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 Status
Claims 1-29 are pending.
Claims 1-13 are withdrawn from examination being part of the nonelected group.
Claims 14-29 are being examined.
There is no amendment of any claim. The rejection is modified from the rejection set forth in the Office action dated 07/21/2025, only to make certain points/issues clearer based on the Applicant’s response while responding to Applicant’s arguments.
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Claim Rejections - 35 USC § 103
Claims 14-17 and 19-29 remain rejected under 35 U.S.C. 103 as being unpatentable over Margolin et al. (Co-expression of human calreticulin significantly improves the production of HIV gp140 and other viral glycoproteins in plants, 2020, Plant Biotechnology Journal, 18:2109-2117) in view of Steinkellner et al. (US 20200080100 A1); and in evidence of Gutternigg et al. (Biosynthesis of Truncated N-Linked Oligosaccharides Results from Non-orthologous Hexosaminidase-mediated Mechanisms in Nematodes, Plants, and Insects, 2021, J. of Biol. Chem., 282: 7825–27840) and Keith et al. (Monocot and dicot pre-mRNAs are processed with different efficiencies in transgenic tobacco, 1986, The EMBO Journal, 5:2419 -2425).
Claim 14 is drawn to a plant cell which is transformed with at least one expression vector, comprising:
a first nucleic acid encoding a mammalian chaperone protein;
a second nucleic acid encoding a polypeptide which increases glycan occupancy;
a third nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell; and
a fourth nucleic acid encoding a heterologous polypeptide of interest.
Margolin et al. teaches a promising approach for production of high yields of appropriately processed and cleaved mammalian viral glycoproteins (Abstract, last 3 lines) and, thus, improving the production of viral glycoprotein-based vaccines in plants (page 2114. Right column, para 1, last 2 lines). Margolin et al. describes transforming Nicotiana benthamiana plants (Abstract, line 10) with at least one expression vector (page 2112, Fig. 2) comprising nucleic acids to efficiently produce heterologous glycoproteins (Abstract, line 9-10 and 14-15; page 2112, Fig. 2). It is understood by an ordinarily skilled artesian that transforming a plant implies transforming cells in the plant.
Margolin et al. describes that coexpression of the mammalian chaperone Calreticulin (CRT) (abstract, line 11), which reads on the first nucleic acid as recited in the claim 14, helped in chaperone-mediated folding (page 2110, left column, para 1, last 4 lines) and enabled production of various appropriately processed and cleaved heterologous glycoproteins (Abstract, last 3 lines).
Margolin et al. also describes expressing a polynucleotide sequence encoding an oligosaccharyltransferase (OST) enzyme (as part of the oligosaccharyltransferase complex), which reads on the second nucleic acid, which adds an oligosaccharide precursor to its polypeptide substrate (page 2110, left column, para 2, line 1-5), and, thus, increases glycan occupancy in its target or substrate polypeptide, as recited in the instant claim 14. The polynucleotide sequences encoding viral glycoproteins (“polypeptide of interest”) comprising HIV gp140 (title; abstract, line 10 and 18), glycoproteins from Epstein-Barr virus (EBV), Rift Valley fever virus (RVFV), and chikungunya virus (CHIKV) (abstract, line 12-13) reads on the fourth nucleic acid, as recited in the instant claim 14. The plant cell is transformed with all the three polynucleotide sequences.
However, Margolin et al. does not describe the “third nucleic acid” which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell.
Steinkellner et al. describes reducing or abolishing plant specific N-glycan residues by using RNAi (page 6, para 0087) to silence or inhibit different beta-hexosaminidase genes (page 6, para 0086) in tobacco (Nicotiana benthamiana) plants (page 8, para 0107 and para 0108). It also teaches that inactivation of beta-hexosaminidase 3 (HEXO3) increases the amount of complex N-glycans in substrate polypeptides (page 6, para 0088). Beta-hexosaminidase 3 enzyme is responsible for formation of truncated glycans, and since the nucleic acid comprising the RNAi construct interferes with this enzyme, this nucleic acid comprising the RNAi construct reads on the “third nucleic acid” recited in claim 14. It is known in the art that hexosaminidases are responsible for producing truncated or paucimannosidic N-linked oligosaccharides in plants (Gutternigg et al., page 27825, right column, para 1, last 4 lines; page 27835, left column, last para; page 27839, left column, para 3, line 3-5), in contrast to mammalian and other vertebrate specific “complex N-glycans”.
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to express a nucleic acid encoding a mammalian chaperone protein, a nucleic acid encoding a polypeptide which increases (general) glycan occupancy, and another nucleic acid encoding a heterologous polypeptide of interest, as described by Margolin et al., while co-expressing one more nucleic acid encoding an RNAi construct to silence hexosaminidase 3 (HEXO3) gene (which produces plant specific N-linked oligosaccharides in a glycoprotein) with a realistic goal to reduce or abolish plant specific N-glycan residues, as described by Steinkellner et al., in the heterologous glycoprotein(s) being expressed in the plant cell. Expressing these nucleotide sequences in a plant cell would have been a promising approach for the production of appropriately processed and cleaved viral glycoproteins for development of viral glycoprotein-based vaccines in plants.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to express: (i) a nucleic acid encoding a mammalian chaperone protein in a plant cell along with (ii) a nucleic acid encoding a polypeptide which increases glycan occupancy, (iii) another nucleic acid encoding a heterologous polypeptide of interest (the viral protein against which the vaccine needs to be raised), and (iv) a forth nucleic acid encoding an RNAi construct to silence hexosaminidase 3 (HEXO3) gene with the realistic goal to reduce or abolish plant specific N-glycan residues in the heterologous glycoprotein intended to be used as a therapeutic agent including as a vaccine.
Regarding claims 15-16, Margolin et al. describes human chaperones including calreticulin (title; abstract, line 9-11).
Regarding claim 17, Margolin et al. describes oligosaccharyltransferase complex which contains oligosaccharyltransferase enzyme that increases glycan occupancy, as discussed above (page 2110, left column, para 2).
Regarding claims 19-20, Steinkellner et al. describes use of different techniques including RNAi to reduce or abolish plant specific N-glycan residues (page 6, para 0087) by mutating or silencing specific genes including beta-hexosaminidase 3 (page 6, para 0088) which is involved in producing plant specific glycans, as discussed above.
Regarding claims 21-22, Margolin et al. describes expressing several heterologous glycoproteins in plants including viral glycoproteins (title; abstract, line 13-15).
Regarding claim 23, Margolin et al. describes expressing various nucleotide sequences using an expression vector pEAQ (Fig. 2). Clearly, there must be a promoter and other regulator(s) (e.g. transcription terminator sequence) operably linked to the nucleic acid sequences to express the nucleotide sequences, as described above, in the host plant cells.
Regarding claims 24-27 and 29, Margolin et al. describes transforming plant cells in tobacco, Nicotiana benthamiana, plants (page 2109, abstract), as described above. It is well known in the art that tobacco is dicotyledonous plant (Keith et al., Abstract).
Regarding claim 28, Steinkellner et al. describes N. benthamiana plants (page 8, para 0108) containing mutations to silence or inhibit glycosylation for plant specific N-glycan residues (page 6, para 0086; para 0087, line 1-6, line 18-20, line 25-29; and para 0088, line 6-11)
Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Margolin et al. in view of Steinkellner et al., as applied to reject claims 14-17 and 19-29 under 35 U.S.C. 103 above, and further in view of Castilho et al. (An oligosaccharyltransferase from Leishmania major increases the N-glycan occupancy on recombinant glycoproteins produced in Nicotiana benthamiana, 2018, Plant Biotechnology Journal, 16:1700–1709).
Claim 18 indirectly depends from claim 14 and is drawn to an oligosaccharyltransferase enzyme, LmSTT3D, from Leishmnia major.
Margolin et al. in view of Steinkellner et al. describes a plant cell which is transformed with at least one expression vector comprising: a first nucleic acid encoding a mammalian chaperone protein; a second nucleic acid encoding a polypeptide which increases glycan occupancy; a third nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell; and a fourth nucleic acid encoding a heterologous polypeptide of interest, as described above.
However, Margolin et al. in view of Steinkellner et al. does not describe the oligosaccharyltransferase enzyme, LmSTT3D, from Leishmnia major.
Castilho et al. teaches that not all potential N-glycosylation sites are recognized in-vivo by various enzymes present in a specific cell and the site occupancy can vary in different expression systems, resulting in under-glycosylation of heterologous glycoproteins (abstract, line 4-6). An oligosaccharyltransferase enzyme, LmSTT3D, from the protozoan Leishmania major have been expressed in Nicotiana benthamiana, to overcome that specific limitation of under-glycosylation (page 1700, abstract, line 4-8).
Before the effective filing date, it would have been obvious to an ordinarily skilled artisan to co-express the oligosaccharyltransferase enzyme LmSTT3D from Leishmania major to increase glycan occupancy to overcome the issue of under-glycosylation of heterologous glycoprotein(s), as described by Castilho et al., while expressing a nucleic acid encoding a mammalian chaperone protein; another nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell; and another nucleic acid encoding a heterologous polypeptide of interest, as described by Margolin et al. in view of Steinkellner et al., as described above.
Before the effective filing date of this invention, an ordinarily skilled artisan would have been motivated to express: i) a nucleic acid encoding a mammalian chaperone protein, ii) another nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell, iii) another nucleic acid encoding a heterologous polypeptide of interest and, iv) co-express (i)-(iii) along with the oligosaccharyltransferase enzyme LmSTT3D from Leishmania major to increase glycan occupancy that would have overcome under-glycosylation of the heterologous glycoprotein(s) in the plant cells.
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.
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Claims 14-16, 21, 23-26 and 29 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claim 6-7 and 10-14 of U.S. Patent No. 11555196B2, in view of Steinkellner et al. (US 20200080100 A1) and Margolin et al. (Co-expression of human calreticulin significantly improves the production of HIV gp140 and other viral glycoproteins in plants, 2020, Plant Biotechnology Journal, 18:2109–2117).
Instant claim 14 is drawn to a plant cell which is transformed with at least one expression vector, comprising:
a first nucleic acid encoding a mammalian chaperone protein;
a second nucleic acid encoding a polypeptide which increases glycan occupancy;
a third nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell; and
a fourth nucleic acid encoding a heterologous polypeptide of interest.
Claim 6 of U.S. Patent No. 11555196B2 (hereafter referred to as ‘196B2) recites a plant cell which is transformed with at least one expression vector, comprising:
a first nucleic acid encoding a mammalian chaperone protein; and
a second nucleic acid encoding a heterologous polypeptide of interest,
wherein the mammalian chaperone protein is selected from calnexin and/or calreticulin.
Claim 7 of ‘196B depends from claim 6, wherein the heterologous polypeptide of interest is a glycoprotein.
However, claims 6-7 of ‘196B2 do not recite (any nucleic acid which interferes with an enzyme which is responsible for the formation of truncated glycans in the plant cell. The claims also do not recite any nucleic acid encoding a polypeptide which increases glycan occupancy.
Steinkellner et al. describes plant and plant cells (page 1, para 0001) with mutated, silenced, or inhibited beta-hexosaminidases (page 6, para 0086) to reduce or abolish plant specific N-glycan residues using RNAi (page 6, para 0087). It also describes that inactivation of beta-hexosaminidase 3 increases the amount of (mammal specific) complex N-glycans in the glycoproteins (page 6, para 0088). It is known in the art that hexosaminidases are responsible for producing plant specific truncated or paucimannosidic N-linked oligosaccharides, as described above. The nucleic acid sequences encoding RNAi constructs targeting beta-hexosaminidase enzymes including beta-hexosaminidase 3 (HEXO3) reads on the third nucleic acid sequence, as recited in claim 14. Therefore, beta-hexosaminidase 3 enzyme is the enzyme that is responsible for the formation of truncated glycans, and since the nucleic acid comprising the RNAi construct interferes with this enzyme, this nucleic acid comprising the RNAi construct reads on the “third nucleic acid” recited in the claim 14.
Margolin et al. describes a promising approach for the production of high yields of appropriately processed and cleaved viral glycoproteins (page 2109, Abstract) to improve
production of viral glycoprotein-based vaccines in plants (page 2114. right column, para 1, last 2 lines). Margolin et al. also describes oligosaccharyltransferase complex adding oligosaccharide precursors to its substrate glycoproteins (page 2110, left column, para 2, line 1-5), and, thus, increases glycan occupancy in the glycoprotein.
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to modify the method described by claims 6-7 of ‘196B2 and express: (i) a nucleic acid encoding a mammalian chaperone protein, (ii) a nucleic acid encoding a heterologous glycoprotein of interest, as recited by claims 6-7 of ‘196B2; and co-expressing (i)-(ii), with (iii) a nucleic acid to silence hexosaminidase gene(s), with a realistic goal to reduce or abolish plant specific N-glycan residues in the heterologous glycoprotein(s), as described by Steinkellner et al., and (iv) one more nucleic acid encoding the oligosaccharyltransferase enzyme to increases glycan occupancy in its target glycoprotein(s), as described by Margolin et al. Expressing these 4 nucleotide sequences in a plant cell would have been a promising approach for the production of appropriately processed and cleaved viral glycoproteins, where the glycosylation pattern of the native (viral or mammalian) protein does not include any plant specific glycosylation and/or would have alerted biological function(s) including immunogenicity in a mammalian system due to plant specific glycosylation, for producing viral glycoprotein-based vaccines in plants.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to express:
(i) a nucleic acid encoding a mammalian chaperone protein in a plant cell,
(ii) a nucleic acid encoding a heterologous glycoprotein of interest,
(iii) a nucleic acid to silence hexosaminidase gene(s) with the realistic goal to reduce or abolish plant specific N-glycan residues in the heterologous glycoprotein, and
(iv) one more nucleic acid encoding the oligosaccharyltransferase enzyme would increases glycan occupancy in its target glycoprotein, to produce of appropriately processed and cleaved viral glycoproteins for development of viral glycoprotein-based vaccines in plants.
Regarding instant claims 15-16, claim 6 of ‘196B2 recites “calnexin and/or calreticulin”.
Regarding instant claim 21, claim 7 of ‘196B2 recites, “the heterologous polypeptide of interest is a glycoprotein”.
Regarding instant claim 23, claim 10 of ‘196B2 recites, “at least one expression vector includes promoters and/or other regulators, operably linked to the first nucleic acid and to the second nucleic acid”. It is well known and widely practiced to operably link several nucleic acid sequences, including the 4 nucleotide sequences described above to reject instant claim 14, with a promoter in expression vector(s) to express it in the host plant.
Regarding instant claim 24, claim 11 of ‘196B2 recites, “the plant cell is from a monocotyledonous or dicotyledonous plant”.
Regarding instant claim 25, claim 12 of ‘196B2 recites, “maize, rice, sorghum, wheat, cassava, barley, oats, rye, sweet potato, soybean, alfalfa, tobacco, sunflower, cotton, and canola”.
Regarding instant claim 26, claim 13 of ‘196B2 recites, “the plant cell is from a tobacco plant”.
Regarding instant claim 29, claim 14 of ‘196B2 recites, “A plant comprising the plant cell of claim 6.”
Response to Applicant’s Arguments
The argument set forth in the Applicant’s replies on 10/27/2025 has been fully considered but is not found persuasive.
The Applicant argues that “Margolin discloses successful expression of viral glycoproteins and improved production. The person of ordinary skill would not have been motivated to modify the disclosure of Margolin, much less with RNAi-mediated interference of hexosaminidase enzymes…” (page 7, para 2). The Applicant continue to argue that, “there would have been no reasonable expectation of success for such a combination” as “co-expression of nucleic acids to produce a heterologous polypeptide of interest is an unpredictable art” (page 7, para 3, line 1-3).
The Examiner disagrees. Glycosylation in different viral and mammalian glycoproteins differ in its pattern of glycosylation. Margolin et al. produced specific glycoprotein, HIV gp140 (abstract) and taught that co-expression of mammalian chaperone (calreticulin, CRT) resulted in producing appropriately processed and cleaved the specific viral (HIV) glycoprotein (gp140), and solved the challenge of “expression yields and appropriate posttranslational modifications along the plant secretory pathway (which) remain(s) a challenge for certain proteins” (abstract, line 3-5). Claims 6-7 of U.S. Patent No. 11555196B2 do include any glycoprotein being co-expressed with calnexin and/or calreticulin. ((In fact, ‘196B2 describes co-expressing specific HIV-1 envelope protein (gp140) from the CAP256 virus (column 14, Example 2) and a soluble antigen (glycoprotein ) from the Rift Valley Fever Virus (RVFV) (column, 16, example 3) with a mammalian chaperone)). An ordinarily skilled artisan would have known that many viral/mammalian glycoproteins having a different glycosylation pattern compared to that of HIV gp140 would not respond similarly to the methods of Margolin et al., and as indicated by. Steinkellner et al. Steinkellner et al. did not express the same HIV gp140, but a very different set of “therapeutically interesting (glyco) proteins” (page 10, para 0134, line 1), for which silencing endogenous beta-hexosaminidase genes (page 6, para 0086) using methods including RNAi (page 6, para 0087) were accomplished in tobacco plants, as discussed above. Silencing of any beta-hexosaminidase gene was not needed for successful production of biologically active gp140 glycoprotein, as described by Margolin et al.
The Applicant is reminded that obviousness may be established by combining or modifying the teachings of the prior art(s) to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, one of ordinary skilled in the art would have arrived at the Applicant’s invention by combining the teachings of the cited arts, as discussed above.
Co-expression of nucleic acids to produce heterologous polypeptides (via stacking) for various purposes including producing mammalian glycoproteins of interest is a standard process and well documented in the art1. Moreover, the Applicant did not provide any evidence that “there would have been no reasonable expectation of success” while co-expressing heterologous polypeptides of interest, as described above. Applicant’s opinion cannot take the place of evidence (MPEP 716.01(c)(II), 2145(I)).
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL. 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.
Communication
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Kallolimath et al. (Engineering of complex protein sialylation in plants, 2016, PNAS, 113: 9498–9503) provides the evidence for co-expression of nucleic acids to produce a heterologous polypeptide in a plant for producing properly glycosylated mammalian proteins (abstract).