DETAILED ACTION
Applicant’s amendment and response received on 12/17/25 has been entered. Claims 1, 5, 7-8, 12, 14-17, 21, 23-24, 26, 28, 30, 32, and 34-35 are currently pending in this application. Of these, claims 8, 12, 16-17, 21, 23-24, 28, 30, and 32 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention and/or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 9/2/22. Claims 1, 5, 7, 14-15, and 34-35 are therefore currently under examination based on the species of genetic modification to the B cell now recited in claim 1, and further based on additional election of species set forth in the previous office action. An action on the merits follows.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . Those sections of Title 35, US code, not included in this action can be found in the previous office action.
Claim Rejections - 35 USC § 112
The rejection of claims 1, 5, 7, 14-15, and 34-35 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention, is maintained in modified form.
Applicant’s amendment to claim 1 to delete the word “strong” overcomes the previous issue of indefiniteness. However, applicant’s amendment to claim 1 has introduced a new issues of indefiniteness as follows.
Independent claim 1 has been amended to recite the phrase, “wherein the genome-edited primary B cell exhibits increased capacity to expand relative to a non-genome edited primary B cell, and wherein binding of the antigen of interest to the BCR results in the generation of long-lived plasma cells, thereby resulting in increased expression of IDUA”. As written, it is unclear whether the “increased expression of IDUA” is present in the plasma cells or the genome-edited primary B cell. While the newly added phrase recites that the “increased capacity” to expand is relative to a non-genome edited primary B cell, the recitation of “increased expression of IDUA” does not provide any point of comparison for the “increased expression”. It is unclear whether the increased expression is intended to reflect 1) increased expression of IDUA in each individual genome-edited primary B cell, whether the applicant intends to claim that 2) IDUA expression is increased in each individual plasma cell which may arise from the gene edited primary B cells, or whether applicant intends to claim that 3) IDUA expression is “increased” because plasma cells are long-lived and therefore express IDUA for longer period of time than a primary B cell. Claim 1 is therefore confusing such that the metes and bounds of the claim cannot be determined. Claims 5, 7, 14-15, and 34-35 depend on claim 1 and are therefore included in this rejection.
In the interests of compact prosecution, the claimed genome-edited primary B cells have been interpreted to encompass any of the three interpretations regarding “increased expression of IDUA” as set forth above.
The rejection of claims 1, 5, 7, 14-15, and 34-35 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for scope of enablement is maintained in modified form in view of applicant’s amendments to the claims.
Independent claim 1 has been amended to delete the previous limitation, “wherein binding of the antigen of interest to the BCR specific for the antigen of interest results in the overexpression of IDUA”, and to introduce the new limitation, “wherein the genome-edited primary B cell exhibits increased capacity to expand relative to a non-genome edited primary B cell, and wherein binding of the antigen of interest to the BCR results in the generation of long-lived plasma cells, thereby resulting in increased expression of IDUA”. As discussed in the rejection the claims under 35 U.S.C. 112(b) above related to the phrase, “thereby resulting in increased expression of IDUA”, this newly added limitation has been interpreted to encompass 1) wherein the increased expression reflects increased expression of IDUA in each individual genome-edited primary B cell, 2) whether the IDUA expression is increased in each individual plasma cell which may arise from the gene edited primary B cells, or 3) whether the IDUA expression is “increased” because plasma cells are long-lived and therefore express IDUA for a longer period of time than a primary B cell. Further, in so far as the claims continue to encompass a genome-edited primary B cell with the structure as claimed that exhibits increased expression of IDUA following the binding of the antigen of interest to the BCR, it is noted that issues raised in regards to lack of enablement for overexpression of IDUA in the genome-edited primary B cells following antigen binding to BCR continue to apply to the claims as amended as increased expression of IDUA following antigen binding to BCR and overexpression of IDUA following antigen binding are considered at least overlapping in scope if not identical in scope.
Based on this analysis of claim interpretation for the amended claims, the scope of enablement has been modified as follows: the specification, while being enabling for a genome-edited primary B cell, wherein the primary B cell comprises a non-clonal cell expressing at least one of CD19, IgM, IgD, CD27+, CD21+, and CXCR5+, wherein the primary B cell comprises a therapeutic cassette comprising a nucleic acid encoding a V, D, or J segment of an endogenous BCR heavy chain, a splice acceptor element, a promoter, a B cell receptor (BCR) specific to an antigen of interest, a ribosomal skipping sequence or an internal ribosome entry site, and a nucleic acid encoding an alpha-L-iduronidase (IDUA) gene, wherein the gene edited primary B cell express both the BCR specific for the antigen of interest and IDUA, does not reasonably provide enablement for 1) a gene edited primary B cell with the structure recited in the claims wherein the genome-edited primary B cell exhibits increased capacity to expand relative to a non-genome edited primary B cell, and 2) wherein either the genome-edited primary B cell itself, or a plasma cell derived from the primary B cell exhibits increased expression of IDUA after antigen binding to the BCR. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
Applicant’s amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the scope of enablement rejection for reasons set forth in detail below. The applicant argues that the expansion capacity of the genome-edited primary B cells is depicted in Figure 9, thus enabling the newly recited functional property of “increased capacity to expand relative to a non-genome edited primary B cell”. The applicant further argues that even though the working examples do not exemplify the expression construct or gene-edited primary B cells comprising the expression construct as claimed that the examples provided disclose methods of transducing B cells with a nucleic acid construct, integration of an expression cassette into the genome of a cell, and expression of a marker protein, and further shows expression of IDUA in 293T cells. According to applicant, these examples bear a reasonable correlation to the scope of the claims, and in combination with the additional guidance in the specification would allow the skilled artisan to make and use the claimed invention without undue experimentation. The applicant also argues that the experiments conducted in the 293T cells show that the introduction of a therapeutic cassette into these cells yielded a 40-fold increase in intracellular IDUA activity and a 14-fold increase in extracellular IDUA activity which provides a reasonable expectation that the genome-edited primary B cells with the claimed construct would exhibit increased expression of IDUA.
In regards to applicant’s comments regarding the legal standard for establishing enablement or lack thereof, it is noted that the scope of enablement set forth above for the claims as amended was identified by the Office after careful analysis of the disclosure provided by the specification. The Office has further analyzed the specification in direct accordance to the factors outlined in In re Wands, namely 1) the nature of the invention, 2) the state of the prior art, 3) the predictability of the art, 4) the amount of direction or guidance present, and 5) the presence or absence of working examples, and presented detailed scientific reasons supported by publications from the prior art for the finding of a lack of enablement for the scope of the instant invention as claimed.
In regards to the lack of enablement for increasing the expression of IDUA in either the genome edited primary B cell comprising the expression cassette as claimed, or in a plasma cell derived therefrom, as the result of binding of an antigen of interest to a BCR specific for the antigen, it is maintained that the specification does not provide sufficient guidance for the structure and elements of a therapeutic cassette comprising nucleotide sequences coding for a BCR and a nucleotide sequence encoding IDUA which when present in a B cell, or in a plasma cell differentiated therefrom, is capable of exhibiting increased expression of IDUA as the result of binding of an antigen of interest to a BCR specific for the antigen. Applicant’s arguments relate to the guidance provided in the specification and the working examples for making gene-edited B cells which can express a BCR and IDUA. However, as can be seen from the statement of the scope of enablement, the issue is not whether one can make a primary B cell comprising the expression cassette as claimed, the question raised is whether the specification enables the claimed functional properties of such a cell- and more specifically, the recited functional property of the genome edited primary B cell comprising the expression cassette as claimed, or in a plasma cell derived therefrom, as exhibiting increased expression of IDUA as the result of binding of an antigen of interest to a BCR specific for the antigen. Applicant’s argument that because the working examples show that a B cell can be gene edited using CRISPR/Cas9, or that a B cell can be successfully modified to comprise an expression cassette that expresses a marker gene GFP in the cell, or that a human embryonic kidney cell (293T cell) can be modified to comprise an expression cassette that expresses IDUA in the cell, that the skilled artisan would find a reasonable correlation between these examples and the claimed B cells is not persuasive because none of these examples provide any evidence that antigen binding to a BCR expressed using an expression cassette in a B cell as claimed would result in increased expression of IDUA. As amended, independent claim 1, the broadest claim, continues to recite the following structural elements for the expression cassette: 1) a nucleic acid encoding a V, D, or J segment of an endogenous BCR heavy chain, 2) a splice acceptor element, 3) a promoter, 4) a B cell receptor (BCR) specific to an antigen of interest, 5) a ribosomal skipping sequence or an internal ribosome entry site, and 6) a nucleic acid encoding an alpha-L-iduronidase (IDUA) gene. It is again noted that the while the B cell comprising the therapeutic cassette is identified as a “genome-edited” primary B cell, the claim does not define or limit how the genome of the B cell has actually been edited. It is also noted that the BCR reads broadly on either membrane bound or soluble BCR. In addition, the claims read broadly on the presence of the therapeutic cassette in the cytoplasm, i.e. in for example a plasmid or other non-integrating vector, or in the genome at any location. The specification does disclose a number of expression cassettes useful for expressing a BCR and IDUA, where either the two nucleotide sequences are operably linked to the same promoters or are each linked individually to different promoters (specification, pages 15-16). The specification also discloses that the two coding sequences can be transcriptionally and/or translationally linked through the use of a single promoter and IRES or 2A sequences separating the two coding sequences (specification pages 15-16). The specification also discloses several promoters for use in the therapeutic cassettes including the MND, CMV, CAG, EF1A, PGK, and FEEK promoters. In some embodiments, the specification discloses that the therapeutic cassette can be inserted into the genome of the B cell at the endogenous heavy chain locus using gene editing, where the therapeutic cassette is inserted near an enhancer found in a constant region (specification, page 15, see also Figure 3A). Figure 3B also depicts “cargo” designs for constructs for insertion into the endogenous BCR locus, one of which contains a promoter, and the other does not. The currently claimed cassette elements appear to correspond to the design of Construct 2 depicted in Figure 3B. However, while Figure 3A does show a potential insertion site for cassette, the claims as written do not indicate that the therapeutic cassette has been inserted into the genome of the cell, or where in the genome the cassette has been placed. It is also noted that while Figure 3A also shows the position of two endogenous enhancers present in the endogenous heavy chain locus, the specification does not teach that either of these transcriptional regulatory elements present at this or any other location are capable of enhancing the expression of the BCR and/or IDUA coding sequences present in claimed cassette regardless of where the cassette is located, i.e. in a cytoplasmic plasmid or viral vector, at any location in the genome, or even at any location within the immunoglobulin heavy chain locus. The specification further does not demonstrate any promoter or enhancer/promoter pair which is further capable of being activated by BCR signaling following antigen binding. There are only two references to antigen activated BCR induced expression of a gene in the specification: the first appears in the bridging paragraph between pages 16-17, “[w]hen, for example, transcription of the nucleic acid encoding the gene to be overexpressed is driven by the same promoter that drives transcription of at least one of the heavy chain or the light chain of the BCR, overexpression of the gene can be controlled by immunizing a subject for the antigen recognized by the exogenous BCR” (specification, pages 16-17, bridging paragraph); and the second on page 19, “[f]or example, a genome-edited primary B cell including a B cell receptor specific for phycoerythrin (PE) and including a nucleic acid encoding alpha-L-iduronidase (IDUA) could be introduced into a subject. The subject could be IDUA deficient. Immunizing the subject with PE could result in differentiation of the genome-edited primary B cell into a long-lived plasma cell and transcription of the nucleic acid encoding IDUA, thereby increasing the expression of IDUA in the genome-edited B cell and body-wide in the patient for cross correction of the disease” (specification, page 19, first paragraph). However, neither of these paragraphs provides any guidance as to any promoters, enhancers, or promoter/enhancer pairs which can in fact be controlled by BCR antigen recognition, where antigen binding by the BCR sends a signal into the cell which can activate the expression of IDUA. The promoters disclosed in the specification, the MND, CMV, CAG, EF1A, PGK, and FEEK promoters are primarily ubiquitous and/or constitutive promoters. The specification does not disclose or demonstrate that any of these promoters can be activated through antigen activated BCR signaling in any type of cell including a B cell. Further, the specification does not teach or demonstrate that the presence of any enhancer at any location in the genome or in the cassette itself could result in transcription of the BCR and IDUA coding sequences through antigen activated BCR signaling in any type of cell, including a B cell. Applicant’s argument do not address the lack of correlation between the disclosed elements of the expression cassette and the recited functional property of increased IDUA expression following antigen binding to the expressed BCR.
Turning to the working examples, the rejection of record pointed out that the specification disclosed the construction and use of a single lentiviral vector comprising an expression cassette comprising an MND promoter operatively linked to nucleic acid sequence encoding a BCR heavy chain, a P2A sequence, a nucleotide sequence encoding a BCR light chain, a P2A sequence and a codon optimized nucleotide sequence encoding IDUA (specification, Example 2 and Figure 6). This expression cassette corresponds to the construct depicted in Figure 6A. The expression cassette used in the working examples does not correspond to the structure of the expression cassette recited in the claims as amended. Further, the working examples demonstrate that transduction of HEK293T cells (human embryonic kidney cells) in cell culture with the lentivirus as described above resulted in the detectable expression of IDUA in the culture media (specification, Example 2, pages 36-37). The applicant refers to working examples using T cells, however, please note that HEK293T cells are not T cells, they are human embryonic kidney cells. The working examples did not disclose transduction of immune cell, let alone a B cell with the lentiviral vectors, and further, contrary to applicant’s arguments, did not disclose or demonstrate that expression of IDUA present in any expression cassette in a B cell or any other cell could be activated by either membrane bound or soluble BCR antigen binding in that cell. The claims, as discussed above, does not simply require the expression of IDUA, the claim requires that the is increased expression is the result of BCR antigen binding.
The rejection of record also provided a detail look at the state of the art of BCR signaling and its effects on gene expression at the time of filing. The rejection of record cited three references. The rejection of record pointed out that at the time of filing, it was well known that antigen binding to membrane bound BCR results in an extremely complex cascade of signaling events which are further complicated by various co-stimulatory pathways that may also be engaged and contribute to intracellular signaling following antigen binding- see for example the diagram provided by Cell Signaling Technologies (B Cell Receptor Signaling (2014 revised), Cell Signaling Technologies, www.cellsignal.com/pathways/b-cell-receptor-signaling#, pages 1-2). Lee et al. further teaches that while antigen binding to membrane bound BCR can result in a signaling cascade that affects gene expression, where upward of 1000 gene were observed to be affected using microarray analysis of RNA obtained from antigen stimulated B cells, the affects on gene expression can be either upregulation or downregulation (Lee et al. (2006) BMC Bioinformatics, Vol. 7:237, pages 1-19, see Figure 1, Table 1, and pages 13-14). Lee et al. also shows that depending in the stimulus provided, different genes are affected (Lee et al., Table I). Lee et al. does identify two genes whose expression is significantly upregulated following BCR antigen recognition, but doesn’t teach any of the transcriptional regulatory sequences present in either gene which are responsible for the BCR signaling induced transcriptional upregulation (Lee et al., Figure 2). Both Cell Signaling Technologies and Lee et al. are specifically concerned with signaling cascades resulting from antigen binding to BCR on the surface of B cells, and thus are extremely relevant to the claimed subject matter. Cells Signaling Technologies and Lee et al. both teach that the signaling cascade of a BCR in B cells following antigen binding is complex and that the effects on gene expression can be negative or positive depending on the genes regulatory elements. Neither reference teaches that regulatory elements responsive to BCR signaling were well known or had been fully elucidated. The rejection of record also cited Tran et al. as evidence that the prior art teaches that the determination of stimulation responsive transcriptional elements for any gene requires substantial experimentation and cannot be determined a priori. Tran et al. detailed attempts to elucidate stimulation responsive elements in the Aicda gene regulatory regions (Tran et al. (2010) Nat. Immunology, Vol. 11(2), 148-155). Tran et al. shows that the regulatory elements of the Aicda gene in B cells are found not only surrounding the promoter region (region 1), but also upstream of the promoter (region 4), intronic between exons 1 and 2 (region 2), and in the 3’ untranslated region of the gene (region 3) (Tran et al., page 149, Figure 1). Tran et al. Tran et al. teaches that each of these regions contains candidate binding motifs for various positive and negative regulatory transcription factors (Tran et al., page 149, Figure 2-4). Tran et al. in an attempt to define elements from the various regions necessary and responsible for stimulation of transcription in response to signaling through a combination of CD40L, IL-4, and/or TGF-beta (CIT), constructed numerous regulatory regions combining and eliminating various candidate transcription factor binding motifs to identify the ones responsible for CIT responsive transcription upregulation of a marker gene (Tran et al., Figures 2-5). Tran et al. identified elements in Region 2 and 4 which either depress or enhance expression as part of sophisticated regulatory system, but states that these results require further confirmation from in vivo mutagenesis studies (Tran et al., page 154). While the Aicda gene is a gene activated through BCR signaling, Tran et al. did not try to specifically elucidate elements which enhance expression. However, Tran et al. does show that attempts to determine elements that enhance expression of this gene following signaling through other B cell surface receptors was a difficult process that required extensive in vitro and in vivo testing. This teaching is clearly relevant to the instant claims, as the claims contain the limitation that antigen binding of the BCR in the B cell induces overexpression of IDUA and the specification fails to provide any specific guidance as to regulatory elements, such as promoters, and/or enhancers, which are activated by BCR signaling and which can activate the expression/overexpression of the IDUA coding sequence present in the expression cassette. Thus, as a whole, the prior art of record teaches that the signaling cascade and plethora of transcription factors affected by antigen induced BCR signaling is complex and further affected by signaling cascades through other B cell surface molecules, that signaling can either upregulate or downregulate gene expression, and that the elucidation of transcription factor binding elements present in the regulatory regions of genes which are positively responsive to receptor signaling complex is difficult to determine and unpredictable without experimentation. The applicant has not provided any evidence, and the specification provides no working example, which rebuts the evidence of record.
Therefore, it is maintained that based on the art recognized complexity of BCR signaling and the unpredictability of identifying transcriptional regulatory elements capable of increasing transcription of gene in responsive to BCR signaling in a B cell, the lack of guidance in the specification for any transcriptional regulatory sequence capable of increasing the transcription of IDUA in response to antigen dependent BCR signaling in a B cell, the limitation in the working examples to expression of IDUA in a non-B cell and without antigen dependent BCR signaling, and the breadth of the claims, it would have required undue experimentation to make and use the B cells with the structure claimed which further exhibit the claimed functional property of increased expression of IDUA as a result of antigen binding to the BCR.
Turing to the newly added limitation, “wherein the genome-edited primary B cell exhibits increased capacity to expand relative to a non-genome edited primary B cell”, while the specification does make a general statement that, “in some embodiments, the gene-edited primary B cell exhibits increased capacity to expand relative a non-genome edited primary B cell in vitro” (instant specification, paragraph 60), this statement is not made specifically in regards to a genome edited primary B cell comprising the claimed expression cassette. The applicant argues that Figure 9 provided evidence of the claimed increased capacity to expand”. However, Figure 9 presents data from an experiment where sorted CD19+ B cells were expanded using a commercially available B cell expansion kit, and compares the expansion of these B cells when plated at a low or high density starting B cell concentration (specification, paragraph 143 and Figure 9). It is unclear what modification if any are present in the CD19+ B cells, though the previous paragraph, paragraph 108, refers to the generation of CRISPR mediated gene editing of the BCL2 locus in stimulated CD19+ B cells. Even supposing the cells expanded in the experiment described in paragraph 143 and Figure 9 are these BCL2 edited CD19+ B cells, Figure 9 only compares the expansion of the same cells plated at different starting densities. Figure 9 does not show that any edited B cell exhibits “an enhanced capacity to expand” compared to an unedited B cell, and further provides no evidence that a genome edited primary B cell comprising the expression cassette as claimed exhibits “an enhanced capacity to expand” compared to an unedited B cell. Figure 9 only shows that sorted CD19+ B cells expanded using a commercially available B cell expansion kit exhibit increased expansion when plated an initial lower density than when plated at a high density. Further, the specification as a whole fails to provide any guidance as to the conditions under which a gene edited primary B cell as claimed exhibits an enhanced capacity to expand compared to an unedited primary B cell. It is also noted that the prior art of record does not teach or suggest that insertion of a cassette for expression of a BCR and IDUA as claimed into a B cell would enhance the proliferative capacity of the cells in vitro or in vivo. As such, in view of the unpredictable state of the prior art for enhancing the expansion capacity of primary B cells by expressing a BCR and IDUA as claimed, the lack of specific guidance for a primary B cells comprising the expression cassette encoding BCR and IDUA as claimed which exhibit enhanced capacity for expansion compared to an unmodified B cell, the lack of working examples which demonstrate enhanced capacity for expansion as claimed, and the breadth of the claims, it would have required undue experimentation to make and use a B cell with this functional property.
some embodiments, whether the
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication from the examiner should be directed to Anne Marie S. Wehbé, Ph.D., whose telephone number is (571) 272-0737. If the examiner is not available, the examiner’s supervisor, Maria Leavitt, can be reached at (571) 272-1085. For all official communications, the technology center fax number is (571) 273-8300. Please note that all official communications and responses sent by fax must be directed to the technology center fax number. For informal, non-official communications only, the examiner’s direct fax number is (571) 273-0737. For any inquiry of a general nature, please call (571) 272-0547.
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Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634