lead antibodies for a target antigen, particularly for use in oligoclonics.  Thus, the claimed transgenic murine mammals do not lack utility for this reason.

    Claim 5 - B cell-specific expression of the transgene

16. The opponent submitted that claim 5 requires the light chain to be expressed in cells of the B cell lineage, which would be required in order for the alleged invention to work.  It argued that expressing the light chain in another cell type of a transgenic mouse would be of no use in the context of the opposed application.  Accordingly, it argued that claims not having this limitation lack utility.

17. Properly construed claim 5 narrows the scope of claims 1-4 by adding a means that restricts transgene expression essentially to cells in the B cells lineage[105].  It does not follow from claim 5 that the B cells of the transgenic murine mammals of the earlier claims do not express the transgene.  To the contrary, properly construed claims 1-4 encompass ubiquitous and constitutive expression the transgene in all cell types in that mammal[106]. 

    [105] DeFranco#1 [57]-[58]; Tarlinton#2 [31]; Goodnow#1 [64].

    [106] Consistent with DeFranco#1 [40], [55], [95].

18. While it can be inferred from Prof DeFranco’s evidence that this might be undesirable[107], I have no evidence before me establishing that the expression of redundant light chains in other cell types necessarily renders the claimed mammal incapable of achieving the promise of the invention.  To the contrary, Prof Brink states that it is possible that if the transgene was expressed in all cells the mouse would still develop normally[108] and this is not disputed by the opponent’s experts.  Consequently, I am not satisfied that the subject matter of claims 1-4 or any dependent claim lacks utility for this reason.

    [107] Consistent with DeFranco#1 [40], [55].

    [108] Brink#1 [60].

    Claim 6 - the certain stage

19. In the context of claim 6, the opponent submitted that there will be certain stages of B cell development during which if expression of the light chain begins, it will be too late to allow the light chain to form part of an antibody.  Furthermore, the promoters may not be active at certain stages or restricted to the immature stages of B cell development.  In these circumstances, the opponent argued that the invention will not work in the manner described in the opposed application.  The opponent submitted that the claims must incorporate some means for ensuring that the transgene is expressed in B cells at the appropriate developmental stage in order that the invention achieve the promised benefit.

20. I have construed claim 6 as limiting the ‘means’ of claim 5 such that transgene expression commences predominantly during the pro-B cell or pre-B cell stages of B cell development and no later than the pre-B cell to immature B cell transition, at which stage it does not significantly interfere with the normal differentiation and/or maturation of the B cell and allows for pairing of the light chain with a heavy chain counterpart.  In this circumstance, I have no reason to believe the transgenic mouse according to claim 6 would not achieve the promise of the invention.

    Utility summary

21. The opponent has not established that any claim lacks utility.

    Novelty

22. Paragraph 18(1)(b)(i) of the Act provides that an invention, so far as claimed in any claim, must be novel.  It is well established that the general test for anticipation is the reverse infringement test.  The classic formulation of this test is that given by Aicken J in Meyers Taylor Pty Ltd v Vicarr Industries Ltd[109]:

    “The basic test for anticipation or want of novelty is the same as that for infringement and generally one can properly ask oneself whether the alleged anticipation would, if the patent were valid, constitute an infringement”

    [109] [1977] HCA 19 [20]; (1977) 137 CLR 228 at 235.

23. This test is satisfied if the alleged anticipation discloses all of the essential features of the invention as claimed[110].  In AstraZeneca AB v Apotex Pty Ltd[111], the majority of the Full Court identified the principles in General Tire[112] as the criteria for determining anticipation by a prior publication.  Most relevant to the present circumstances are those are those relating to inherency and inevitable result:

    “When the prior inventor’s publication and the patentee’s claim have respectively been construed by the Court in the light of all properly admissible evidence ... the question whether the patentee’s claim is new ... falls to be decided as a question of fact.  If the prior inventor’s publication contains a clear description of, or clear instructions to do or make, something that would infringe the patentee’s claim if carried out after the grant of the patentee’s patent, the patentee’s claim will have been shown to lack the necessary novelty, that is to say, it will have been anticipated.  The prior inventor, however, and the patentee may have approached the same device from different starting points and may for this reason, or it may be for other reasons, have so described their devices that it cannot be immediately discerned from a reading of the language which they have respectively used that they have discovered in truth the same device; but if carrying out the directions contained in the prior inventor’s publications will inevitably result in something being made or done which, if the patentee’s patent were valid, would constitute an infringement of the patentee’s claim, this circumstance demonstrates that the patentee’s claim has in fact been anticipated.

    … To anticipate the patentee’s claim the prior publication must contain clear and unmistakable directions to do what the patentee claims to have invented ... a signpost, however clear, upon the road to the patentee’s invention will not suffice. The prior inventor must be clearly shown to have planted his flag at the precise destination before the patentee.”

    [110] Nicaro Holdings Pty Ltd v Martin Engineering Co [1990] FCA 40; (1990) 91 ALR 513 at 517 [19].

    [111] [2014] FCAFC 99 at [293].

    [112] [1972] RPC 457 at 486.

24. The opponent relied on two prior art documents to establish lack of novelty, which are:

    Sirac, C. et al. (2006) Blood 108: 536-543 (Sirac)

    WO 2006/117699 A2 (Innate Pharma S.A. & Inserm (Institut national de la santé et de la recherché medicale)) 9 November 2006 (WO’699)

25. The priority date of the opposed application was not in dispute.  Sirac and WO’699 form part of the prior art base.  However, although they were mentioned in and filed with the SGP, these documents have not been filed as evidence in this opposition.  Nevertheless, copies of Sirac and WO’699 are available in the patent office and both parties had access to them.  The experts have addressed Sirac and WO’699 in the evidence in support, answer and reply, as did the parties in their written submissions filed prior to the hearing.  Thus at the hearing, pursuant to reg 5.23, I gave the parties notice that I intended to consult WO’699 and Sirac and they could make any further representations about these documents at the hearing.

26. Consistent with my advice to the parties on 11 November 2016, in considering the inherent characteristics of the transgenic mice disclosed in Sirac, I have had regard to the following additional publications by the same research group that further characterise these mice:

    Sirac, C. et al. (2011) Contrib. Nephrol. 169: 247-261 (Sirac 2011);

    Sirac, C. et al. (2006) PNAS 103(20): 7747-7752 (Sirac PNAS); and

    Aucouturier, P. et al. (1993) J. Immunol. 150(8): 3561-3568 (Aucouturier).

27. Sirac 2011 was filed with the reply evidence as Exhibit ALD-5.  Sirac PNAS and Aucouturier (Exhibits CCG-3/ALD-6 and RB-10, respectively) were filed under the provisions of reg 5.23(2)(c), in response to my direction of 16 September 2016 allowing the parties to file further information and/or submissions regarding the specificity and use of the B220 marker in the flow cytometric analyses that are disclosed in Sirac and which form the basis for Figures 2 and 6 in that document.

28. Although Sirac 2011 was published after the priority date of the opposed application, it relates to the transgenic mouse model disclosed in Sirac[113] and provides additional information regarding the inherent characteristics of these mice.  Thus, contrary to the applicant’s submission, Sirac 2011 is admissible in this opposition, insofar as it is relevant to establishing factual matters regarding the transgenic mice disclosed in the earlier Sirac document.

    [113] Goodnow#2 [14]; DeFranco#3 [23]; Brink#4 [37].

29. For convenience, I have divided claim 1 into three parts for consideration of novelty and inventive step, based on the genetic and functional characteristics of the transgenic light chain and the result to be achieved.

    Sirac

30. The opponent submitted that claims of the application lack of novelty in light of Sirac. 

31. This journal article is titled “Role of the monoclonal k chain V domain and reversibility of renal damage in a transgenic model of acquired Fanconi syndrome”.  Fanconi Syndrome in humans typically arises as a complication of excess free monoclonal immunoglobulin kappa light chains produced by malignant plasma B cells in the subject, which crystallise in the proximal tubule cells (PTCs) of the kidney causing generalised renal dysfunction[114].  Seeking to make a mouse model of Fanconi Syndrome[115], the Sirac researchers replaced part of the endogenous mouse kappa light chain gene with a human VkJk rearranged gene segment dubbed the ‘CHEB’ variable region signifying the patient with myeloma-associated Fanconi Syndrome from which it was derived[116].  The resulting transgene encodes a hybrid kappa light chain comprising the endogenous mouse kappa constant region linked to the human CHEB variable region, which I will refer to in this decision as the ‘k-CHEB light chain’. 

    [114] Sirac, the Abstract; Hudson#1 [61]; Brink#1 [36].

    [115] Tarlinton#1 [56].

    [116] Sirac Abstract, page 537 para 1 and Figure 1; DeFranco#1 [109].

1. The Sirac authors then created mice homozygous for (i.e. having two copies of) the transgene (which they identify as‘k-CHEB’ or ‘k-CH’ mice) and subsequently, by deleting one copy, hemizygous mice (‘k-C/k‑D’ mice)[117].  I will refer to the homo- and hemizygous mice collectively as ‘the Sirac k-CHEB mice’.  There was no possible expression of endogenous kappa light chains in these transgenic mice[118] and expression of the k-CHEB light chain was associated with nephrotoxic effects similar to those seen in humans with Fanconi Syndrome [119]. Normal litter mates served as Controls[120].  Sirac also reports data for intermediate transgenic ‘k-NH’ mice which retain the complete gene targeting cassette[121] and as a consequence demonstrate poor expression of the kappa light chain[122]. 

   [117] Sirac Abstract, page 537 para 1 and Figure 1; DeFranco#1 [109].

   [118] Sirac PNAS Abstract; page 7748 right column, first full para; and consistent with DeFranco#2 [69], second sentence.

   [119] Sirac, Abstract; and consistent with Hudson#1 [60]-[61].

   [120] Sirac page 537, first sentence under the heading “ELISA assays”.

   [121] The Sirac Figure 2 legend and the 1st sentence under the heading ‘ELISA assays’ both indicate that the mice identified as k-NH mice are homozygous k-Neo mice.  Sirac page 537 Figure 1 and text under the heading ‘Gene targeting’ identifies the nature of the gene targeting construct (which comprises a LoxP-flanked neomycin resistance cassette upstream of a pVH promoter and the coding sequence of the rearranged VkJk CHEB gene segment, followed by a third LoxP site) and the resulting gene locus.

   [122] Sirac page 538 under the heading ‘Results’ states that the transgenic kappa light chain is poorly expressed when the neo^rcassette is still present.

2. Clearly, Sirac relates to a different field of research than the present patent application[123].  However, the transgenic murine mammal specified in claim 1 is not limited to any subsequent use.  For novelty purposes, the question is whether the transgenic mouse disclosed by Sirac fulfils the requirements set out in the applicant’s claims.  The genetic requirements in claim 1 are:

   “A transgenic murine mammal comprising, integrated in its genome, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region,   …  and wherein said light chain further comprises a murine light chain constant region.”

   [123] Consistent with Brink#1 [36], Hudson#1 [84].

3. Consistent with the evidence[124], there was no dispute that Sirac discloses a transgenic murine mammal comprising, integrated in its genome at the endogenous light chain locus, a nucleic acid molecule encoding part of a human immunoglobulin, and wherein the mammal’s light chain further comprises a murine light chain constant region.  

   [124] Sirac: the Abstract, page 537 para 1 lines 14-18, page 537 Material and methods section under the heading “Gene targeting” and Figure 1; and DeFranco#1 [109] & Tarlinton#1 [58]-[59] which is not disputed by the applicant’s experts.

4. The parties disagreed on whether the nucleic acid molecule encoded a ‘rearranged’ human immunoglobulin ‘light chain variable region’, with the applicant submitting that the k-CHEB light chain cannot be considered as such, given its unusual biophysical properties. 

5. In the following passages, the Sirac authors explicitly describe the nucleic acid molecule encoding the CHEB immunoglobulin light chain variable region, as both ‘rearranged’ and encoding a ‘human variable domain’: 

   “… we have generated a transgenic model by targeted insertion of the rearranged VkJk gene CHEB in the k locus.  These mice express a hybrid k Ig LC comprising the human V domain and the mouse C region.” [125]

   “We engineered transgenic mice in which the endogenous mouse Jk cluster was replaced by a rearranged gene cloned from a patient with smoldering myeloma-associated [Fanconi Syndrome]”[126]

   [125] Sirac, page 537 para 1, lines 14-18.

   [126] Sirac Abstract.

6. Three of the opponent’s experts repeatedly describe the k-CHEB variable region in the transgene as ‘rearranged’[127] - many of those references appear in the supporting evidence and are not disputed by the applicant’s experts[128]. Prof Tarlinton and Prof DeFranco understand the transgenic k-CHEB light chain to encode a human immunoglobulin light chain variable region [129]. Dr Hudson and Prof Brink acknowledge the ‘human light chain variable region’ encoded by the transgene, albeit that they variously describe it as ‘aberrant’, ‘dysfunctional’, ‘unusual’ and not a ‘normal’ light chain variable region[130]. 

   [127] Tarlinton#1 [58]-[59], #2 [86]-[87]; DeFranco#1 [109], [120]-[121], #2 [59]-[60], [62]-[63], [67]; Goodnow#1 [113]-[115].

   [128] Dr Hudson#1 [64] comments explicitly on Prof Tarlinton’s evidence at [58].

   [129] DeFranco#1 [107], [109]; Tarlinton#1 [58], #2 [87].

   [130] Hudson#1 [61]-[62]; Brink#1 [37], [39], [41].

7. Based on the explicit disclosure in Sirac and the expert evidence, I find that Sirac discloses a transgenic murine mammal comprising, integrated in its genome, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region, wherein said light chain further comprises a murine light chain constant region.  The nature of this light chain is best dealt with in the context of the functional requirements of the k-CHEB light chain variable region set out in claim 1, which are:

   “…said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, murine mammal …”

8. There was no dispute that the CHEB light chain variable region expressed by Sirac’s k-CHEB transgenic mice is unusual in that it is resistant to proteolytic digestion[131] and is able to form dimers and higher order crystal structures which accumulate in the PTCs of the kidney[132] reproducing the renal manifestations of Fanconi Syndrome[133].  

   [131] Sirac page 536 second column; Hudson#1 [61]; Brink#4 [13].

   [132] Sirac page 536 right column; Tarlinton #1 [56], [60]; Hudson#1 [61].

   [133] Sirac page 537 para 1; Hudson#1 [60]-[61]; Brink#1 [36], #4 [6].

9. It is convenient to note here that although much of the parties submissions and evidence in relation to the Sirac transgenic mice were directed to whether B cell development was ‘normal’ or ‘not normal’ in these mice, I do not consider it necessary to decide this point.  Notwithstanding its idiosyncrasies, what must be determined is whether the transgenic k-CHEB light chain variable region is capable of pairing with at least two different heavy chain variable regions in the k‑CHEB transgenic mice.  The opponent submitted that the skilled addressee would understand Sirac to implicitly disclose this feature.  The applicant’s submissions are essentially that the Sirac document does not disclose that the k-CHEB light chain will pair with at least two different heavy chain variable regions, and even if it would, it is unlikely to do so in such a way as to act as a functional antigen binding site.  In particular, the applicant argued that since the k-CHEB light chain is: (i) produced and secreted as a free light chain and has such a strong affinity for itself that it forms crystals; (ii) completely resistant to proteolytic digestion; and (iii) does not lead to allelic exclusion; it cannot be considered a functional light chain variable region.

10. In this regard, it is useful to consider the nature of the CHEB light chain variable region and its role in the pathological process leading to Fanconi Syndrome.  In Sirac, the authors refer to Aucouturier for this purpose[134].  Aucouturier details the cloning, sequencing and subsequent investigation of the monoclonal kappa light chain from the ‘CHEB’ patient with low-mass myeloma (a cancer of plasma B cells) causing Fanconi Syndrome[135].  In this patient, free kappa light chains were present in urine as monomers and dimers in equivalent amounts, without detectable polymers[136].  Protein fragments corresponding to the subsequently cloned CHEB variable domain (Vk fragments) were required in an appropriate excess for spontaneous crystallization to occur in vitro[137], and crystals morphologically similar to those found in the patient’s PTCs contained the Vk fragments and a low proportion of entire kappa light chain[138].  Since bone marrow cells expressed only full length RNA transcripts, the urinary Vk fragment was thought to be a post synthetic product[139], with the mostly membrane-bound intracellular crystals accumulating in proximal tubule cells in the kidney, macrophages and plasma B cells, as a result of intracellular degradation of the monoclonal kappa light chains leaving the intact Vk fragment which promoted auto-aggregation and crystallisation[140].  Thus, although the monoclonal kappa light chain in the CHEB patient is capable of self-dimerisation, it requires proteolytic digestion to free the variable domain fragment before crystallisation occurs.

    [134] Sirac, page 536 right column, lines 3-4; as noted by Prof Hudson at #1 [61].

    [135] Aucouturier Abstract and page 3562 right column, 3^rd full para. 

    [136] Aucouturier page 2564 last para.

    [137] Aucouturier page 3565 first full para, and last para bridging pages 3564-65, which is consistent with Sirac page 537, para 1.

    [138] Consistent with Aucouturier page 3565 first full para and last para bridging pages 3564-65, and confirmed by Sirac page 536, right column of the Introduction, first full para.

    [139] Aucouturier page 3566 para 1.

    [140] Aucouturier page 3566 left column and para bridging pages 3566-67, and consistent with Sirac page 536 in the Introduction.

11. In construing claim 1, I have found that the presence of a transgenic light chain on the surface of a B cell outside the bone marrow is prima facie evidence that the light chain expressed by that B cell (including its variable region), is paired with a heavy chain (including its variable region).  Nevertheless, I accept the applicant’s submissions that the potential for non-specific adsorption of the light chain onto the surface of splenocytes (spleen cells) and/or splenic B cell survival due to co-expression of lambda light chains (failure of allelic exclusion), must be considered when deciding whether or not the transgenic light chain is paired with heavy chains. 

12. The opponent relied on Figures 2 and 6 in the Sirac document to establish that the transgenic light chain variable region in the Sirac k-CHEB mice is capable of pairing with at least two different heavy chain variable regions.  These Figures are reproduced below.

    Figure 2:

13. The Figure 2 data is derived from assays employing an antibody that detects the presence of mouse kappa light chain constant regions[141].  This antibody will detect the transgenic kappa light chain as well as any endogenous kappa light chains[142].  

    [141] Sirac page 537, under the headings ‘Flow cytometric analysis’ and ‘ELISA assays’.

    [142] Consistent with Tarlinton#2 [112].

14. Figure 2A depicts the results of flow cytometric analysis of splenocytes, which are an heterogeneous group of cells comprising not just B cells but also other cells types, including T cells, NK cells, dendritic cells and macrophages[143].  For an analyte to be detectable in flow cytometry, it must be on the surface of the cells analysed[144].  It follows that the flow cytometric analysis presented in Figure 2A identifies any and all spleen cells having kappa light chains on the cell surface, whether this is achieved by the light chain pairing with a heavy chain or by other means such as non-specific adsorption of the light chain to the cell surface[145]. 

    [143] Brink#1 [42], #3 [3].

    [144] DeFranco#1 [110] and consistent with Tarlinton#1 [58]; Hudson#1 [87].

    [145] Hudson#1 [64], [87]; Brink#1 [39]; Tarlinton#2 [113].

15. Figure 2B presents the results of an immunoassay analysis detecting kappa light chains in mouse serum[146]. 

    [146] Sirac Figure 2 legend and page 537, under the heading ‘ELISA assays’.

    Figure 6:

16. Figure 6 relates to experiments undertaken on the homozygous k-CHEB mice before and after deletion from its genome of the gene sequence encoding the CHEB variable region.  As indicated in the Figure legend, Figure 6A demonstrates the presence of the transgene in the genome of homozygous mice at Day 0 and the subsequent deletion of its variable region by Day 4[147].  

    [147] This is evident from the loss of the larger 1.2 kb band in the transgenic k-CHEB light chain at days 4 and 10, which is replaced by a more prominent 0.4 kb band in lanes 8-9, which is equivalent to that seen in the homozygous k-Del mice (which lack a light chain variable region) in lane 3.

17. Figure 6B provides the results of flow cytometric analyses of splenocytes in the same mice staining for both the B220 marker and kappa light chains - the top right hand quadrant in each panel identifies the proportion of splenocytes that have both B220 and kappa light chains present on the cell surface. 

    Are the kappa light chains present specifically on the surface of B cells?

18. As noted above, the data presented in Figure 2 of Sirac was generated by detecting kappa light chains, while that in Figure 6B was the result of detecting both kappa light chains and B220 on the B cell surface.  Although B220 is commonly used as a B cell marker[148], its expression is not exclusive to B cells[149] and other B220-positive cell types are present in the spleen albeit at a much lower frequency than B cells[150]. 

    [148] Tarlinton#2 [118]; Goodnow#2 [4]; DeFranco#2 [60] & #3 [7].

    [149] Goodnow#2 [8]; Brink#3 [8], #4 [3]-[5]; DeFranco#2 [60], #3 [6].

    [150] Goodnow#2 [8]; DeFranco#3 [7].

19. Since B220-positive (B220⁺) splenocytes are not necessarily B cells, the applicant submitted that it is not possible to conclude from the Sirac data that the k-CHEB light chain is being detected specifically on the surface of B cells, rather that other cell types in the spleen.  In this regard the experts are divided.  The opponent’s experts understand Figures 2 and 6 in Sirac to demonstrate B cell-specific cell-surface expression of paired light and heavy chain variable regions in mice expressing the k-CHEB light chain[151].  The applicant’s experts consider an equally plausible interpretation of this data is that the transgenic light chain is adhering non-specifically to the cell surface of any one of the cell types in the splenocyte sample[152]. 

    [151] Tarlinton#1 [58], #2 [86], [89]-[90]; DeFranco#1 [110]-[111], #3 [9]-[11]; Goodnow#2 [5]-[9], [11].

    [152] Brink#1 [39], [42]; Hudson#1 [63]-[64], [87].

20. Whether or not the proportion of dual kappa⁺/B220⁺ splenocytes[153] reported in Sirac reflects the proportion of B cells present in the splenocyte sample is a factual matter, can be resolved by having regard to Sirac PNAS.  Sirac PNAS discloses flow cytometric analysis of splenocytes from the Sirac k-CHEB transgenic mouse model[154], detecting kappa light chains and the CD19 marker.  Consistent with the expert evidence[155], both parties acknowledge CD19 as a B cell-specific marker.  The comparative data from Sirac and Sirac PNAS is reproduced in the Table below.

    [153] That is splenocytes staining positive for both kappa light chains and the B220 marker on the cell surface.

    [154] Goodnow#2 [15]; DeFranco#3 [23]; Brink#4 [37].

    [155] Goodnow#2 [18]; DeFranco#3 [26], #4 [9]; Brink#3 [9].

Proportion of spleen cells expressing the marker(s)
Source	Marker(s) detected	Control mice	Hemizygous k-CHEB/k-Del mice	Homozygous k-CHEB mice
Sirac Fig 2A	k light chains	38%	19%	27%
Sirac Figure 6B (Day 0)	k light chains & B220	24.4%
Sirac PNAS Figure 1C	k light chains & CD19	43.7%	16.8%	23.7%

1. Sirac PNAS reports that approximately 44% of splenocytes in Control mice stain positive for both CD19 and kappa light chains, thus establishing the proportion of B cells in the splenocyte pool with kappa light chains on the cell surface[156].  For the transgenic mice, Sirac PNAS establishes that approximately 17% and 24% of splenocytes in mice hemizygous and homozygous for the k‑CHEB transgene, respectively, are B cells with k-CHEB light chains on the cell surface.  The data reported in Sirac is substantially consistent with that reported in Sirac PNAS[157], establishing that only a small proportion of kappa light chain-positive splenocytes in the mice hemizygous and homozygous for the k-CHEB light chain are other than B cells[158].  Thus, Sirac PNAS confirms the opinion of the opponent’s experts[159] that the transgenic k-CHEB light chains in the homozygous and hemizygous mice are predominantly present on the surface of B cells rather than any other cell type in the spleen[160]. 

   [156] Consistent with Goodnow#2 [18]; DeFranco#3 [26], #4 [9]; Brink#3 [9].

   [157] Goodnow#2 [16], [18]; DeFranco#3 [25]-[26].

   [158] Consistent with Prof DeFranco’s reasoning at para [10] of his third declaration, in the context of kappa light chain and B220 staining of splenocytes. 

   [159] Tarlinton#2 [117]; DeFranco#3 [13]-[16], #4 [9]; Goodnow#2 [13]. I accord less weight to Prof Brink’s contrary opinion (Brink#4 [7]-[8], [26]), which is based solely on his review of the Sirac data without regard to the corroborating information in Sirac PNAS.

   [160] Consistent with Goodnow#2 [16]-[18]; DeFranco#3 [25]-[26]; which is not directly disputed by Prof Brink in his responding evidence.

   Are the k-CHEB light chains simply adsorbed (adhered) onto the B cell surface?

2. I have found above that Sirac PNAS confirms essentially B cell-specific expression of the transgenic k-CHEB light chains in the k-CHEB mouse model disclosed in Sirac.  The opponent’s experts believe the Sirac data inconsistent with non-specific adsorption.  Having regard to (i) the serum levels of kappa light chains in the hemizygous and homozygous k-CHEB mice, (ii) the number of cells staining positive and (iii) the intensity of kappa staining depicted in Figure 2A for these mice, Prof Tarlinton concludes the only plausible explanation is actual surface expression of the light chain immunoglobulin on B cells[161].  Supporting this conclusion, Prof Goodnow and Prof DeFranco consider the rapid and substantial reduction in the proportion of dual kappa⁺/B220⁺ splenocytes demonstrated in Figure 6B[162] in response to deletion of the coding sequence for the CHEB variable region, is inconsistent with non-specific adsorption of the k-CHEB light chain to the cell surface and can only be explained by the k-CHEB light chains being produced by B cells and then pairing with heavy chains as a functional surface immunoglobulin[163].  

   [161] Tarlinton#2 [116]-[119].

   [162] From 24% on Day 0 down to 2% on Day 4 after deletion of the k-CHEB light chain variable region.

   [163] Goodnow#2 [13]; DeFranco#3 [13]-[16].

3. I am not persuaded otherwise by Prof Brink’s evidence, based on the Sirac data alone, that B-cell specific expression of k-CHEB light chains simply reflects non-specific adsorption onto the secreting B cell which is the cell in closest proximity to the light chain when it is secreted in free form[164].  Relevantly, Figure 2B in Sirac establishes that there are substantial serum levels of k-CHEB light chain in the transgenic mice, which would be available to deposit onto other cell types should non-specific cellular adsorption be occurring[165].  Prof Brink has provided no cogent explanation of why these circulating k-CHEB light chains would adsorb onto B cells but not, or to a much lesser extent, on other cell types in the splenocyte pool. 

   [164] Brink#4 [7].

   [165] Consistent with Tarlinton#2 [117]; DeFranco#3 [9], [10], [11] (first 2 sentences) and [13].

4. On balance, I am satisfied that the transgenic k-CHEB light chains in the Sirac k-CHEB mice are not to any relevant degree simply adsorbed onto the surface of either splenocytes generally or splenic B cells in particular.    

   Co-expression of lambda light chains (failure of allelic exclusion)

5. ‘Allelic exclusion’ is the process by which expression of a functional immunoglobulin light chain in a developing B cell prevents subsequent rearrangements and expression of the other light chain loci in that B cell[166].  A failure of allelic exclusion may be caused by a non-functional light chain, delayed onset of expression of the pre-rearranged transgenic kappa light chain or expression at too low a level[167], and leads to ‘light chain inclusion’ i.e. the presence in a single B cell of both kappa and lambda light chains[168].

   [166] DeFranco#1 [43], #2 [18]; and consistent with Brink#4 [40]-[44].

   [167] DeFranco#1 [43], #2 [18]; and consistent with Brink#4 [40]-[44].

   [168] Brink#4 [39].

1. Notwithstanding the opponent’s submissions, there are claims in the specification defining the monopoly sought by the applicant.  Above in this decision, I have construed the claims and found their scope capable of resolution.  Thus, the claims define the invention for the purposes of paragraph 40(2)(b).

   Fair basis

2. Subsection 40(3) relevantly requires that the claim or claims in a patent specification are clear and fairly based on the matter described in the specification.

3. As the test for fair basis, the High Court in Lockwood Security Products Pty Ltd v Doric Products Pty Ltd[267] (Lockwood) at [69] approved the words of Gummow J in Rehm Pty Ltd v Websters Security Systems (International) Pty Ltd[268]:

   “The circumstance that something is a requirement for the best method of performing an invention does not make it necessarily a requirement for all claims; likewise, the circumstance that material is part of the description of the invention does not mean that it must be included as an integer of each claim. Rather, 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.”

   [267] [2004] HCA 58; (2004) 217 CLR 274.

   [268] [1988] FCA 162; (1988) 81 ALR 79 at 95 [54].

4. In Lockwood, the High Court observed that the phrase “real and reasonably clear disclosure” compels attention “to the construction of the specification as a whole, putting aside particular parts which, although in isolation they might appear to point against the “real” disclosure, are in truth only loose or stray remarks”[269].  The High Court has also noted with approval[270] the following statement of principle by Barwick J in Olin Corporation v Super Cartridge Co Pty Ltd[271]:

   “The question whether the claim is fairly based is not to be resolved ... 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 being new, useful, and inventive, that is to say, the claim as expressed, travels beyond the matter disclosed in the specification.”

   [269] Lockwood No 2 [2004] HCA 58; (2004) 217 CLR 274 at [69].

   [270] Kimberly-Clark Australia Pty Ltd v Arico Trading International Pty Ltd [2001] HCA 8; (2001) 207 CLR 1 at 12 [15] and Lockwood No 2 [2004] HCA 58; (2004) 217 CLR 274 at [57].

   [271] (1977) 180 CLR 236 at [240].

5. The High Court in Lockwood also warned against the application of erroneous principles:

   “The comparison which s 40(3) calls for is not analogous to that between a claim and an alleged anticipation or infringement.  It is wrong to employ “an over meticulous verbal analysis”.  It is wrong to seek to isolate in the body of the specification “essential integers” or “essential features” of an alleged invention and to ask whether they correspond with the essential integers of the claim in question.”[272]

   [272] [2004] HCA 58; (2004) 217 CLR 274 at [68], referring to CCOM Pty Ltd v Jiejing Pty Ltd (1994) 51 FCR 260 at 281 per Spender, Gummow and Heerey JJ.

6. The opponent submitted that the claims are not fairly based insofar as they omit the following features:

   i.       the rearranged light chain-encoding sequence is resistant to further rearrangement and somatic hypermutation in order that the light chain polypeptide has the same fixed amino acid sequence and makes no contribution to variety in specificity; and

   2. the endogenous light chain is silenced. 

7. I will address each of these submissions in turn.

   Are the claims fairly based where they do not explicitly require that the rearranged human immunoglobulin light chain variable region is resistant to further (secondary) rearrangement and somatic hypermutation?

8. I have found above that the terms of claim 1 do not preclude the possibility of further (or secondary) rearrangements or somatic hypermutations in the light chain.  In this regard, the opponent submitted that the claims are not fairly based and travel beyond the the matter disclosed in the specification insofar as they do not expressly require, or provide means for ensuring, that the nucleic acid encoding the rearranged human light chain variable region is unable to undergo further (secondary) rearrangement or hypermutation.

9. I understand from its submissions that the opponent equates references in the body of the specification to the transgenic light chain-encoding molecule being resistant to rearrangement and/or somatic hypermutation, with the need to prevent these processes acting on the rearranged light chain.  Such a narrow construction is inconsistent with the plain meaning of ‘resist’[273], which does not necessarily require that a resisted action is ultimately prevented.  A more reasonable construction is that provided by Prof Brink who, in the context of rearrangement, understands a “resistance to” the process to mean the process is inhibited[274].  The quantum or degree of resistance is not defined in the specification, and it could encompass any amount from minor inhibition up to and including total inhibition (i.e. prevention) of rearrangements and/or somatic hypermutation.  

   [273] “To withstand, strive against, or oppose.” - The Macquarie Dictionary, Revised Edition 1985

   [274] Brink#2 [21], [22]-[24].

10. The opponent primarily relied on the following paragraph in the description to establish that the transgenic (rearranged) light chain specified in the claims must be prevented from undergoing both rearrangement and somatic hypermutation, in order that the specificity of the encoded antibody is purely a function of the heavy chain:

    “Preferably the immunoglobulin chain produced in a manner resistant to rearrangements and hypermutation is a light chain capable of pairing with different heavy chains encoded by the non-human mammal. The light chain will then be the same (and less immunogenic) in all antibodies, but variety in specificity is retained through rearrangements and hypermutations in the heavy chains.” [275] 

    [275] Specification page 9, lines 10-15.

11. In that paragraph and others[276], the description explicitly discloses preferred embodiments having an invariant ‘fixed’ light chain, as a result of the transgene being essentially incapable of undergoing further rearrangement and somatic hypermutation.  However, the description discloses additional and distinct embodiments of the invention, in which the means renders the transgenic light chain resistant to only one of these processes.  For example:

    “According to the invention the reduction of immunogenicity is at least partially achieved by providing a transgenic non-human mammal comprising, at least in its B cell lineage, a nucleic acid encoding at least an immunoglobulin light chain …, wherein the … light chain encoding sequence is provided with a means that renders it resistant to DNA rearrangements and/or somatic hypermutations, …”[277] (emphasis added)   

    “The invention further provides progeny of a transgenic non-human animal according to the invention, the progeny comprising, at least in its B-cell lineage, a … light chain encoding sequence together with a means that renders the sequence resistant to DNA rearrangements and/or somatic hypermutations.”[278] (emphasis added)

    [276] Specification page 14, lines 17-2; page 16, para 4.

    [277] Specification page 6, lines 18-24

    [278] Specification page 23, lines 9-13.

12. Relevant to somatic hypermutation during B cell development, the description discloses embodiments in which the transgenic nucleic acid sequences encoding the light chain variable region are characterized by “no or very few mutations” or that are “not or marginally subject to somatic hypermutation” (emphases added), from which I conclude that the light chain variable region need not necessarily be incapable of further rearrangement or somatic hypermutation.

13. Regarding rearrangement, where a light chain polypeptide having a rearranged human light chain variable region is capable of functionally pairing with an endogenous heavy chain in a B cell, further rearrangement of the already rearranged gene sequence is inhibited by innate mechanisms during the normal B cell maturation process[279].  To this extent, a rearranged light chain gene sequence is inherently resistant to further rearrangement[280].  Nevertheless, further rearrangements may occur (i) where the rearranged light chain does not pair functionally with a heavy chain[281], or (ii) as part of the editing process which is triggered in the event that an autoimmune response is generated by self-reactive antibodies[282].  The question is whether the potential for further rearrangement of the rearranged human light chain variable region renders the claim lacking fair basis? 

    [279] The Primer page 3 paras 1-2; and Brink#2 [24] and Hudson#2 [10], which is not disputed by the opponent’s experts.

    [280] Brink#2 [21], [24]; Hudson#2 [10], [15].

    [281] Primer page 3, first two paras.

    [282] Goodnow#1 [83]; and the Primer page 2 last para.

14. The specification explicitly discloses that strategies that prevent light chain rearrangements may also prevent the heavy chain rearranging, the latter being necessary in order to retain variety in antibody specificity in the mouse[283].  An alternative strategy disclosed in Example 22 of the opposed specification is to use the immunised transgenic mice as a source of a repertoire of heavy chain variable regions, which are paired back to the original human rearranged IGKV1-39 light chain variable region to identify those that bind the immunogen[284].  This circumvents the effect of any secondary rearrangement or somatic hypermutation of the transgenic light chains that may occur in the mouse[285].  It follows that in Example 22, the description provides a real and reasonably clear disclosure of a transgenic murine mammal in which rearrangement and somatic hypermutation of the heavy chain genes leads to variety in specificity of the antibodies in the mouse.  Although the transgenic light chain in these mice may also be subject to further rearrangement or somatic hypermutation, I have found above that this is not precluded by the opposed claims.

    [283] Specification page 7, para 3.

    [284] DeFranco#1 [44]; Hudson#1 [42]-[43], [79] (last two sentences), Hudson#2 [14]; Brink#1 [26]; Tarlinton #2 [16].

    [285] Consistent with Hudson#1 [43], #2 [14]; Brink#1 [26], #2 [14], Tarlinton#2 [72], and para [73] in the context of the Example 2 disclosure of oligoclonics.

15. Supporting this conclusion, I note that although Prof Tarlinton considers the focus of the invention to be “a mouse expressing a transgenic light chain that is unable to rearrange and/or somatically hypermutate”[286], he acknowledges this is not what the inventors have demonstrated in the specification and his opinion appears to be based on his view that such a mouse would be more beneficial[287].

    [286] Tarlinton#2 [12].

    [287] Tarlinton#2 [12], [16].

16. On balance, I am satisfied that the body of the opposed specification provides a real and reasonably clear disclosure of the transgenic murine mammal specified in claim 1, in which the rearranged human immunoglobulin light chain variable region is not necessarily resistant to further rearrangement and somatic hypermutation. 

    Are the claims fairly based where they do not explicitly require silencing of the endogenous light chain?

17. The opponent submitted that insofar as claims 1-10 do not require silencing of the endogenous light chain the claimed invention is not fairly based.  The opponent noted that Figure 27 of the opposed specification demonstrates that most of the B cells in the transgenic mice exemplified in the specification express both the transgenic and endogenous light chains, the latter of which will rearrange and somatically hypermutate and make no contribution to producing antibodies that are less immunogenic as a result of the non-immunogenic fixed light chain.  Responding, the applicant argued that silencing of the endogenous light chain is described as a preferred embodiment, which may be rendered unnecessary by allelic exclusion[288]. 

    [288] Specification page 9, lines 15-17.

18. Profs DeFranco and Tarlinton consider it important to silence the endogenous light chain loci, in order to maximise the production of antibodies including the transgenic light chain[289].  However, their evidence appears to view of the transgenic mouse necessarily as the antibody production system rather than as a source of heavy chains for further engineering.

    [289] DeFranco#1 [79]-[81]; and consistent with Tarlinton#1 [62] & DeFranco#1 [36].

19. As discussed above in this decision, Example 22 of the specification discloses that the transgenic mice, once immunised, can be used as a source of a repertoire of heavy chain variable regions, which are paired with the original human rearranged IGKV1-39 light chain variable region for subsequent identification of antibodies that bind immunogen [290]. The evidence establishes that the endogenous light chain loci are not silenced in these mice[291].

    [290] Hudson#1 [42]-[43], [79] (last two sentences); Brink#1 [26]; Tarlinton #2 [16].

    [291] DeFranco#1 [81]; and consistent with Tarlinton#1 [62] & DeFranco#1 [36].

20. I can only conclude that the specification provides a real and reasonably clear disclosure of the transgenic murine mammal specified in claim 1, in which the endogenous light chains are not silenced.

    Fair basis conclusion

21. The opponent has not established that any claim lacks fair basis.

    Clarity

22. Subsection 40(3) of the Act requires that the claim or claims of a specification are clear.  A claim is clear if a third party could ascertain, without difficulty, whether or not what he or she proposes to do would fall within the ambit of the claim (Monsanto Co v Commissioner of Patents (1974) 48 ALJR 59 at 60). However, a claim does not lack clarity because it uses inexact language or is difficult to construe, as long as it provides a workable standard suitable to the intended use (Minnesota Mining & Manufacturing Co v Beiersdorf (Australia) Ltd [1980] HCA 9; (1980) 144 CLR 253 at 274 [46]).

23. The opponent submitted that claims 6 and 14-15 lacked clarity.  Regarding claim 6, the opponent submitted that it is not clear what the term “a certain stage of the development of B cells” relates to.  The opponent noted that for the light chain to pair with a heavy chain and be part of an antibody of the mouse, the light chain must be expressed at the correct stage of B cell development, and then continue to be expressed throughout B cell development and as a consequence, it is important that the means allow expression over multiple stages. 

24. With respect to claims 14-15, the opponent submitted that the opposed specification refers throughout to ‘germline’ or ‘germline-like’ or ‘near germline’ or ‘germline gene (optimized)’.  It argued that whilst claims 14-15 simply refer to ‘germline’, the specification exemplifies light chain encoding sequences that would be considered ‘germline-like’, rather than strictly germline sequences that appear as they would in the endogenous germline from the human from which they are obtained. 

25. I have construed claims 6 and 14-15 above and have been able to give them a meaning.  In doing so I have addressed the opponent’s concerns regarding these claims.  Furthermore, I am satisfied that each of these claims provides a workable standard such that a third party could determine whether any proposed course of action would fall within the scope of one or more of these claims.

    Conclusion

26. The opposition is successful, claims 1-3, 5-7, 9-13 and 24-26 have been found to lack novelty.

27. It is usual in matters before the Commissioner that in the event that an opposition to the grant of a patent is successful, the applicant is allowed the opportunity to propose amendments to the claims.  Therefore, I will allow the applicant a period of time to propose suitable amendments.

    Costs

28. It is normal in matters before the Commissioner that costs should follow the event.  Although both parties sought an award of costs in their favour, the opponent has been successful in this opposition, and I consider it appropriate in the circumstances to award costs against the applicant.    

    Dr Barbara Akhurst

    Delegate of the Commissioner of Patents

    ANNEXURE A: The claims

    1.A transgenic murine mammal comprising, integrated in its genome, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region, wherein said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, murine mammal, such that variety in specificity of antibodies is retained through rearrangements and hypermutations in the heavy chains, and wherein said light chain further comprises a murine light chain constant region.

    2. A transgenic murine mammal according to claim 1, which is a mouse.

    3. A transgenic murine mammal according to claim 1, wherein the integration is in a locus that is resistant to silencing.

    4. A transgenic murine mammal according to claim 3, wherein the integration is in the Rosa-locus.

    5. A transgenic murine mammal according to any one of claims 1-4, wherein the human immunoglobulin light chain variable region encoding nucleic acid molecule is provided with a means that allows expression of said nucleic acid molecule essentially limited to cells of B cell lineage.

    6. A transgenic murine mammal according to claim 5, wherein the human immunoglobulin light chain variable region encoding nucleic acid molecule is provided with a means that allows expression of the light chain encoding nucleic acid molecule predominantly during a certain stage of the development of B cells.

    7. A transgenic murine mammal according to claim 6, wherein said means comprises a promoter selected from the group of CD19, CD20, μHC, VpreBl, VpreB2, VpreB3, l5, Iga, Igb, kLC, lLC, and BSAP (Pax5).

    8. A transgenic murine mammal according to claim 6 or 7, wherein said means comprises a cre‑lox system.

    9. A transgenic murine mammal according to any one of claims 1-8, wherein said light chain is capable of pairing with at least two murine heavy chains.

    10. A transgenic murine mammal according to any one of claims l-8, wherein said light chain is capable of pairing with at least two human heavy chains.

    11. A transgenic murine mammal according to any one of claims 1-10, wherein at least one of the endogenous loci encoding an endogenous light chain is functionally silenced.

    12. A transgenic murine mammal according to any one of claims 1-11, wherein the endogenous k light chain locus is functionally silenced.

    13. A transgenic murine mammal according to any one of claims 1-12, wherein the sequence of the light chain encoding sequence is a human vk sequence.

    14. A transgenic murine mammal according to claim 13, wherein the light chain encoding sequence is a germline sequence.

    15. A transgenic murine mammal according to claim 14, wherein the germline sequence is based on O12.

    16. A transgenic murine mammal according to claim 1, wherein the human immunoglobulin light chain encoding nucleic acid molecule comprises in 5’-3’ direction: a vk promoter, a human leader, a human V gene, optionally a MoEki enhancer, a rat constant region (k) and optionally a (truncated) MoEk3’ enhancer.

    17. A transgenic murine mammal according to any one of claims 1-15, which has been provided with an expression cassette which comprises in 5’-3’ direction: a Vk promoter, a leader, a human V gene, and a rat constant region (k).

    18. A transgenic murine mammal according to claim 17, which has been provided with an expression cassette which comprises in 5’-3’ direction: a Vk promoter, a leader, a human V gene, a MoEki enhancer, a rat constant region (k) and a MoEk3’ enhancer.

    19. A transgenic murine mammal according to claim 18, wherein the MoEk3’ enhancer is truncated.

    20. A method for producing a desired antibody comprising exposing a murine mammal according to any one of claims 1-19 to an antigen such that an antibody response is induced and isolating the antibodies specific for the antigen.

    21. A method for producing a desired antibody comprising exposing a murine mammal according to any one of claims 1-19 to an antigen such that an antibody response is induced and isolating cells producing such antibodies, culturing said cells and harvesting said antibodies.

    22. A method according to claim 21, further comprising immortalizing said cells prior to harvesting said antibodies.

    23. A method for producing a desired antibody comprising exposing a murine mammal according to any one of claims 1-19 to an antigen such that an antibody response is induced and isolating a nucleic acid molecule encoding at least part of such an antibody, inserting said nucleic acid molecule or a copy or a derivative thereof in an expression cassette and expressing said antibody in a host cell.

    24. Progeny of a transgenic murine animal according to any one of claims 1-19, the progeny comprising, at least in its B-cell lineage, a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region.

    25. A cell that is isolated from a transgenic murine animal according to any one of claims 1-19 or 24, the cell comprising a rearranged human immunoglobulin light chain variable region.

    26. A method for producing a transgenic murine mammal according to any one of claims 1-19, comprising inserting a nucleic acid molecule encoding a rearranged human immunoglobulin light chain variable region into the genome of said mammal, wherein said light chain variable region is capable of pairing with at least two different heavy chain variable regions encoded by said transgenic, murine mammal.

    27. A transgenic murine mammal according to claim 1, substantially as hereinbefore described.

    28. A method according to any one of claims 20 to 23, substantially as hereinbefore described.

    29. Progeny according to claim 24, substantially as hereinbefore described.

    30. A cell according to claim 25, substantially as hereinbefore described.

    31. A method according to claim 26, substantially as hereinbefore described.

    ANNEXURE B: Extract from Exhibit ALD-3