Office Action 2: Final Rejection (2024-07-16)
Rejection types: 112 - Written Description/Enablement, Double Patenting

CLAIMS:
Listing of Claims:

This listing of claims will replace all prior versions, and listings, of claims in the application.

1\. (Canceled)

2\. (New) A polynucleotide encoding a light chain of an antibody, or antigen-binding fragment thereof, that immunospecifically binds to platelet factor 4 (PF4), wherein the light chain or antigen-binding fragment thereof comprises a light chain CDR and framework region comprising the amino acid sequence of SEQ ID NO: 4.

3\. (New) The polynucleotide of claim 2, wherein the light chain or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 6.

4\. (New) The polynucleotide of claim 2, wherein the light chain or antigen-binding fragment thereof comprises a light chain variable region comprising the amino acid sequence of SEQ ID NO: 5.

5\. (New) An expression vector comprising the polynucleotide of claim 2.

6\. (New) An expression vector comprising the polynucleotide of claim 3.

7\. (New) An expression vector comprising the polynucleotide of claim 4.

8\. (New) A host cell comprising the expression vector of claim 7.

9\. (New) The host cell of claim 8, wherein the host cell is a eukaryotic cell, a yeast cell, a plant cell or a bacterium.

10\. (New) The host cell of claim 9, wherein the eukaryotic cell is a 293T cell or a Chinese Hamster Ovary (CHO) cell.

11\. (New) A polynucleotide encoding a heavy chain of an antibody, or antigen-binding fragment thereof, that immunospecifically binds to platelet factor 4 (PF4), wherein the heavy chain or antigen-binding fragment thereof comprises a heavy chain CDR and framework region comprising the amino acid sequence of SEQ ID NO: 10.

12\. (New) The polynucleotide of claim 11, wherein the heavy chain or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 12.

13\. (New) The polynucleotide of claim 11, wherein the heavy chain or antigen-binding fragment thereof comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 11.

14\. (New) An expression vector comprising the polynucleotide of claim 11.

15\. (New) An expression vector comprising the polynucleotide of claim 12.

16\. (New) An expression vector comprising the polynucleotide of claim 13.

17\. (New) A host cell comprising the expression vector of claim 16.

18\. (New) The host cell of claim 17, wherein the host cell is a eukaryotic cell, a yeast cell, a plant cell or a bacterium.

19\. (New) The host cell of claim 18, wherein the eukaryotic cell is a 293T cell or a Chinese Hamster Ovary (CHO) cell.

20\. (New) A composition comprising:a polynucleotide encoding a light chain of an antibody, or antigen-binding fragment thereof, that immunospecifically binds to platelet factor 4 (PF4), wherein the light chain or antigen-binding fragment thereof comprises a light chain CDR and framework region comprising the amino acid sequence of SEQ ID NO: 4 and a polynucleotide encoding a heavy chain of an antibody, or antigen-binding fragment thereof, that immunospecifically binds to PF4, wherein the heavy chain or antigen-binding fragment thereof comprises a heavy chain CDR and framework region comprising the amino acid sequence of SEQ ID NO: 10.

21\. (New) The polynucleotide of claim 20, wherein the light chain or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 6 and the heavy chain or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 12.

22\. (New) The polynucleotide of claim 20, wherein the light chain or antigen-binding fragment thereof comprises a variable domain comprising the amino acid sequence of SEQ ID NO: 5 and the heavy chain or antigen-binding fragment thereof comprises a variable domain comprising the amino acid sequence of SEQ ID NO: 11.

23\. (New) An expression vector comprising the polynucleotide of claim 22.

24\. (New) A host cell comprising the expression vector of claim 23.

OFFICE ACTION:
DETAILED ACTION
Notice of Pre-AIA  or AIA  Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim 1 has been cancelled.  Claims 2-24 have been newly added.
Applicant's arguments filed 6/26/2024 have been fully considered but they are not persuasive.
The prior art of record does not disclose or suggest polynucleotides encoding the light chain and heavy chain anti-platelet factor 4 (PF4) antibodies or antigen binding fragments recited in the claims.  The prior art of record does not disclose or suggest expression vectors or host cell containing them.  SEQ ID NO: 4 is 74 amino acids and contains the light chain CDRs of SEQ ID NOS: 1, 2, and 3 and the second and third framework regions. SEQ ID NO: 4 is contained within SEQ ID NOS: 5 and 6. SEQ ID NO: 10 is 83 amino acids and contains the heavy chain CDRs of SEQ ID NOS: 7, 8, and 9 and the second and third framework regions. SEQ ID NO: 10 is contained within SEQ ID NOS: 11 and 12. See at least Table 2.
Specification
The substitute specification filed 5/16/2023 has been entered.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA  as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 2-4, 11-13, and 20-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 and 10-12 of U.S. Patent No. 11,524,999. Although the claims at issue are not identical, they are not patentably distinct from each other because issued claims 10-13 are directed to recombinant cells comprising polynucleotides encoding sequences comprising SEQ ID NOS: 4 and 10.  Issued claims 1-5 are directed to antibodies comprising SEQ ID NOS: 4 and 10; SEQ ID NOS: 5 and 11; and SEQ ID NOS: 6 and 12.  SEQ ID NOS: 4-6 and 10-12 correspond to instant SEQ ID NOS: 4-6 and 10-12.  Issued claims 10-12 contain the polynucleotides of instant claims 2, 11, and 20.  The issued claims comprise these polynucleotides and fairly include polynucleotides encoding the polypeptides of SEQ ID NOS: 5-6 and 11-12 recited in issued claims 2-5.
The issued claims are not patentably distinct from the instant claims.
Claims 5-10, 14-19, and 23-24 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 and 10-12 of U.S. Patent No. 11,524,999 in view of Cabilly et al. U.S. Patent No. 4,816,567 (of record).
The issued claims are as described above.  Issued claims 12-13 disclose the host cells of instant claims 9-10 and 18-19.  The issued claims do not specifically disclose an expression vector.
Cabilly et al. discloses using expression vectors when recombinantly producing antibodies from polynucleotides encoding the heavy or light chain.  Polynucleotides encoding both chains can be in the same expression vector.  See at least claims and column 5, lines 35-46; column 8, lines 20-45; and column 12, lines 57-65.
It would have been obvious to use an expression vector as the vector in the recombinant cells of the issued claims.  One would have been motivated to do so in order to recombinantly produce the encoded proteins.
The issued claims in view of Cabilly et al. are not patentably distinct from the instant claims.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA  35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 20-24 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA  35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 20-24 are not original claims.  They were added by amendment on 6/24/2024.  No specific basis for these claims was pointed to and none is apparent.
The specification does not appear to disclose a composition of two discrete polynucleotides as recited in claim 20 and dependent claims 21-22.  The specification does not appear to disclose a single expression vector containing the two polynucleotides of claim 22 as recited in claim 23 or a host cell containing such an expression vector as recited in claim 24.
These claims constitute new matter.  Applicant should point to page and line number in the specification to provide support for these claims.
The following is a quotation of 35 U.S.C. 112(b):
(b)  CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 21-24 are rejected 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.
Claims 21-24 depend upon claim 20 which is directed to a composition.  Claims 21-22 incorrectly refer to the polynucleotide of claim 20 rather than the composition of claim 20.  Claim 23 refers to the polynucleotide of claim 22.  It is noted that an expression vector cannot contain a composition having two discrete elements as in claim 22.  It appears that this claim should recite an expression vector comprising a polynucleotide encoding SEQ ID NO: 5 and a polynucleotide encoding SEQ ID NO: 11.
Conclusion
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 extension fee 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 date of this final action.

APPLICANT REBUTTAL: REMARKS
Claims 2-24 are pending. Claims 20-23 are amended herein. Support for these
amendments is found throughout the specification and claims as originally filed. No new subject matter has been added.
Applicant submits that the reply is consistent and compliant with the Patent Office's
After Final Consideration Pilot Program and the goals of the compact prosecution. Form SB 434 is submitted with this reply.
Claim Rejections - Double Patenting
I.
Claims 2-4, 11-13, and 20-22 stand rejected for non-statutory double patenting as
allegedly being unpatentable over claims 1-5 and 10-12 of U.S. Patent No. 11,524,9991. Applicant respectfully disagrees.
Although Applicant does not concede the correctness of the non-statutory double
patenting rejections, a terminal disclaimer with respect to U.S. Patent No. 11,524,999 is being filed concurrently with this reply.
Accordingly, Applicant respectfully requests that the non-statutory double patenting rejections be reconsidered and withdrawn.
II.    Claims 5-10, 14-19, 23, and 24 stand rejected for non-statutory double patenting as allegedly being unpatentable over claims 1-5 and 10-12 of U.S. Patent No. 11,524,999 in view of U.S. Patent No. 4,816,5672.
Although Applicant does not concede the correctness of the non-statutory double
patenting rejections, a terminal disclaimer with respect to U.S. Patent No. 11,524,999 is being filed concurrently with this reply.
1 Office Action, at 4.
2 Office Action, at 5.
Accordingly, Applicant respectfully requests that the non-statutory double patenting rejections be reconsidered and withdrawn.
Claim Rejections - 35 U.S.C. § 112
I.
Claims 20-24 stand rejected under 35 U.S.C. § 112(a) as allegedly failing to comply with
In particular, the Office Action contends the specificationdoes not appear to disclose a composition of two discrete polynucleotides as recited in claim 20 and dependent claims 21-22. Applicant respectfully disagrees with the rejection. Solely to advance prosecution, however, and without conceding the correctness of the rejections, claim 20 is amended to replace "composition" with "combination of polynucleotide." To the extent that the rejections are maintained in view of the amendments, Applicant traverses the rejections.
Paragraph [0090] of the instant specification states that "[t]he heavy chain and light chain sequences were synthesized and cloned into pSectag vectors using the QuickChange® mutagenesis kit" and that "[d]ifferent combinations of heavy chain and light chain plasmids were then co-transfected into 293T cells or expi-CHO cells for expression." (Application at [0090]; emphasis added). In other words, to express the antibodies, a combination of polynucleotides (one encoding a light chain or antigen-binding fragment thereof and one encoding a heavy chain or antigen-binding fragment thereof) were used. As such, the instant specification provides support for claim 20 and the claims that depend therefrom. Applicant respectfully requests reconsideration and withdrawal of the rejections to claims 20-22 under 35 U.S.C. § 112(a).
II.    Claims 21-24 stand rejected under 35 U.S.C. § 112(b) as being indefinite4. The preamble of claims 21-23 are amended to align with claim 20, and claim 24 is amended to depend from claim 20. Accordingly, Applicant respectfully requests reconsideration and withdrawal of the rejections.
3 Office Action, at 6.
4 Office Action, at 6.
CONCLUSION

NEXT OFFICE ACTION: EXAMINER'S AMENDMENT
An examiner’s amendment to the record appears below. Should the changes and/or additions be unacceptable to applicant, an amendment may be filed as provided by 37 CFR 1.312. To ensure consideration of such an amendment, it MUST be submitted no later than the payment of the issue fee.
Authorization for this examiner’s amendment was given in an interview with Dr. Elizabeth A. Browning on 27 September 2024.
The application has been amended as follows:
Claims 20-24 have been cancelled.
Reasons for Allowance
The following is an examiner’s statement of reasons for allowance:
Claims 20-24 as originally filed on 6/24/2024 constituted new matter for reasons of record.  The amendments proposed in the 9/17/2024 after final response did not have basis and did not overcome the new matter rejection for these claims.  Applicant elected to cancel these claims.
The terminal disclaimer filed on 9/23/2024 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of U.S. Patent No. 11,524,999 has been reviewed and is accepted.  The terminal disclaimer has been recorded.  The double patenting rejection of record has been withdrawn.
The prior art of record does not disclose or suggest polynucleotides encoding the light chain and heavy chain anti-platelet factor 4 (PF4) antibodies or antigen binding fragments recited in the claims. The prior art of record does not disclose or suggest expression vectors or host cell containing them. SEQ ID NO: 4 is 74 amino acids and contains the light chain CDRs of SEQ ID NOS: 1, 2, and 3 and the second and third framework regions. SEQ ID NO: 4 is contained within SEQ ID NOS: 5 and 6. SEQ ID NO: 10 is 83 amino acids and contains the heavy chain CDRs of SEQ ID NOS: 7, 8, and 9 and the second and third framework regions. SEQ ID NO: 10 is contained within SEQ ID NOS: 11 and 12. See at least Table 2.
Claims 1 and 20-24 have been cancelled.  Claims 2-19 are allowable.
Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee.  Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.”
Conclusion

CITED REFERENCE SUMMARIES: Ref US11524999: Claims:
1. An isolated antibody, or antigen-binding fragment thereof, that immunospecifically binds to platelet factor 4 (PF4), the antibody or antigen-binding fragment thereof comprising a light chain CDR and framework region comprising SEQ ID NO: 4 and a heavy chain CDR and framework region comprising SEQ ID NO: 10.
2. The isolated antibody, or antigen-binding fragment thereof, of claim 1, wherein the isolated antibody or antigen-binding fragment thereof has a light chain variable domain comprising the amino acid sequence of SEQ ID NO: 5 and a heavy chain variable domain comprising the amino acid sequence of SEQ ID NO: 11.
3. The isolated antibody, or antigen-binding fragment thereof, of claim 2, wherein the light chain variable domain has the amino acid sequence of SEQ ID NO: 5 and the heavy chain variable domain has the amino acid sequence of SEQ ID NO: 11.
4. The isolated antibody, or antigen-binding fragment thereof, of claim 1, wherein the isolated antibody or antigen-binding fragment thereof has a light chain comprising the amino acid sequence of SEQ ID NO: 6 and a heavy chain comprising the amino acid sequence of SEQ ID NO: 12.
5. The isolated antibody, or antigen-binding fragment thereof, of claim 4, wherein the light chain has the amino acid sequence of SEQ ID NO: 6 and the heavy chain has the amino acid sequence of SEQ ID NO: 12.
6. The isolated antibody, or antigen-binding fragment thereof, of claim 1, wherein the antibody isotype is IgG.
7. The isolated antibody, or antigen-binding fragment thereof, of claim 1, wherein the antigen-binding fragment is a Fv, Fab, Fab', Fab'-SH or F(ab')2.
8. The isolated antibody, or antigen-binding fragment thereof, of claim 1, wherein the antibody is a single chain antibody, a diabody, or a multispecific antibody formed from more than one antigen-binding fragment.
9. A pharmaceutical composition comprising the isolated antibody or the antigen-binding fragment of claim 1 and a pharmaceutically acceptable carrier.
10. A recombinant cell comprising:
(a) a vector comprising a nucleic acid molecule encoding a heavy chain CDR and framework region comprising SEQ ID NO: 10;
(b) a vector comprising a nucleic acid molecule encoding a light chain CDR and framework region comprising SEQ ID NO: 4; or
(c) the vectors of both (a) and (b).
11. A recombinant cell comprising:
(a) a vector comprising a nucleic acid molecule encoding a heavy chain comprising SEQ ID NO: 12;
(b) a vector comprising a nucleic acid molecule encoding a light chain comprising SEQ ID NO: 6; or
(c) the vectors of both (a) and (b).
12. The recombinant cell of claim 11, wherein the recombinant cell is a eukaryotic cell, a yeast cell, a plant cell or a bacterium.
13. The recombinant cell of claim 12, wherein the eukaryotic cell is a 293T cell or a Chinese Hamster Ovary (CHO) cell.
14. A method of reducing thrombosis in a subject having heparin-induced thrombocytopenia (HIT), the method comprising administering to the subject a therapeutically effective amount of the isolated antibody or antigen-binding fragment thereof of claim 1, thereby reducing thrombosis.
15. The method of claim 14, wherein the isolated antibody or antigen-binding fragment thereof is administered with heparin.
16. The method of claim 15, wherein the heparin is heparin fragment, low-molecular-weight heparin or unfractionated heparin.
17. The method of claim 14, wherein the isolated antibody or antigen-binding fragment thereof is administered with a heparin mimic.
18. The method of claim 17, wherein the heparin mimic is fondaparinux.
Ref US4816567: Claims:
1. A method comprising(a) preparing a DNA sequence encoding a chimeric immunoglobulin heavy or light chain having specificity for a particular known antigen wherein a constant region is homologous to the corresponding constant region of an antibody of a first mammalian species and a variable region thereof is homologous to the variable region of an antibody derived from a second, different mammalian species; (b) inserting the sequence into a replicable expression vector operably linked to a suitable promoter compatible with a host cell; (c) transforming the host cell with the vector of (b); (d) culturing the host cell; and (e) recovering the chimeric heavy or light chain from the host cell culture.
2. The method of claim 1 wherein the first mammalian species is human.
3. A composition comprising a chimeric immunoglobulin heavy or light chain having specificity for a particular known antigen having a constant region homologous to a corresponding constant region of an antibody of a first mammalian species and a variable region homologous to a variable region of an antibody derived from a second, different mammalian species.
4. The chimeric heavy or light chain of clain 3 wherein the constant region is human.
5. A replicable expression vector comprising DNA operably linked to a promoter compatible with a suitable host cell, said DNA encoding a chimeric immunoglobulin heavy or light chain having specificity for a particular known antigen and having a constant region homologous to a corresponding region of an antibody of a first mammalian species and a variable region homologous to a variable region of an antibody derived from a second, different mammalian species.
6. The vector of claim 5 wherein the first mammalian species is human.
7. Recombinant host cells transformed with the vector of claim 5.
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