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 .
Response to Amendment/Status of Claims
Receipt of Arguments/Remarks filed on 05/28/2026 is acknowledged. Claims 1-54,57,62,63,71,72 and 74 stand cancelled. No claims were amended. Claims 55,56,58-61,64-70,73 and 75-84 are pending. Claim 70 remains withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/24/2024. Claims 55,56,58-61,64-69,73 and 75-84 are directed to the elected invention and are under examination.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged, and claim for foreign priority under 35 U.S.C. 119 (a)-(d) is acknowledged. This application is a continuation of PCT/EP2019/086019 filed on 12/18/2019, which claims the benefit of Application Nos. EP19208066.1 filed on 11/08/2019 and EP18214221.6 filed on 12/19/2018. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Maintained Objections and Rejections
Specification
The use of the terms which are trade names or marks used in commerce, has been noted in this application. Below is a non-exhaustive list of terms identified in the application:
-UniProt, page 18, line 17 (also on pages 22-30 and throughout the specification)
-Agilent Technologies, page 31, line 20
-Invitrogen, page 31, line 20
-Promega, page 31, line 21
-Invivogen, page 31, line 21
Applicant is advised to review the entire specification for trade names or marks used in commerce and correct them appropriately. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM or ® following the term. Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. There are numerous instances in the specification reciting an embedded hyperlink and/or browser-executable code. See at least pages 51,102,107-112. Applicant should review the entire specification and correct all instances of hyperlinks or browser-executable code.
Response to Arguments
Applicant’s arguments, see page 1, filed 05/28/2026, with respect to the amendments to the specification have been fully considered but are not persuasive. Applicant argues that a substitute specification has been submitted herewith including a marked-up copy and clean copy. The specification that is filed 05/28/2026 is only one page and recites that the specification objections have been addressed in the accompanying marked and clean copies of the specification, and Applicant has revised trade names and commercial marks and embedded hyperlinks and browser-executable code have been removed. However, other than this one page, there is no other specification filed 05/28/2026 in the file wrapper that includes marked up and clean copies as Applicant asserts and therefore the objections to the specification remain.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 55,56,59-61,64 and 77-83 are rejected under 35 U.S.C. 103 as being unpatentable over Guler-Gane, et al. (PLOS ONE, Vol 11 No 5, 19 May 2016) in view of Alonso et. al. (US 2012/0093775; Published: Apr. 19,2012; Effectively filed: Mar. 26, 2010 and Hempstead et. al. (US 2008/0025978 A1; Published: Jan. 31, 2008; Effectively filed: Jul. 27, 2007).
Regarding claim 55, Guler-Gane teaches a composition comprising an expression vector, called “pDest12.20riP CD33 SEAP -FLAGI10His” (page 3, paragraph “Generation of expression vectors”), which encodes a recombinant RNA construct. Further, Guler-Gane teaches that the expression vector encodes a CD33 signal peptide connected to the SEAP gene (page 5, paragraph 2, lines 3-6), which is a first nucleic acid sequence encoding a signal peptide operably linked to a second nucleic acid sequence encoding a protein, wherein the second nucleic acid sequence encoding the protein comprises a coding sequence of a mature protein of the protein. Guler-Gane teaches that by replacing the signal peptide the level of expression of the protein can be modified. Indeed, this has shown to be the case in a number of studies, where replacement of the native signal peptides with those from proteins that are known to secrete at high levels (e.g. luciferase, tissue plasminogen activator) can significantly improve secreted levels, and the potential posed by utilizing heterologous signal peptides from highly secreted proteins to improve protein yields is an attractive one (page 2, bottom).
The specification of the instant application discloses, in reference to human IGF1, that the sequence encoding the mature protein is 70 amino acids (nucleotides 145-354), which is downstream and separate from the sequences encoding the signal peptide and propeptide (page 22, lines 24-30), and additionally, that “the term "mature protein" refers to the protein synthesized in the endoplasmic reticulum and secreted via the Golgi apparatus in a cell expressing and secreting the protein” (page 23, lines 11-12). Guler-Gane uses the same definition of a mature protein in reference to SEAP. They reference that a mature protein is synthesized and processed (signal peptide removed) in the endoplasmic reticulum and secreted via trafficking through the Golgi network (page 2, paragraph 2), and that the SEAP protein linked to the CD33 signal peptide is that of the mature SEAP protein sequence (page 5, paragraph 2).
Guler-Gane also teaches the signal peptide is a signal peptide heterologous to the protein, with the proviso that the protein is not an oxidoreductase. The specification of the instant application defines “signal peptide heterologous to the protein” on page 18, lines 31-33 as “a naturally occurring signal peptide which is different to the naturally occurring signal peptide of the protein, i.e. the signal peptide is not derived from the same gene of the protein.” The CD33 signal peptide and SEAP protein of Guler-Gane are heterologous as the CD33 signal peptide is not the naturally occurring signal peptide of SEAP (page 5, paragraph 2, lines 1-2), and SEAP is a phosphatase (secreted alkaline phosphatase) (page 3, paragraph 1, lines 1-3), which is not an oxidoreductase.
Guler-Gane does not teach a recombinant RNA construct that encodes a protein comprising an amino acid sequence with at least 85% sequence identity to the amino acid sequence encoded by SEQ ID NO: 7 or SEQ ID NO: 8; and wherein the signal peptide is the signal peptide of brain-derived neurotrophic factor (BDNF).
The instant specification discloses that in a preferred embodiment of the present invention the mRNA comprising a nucleic acid sequence encoding human insulin-like growth factor 1 (IGF1) and the signal peptide of the brain-derived neurotrophic factor (BDNF) comprises a nucleic acid sequence transcribed from the DNA sequence as shown in SEQ ID NO: 7 comprises: (i) a nucleic acid sequence encoding the propeptide (also called pro-domain) of human IGF1 having 27 amino acids as shown in SEQ ID NO: 38, (ii) a nucleotide acid sequence encoding the mature human IGF1 having 70 amino acids as shown in SEQ ID NO: 39, and (iii) a nucleic acid sequence encoding the signal peptide of the brain-derived neurotrophic factor (BDNF), preferably, a nucleotide acid sequence encoding the signal peptide of the brain- derived neurotrophic factor (BDNF) as shown in SEQ ID NO: 30 (see page 88,1-14, page 89, lines 3-8).
In addition, Table 1 on page 105 of the specification shows the amino acid sequences, DNA sequences and RNA sequences of each of the signaling peptide and protein for Cpd. No. 4 which is the compound that is claimed. See below:
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78
599
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45
596
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Alonso et. al. discloses a recombinant nucleic acid construct that has 100% sequence similarity to the sequence encoding the propeptide and mature protein of human IGF1 comprised in SEQ ID NO: 7 in the instant application (see alignment below).
Alignment of Instant SEQ ID NO: 7 (Qy) to Alonso’s SEQ ID NO: 2 (Db):
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463
804
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Alonso further discloses that such a nucleic acid construct comprising a nucleotide sequence encoding IGF1 presents therapeutic benefits for the treatment of diseases such as cirrhosis [0004]; [0083]; [0053]. Alonso also discloses that it is possible to include a polynucleotide encoding the IGF1 fused to a heterologous signal sequence that is synthetically derived or isolated from another gene that directs the protein into the endoplasmic reticulum from which it is discharged to the appropriate destination [0058]. Therefore Alonso et al. suggests using a heterologous signal sequence with IGF1.
Alonso et. al. discloses a recombinant nucleic acid construct that has 100% sequence similarity to the sequence encoding the propeptide and mature protein of human IGF1 comprised in SEQ ID NO: 8 in the instant application (see alignment below).
Alignment of Instant SEQ ID NO: 8 (Qy) to Alonso’s SEQ ID NO: 2 (Db):
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444
805
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Alonso does not disclose a BDNF signal peptide operably linked to a protein of interest and wherein the RNA construct encodes a protein comprising an amino acid sequence with at least 85% sequence identity to SEQ ID NO: 7 or 8.
However, Hempstead discloses an amino acid sequence encoding a signal peptide that has 100% sequence identity to the sequence encoding the BDNF signal peptide in SEQ ID NO: 7 (SEQ ID NO: 30) (See sequence alignment below).
Hempstead further discloses any of the pro-domains described above optionally comprise a signal sequence, and that the signal sequence characteristically includes a stretch of hydrophobic amino acid residues that facilitates transport into the ER and facilitates secretions from cells, and the signal sequences found at the N-terminus of BDNF (SEQ ID NO: 93)…..constitute suitable signal sequences (paragraph 0080).
Alignment of instant SEQ ID NO: 30 to Hempstead’s SEQ ID NO: 93.
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822
753
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It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the composition of Guler-Gane with Alonso’s construct encoding the IGF1 protein and Hempstead’s heterologous BDNF signal peptide. There is a reasonable expectation of success because Alonso teaches that it is possible to fuse IGF1 to a heterologous signal sequence, and therefore an ordinary artisan would be motivated to try any heterologous signal sequence including a signal sequence from BDNF. One would have been motivated to substitute Guler-Gane’s SEAP protein and CD33 signal peptide with Alonso’s IGF1 protein and Hempstead’s BDNF signal peptide because Alonso teaches that IGF1 has therapeutic benefits for diseases such as cirrhosis and that a heterologous signal peptide can be fused to IGF1 to facilitate transport into the endoplasmic reticulum, and facilitate secretion from cells, and because Hempstead teaches the pro-domains may comprise a signal sequence which characteristically includes a stretch of hydrophobic amino acid residues that facilitates transport into the ER and facilitates secretions from cells, and the signal sequences found at the N-terminus of BDNF (SEQ ID NO: 93) constitute suitable signal sequences (paragraph 0080).
Regarding claim 56, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above. Alonso and Hempstead teach nucleic acid construct sequences that have 100% sequence similarity to the SEQ ID: NO 28, SEQ ID NO: 29, and SEQ ID NO: 30 all of which are comprised within SEQ ID NO: 7.
Regarding claim 61, The teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Guler-Gane teaches that SEAP is secreted, and that the quantity of secreted SEAP protein using a heterologous CD33-AA signal peptide (the CD33 signal peptide modified by insertion of 2 alanine residues at its C-terminal end) is higher than the quantity of secreted SEAP protein using its natural signal peptide (page 5, paragraph 2, lines 9-16; page 6, Figure 1; page 7, Table 1), which is a “signal peptide homologous to the protein” as defined in the specification of the instant application on page 19, lines 22-24. Guler-Gane also teaches that SEAP is secreted when expressed in a cell, and that the quantity of secreted SEAP protein using a heterologous CD33-AA signal peptide (the CD33 signal peptide modified by insertion of 2 alanine residues at its C-terminal end) is higher than the quantity of secreted SEAP protein using its natural, homologous signal peptide when expressed in a cell (page 5, paragraph 2, lines 9-16; page 6, Figure 1; page 7, Table 1).
Regarding claims 59-60, The teachings of Guler-Gane, and Alonso as applied to claim 55 are discussed above.
Guler-Gane and Alonso do not disclose the composition of claim 55 wherein the signal peptide of BDNF comprises the amino acid sequence of SEQ ID NO: 31.
Hempstead discloses an amino acid sequence encoding a signal peptide that has 100% sequence identity to the sequence encoding the BDNF signal peptide as shown in SEQ ID NO: 31 (see sequence alignment below). Hempstead further discloses the signal sequence facilitates transport into the endoplasmic reticulum, and facilitates the secretion from cells [0080].
Alignment of Instant SEQ ID NO: 31 to Hempstead’s SEQ ID NO: 93.
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682
730
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It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the compositions of Guler-Gane and Alonso with Hempstead’s heterologous BDNF signal peptide. One would have been motivated to substitute Guler-Gane’s and Alonso’s composition with Hempstead’s BDNF signal peptide because Hempstead teaches that a heterologous signal peptide can be fused to IGF1 to facilitate transport into the endoplasmic reticulum, and facilitate secretion from cells. There is a reasonable expectation of success because Alonso teaches that it is possible to fuse IGF1 to a heterologous signal sequence.
Regarding claim 64, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Alonso and Hempstead together teach nucleic acid construct sequences that have 100% sequence similarity to the SEQ ID: NO 28, SEQ ID NO: 29, and SEQ ID NO: 30 all of which together make up SEQ ID NO: 7. It is noted that instant SEQ ID NO: 8 is the RNA sequence that corresponds to the DNA sequence of SEQ ID NO: 7.
Regarding claim 77, and 79-80, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Hempstead discloses an amino acid sequence encoding a signal peptide that has 100% sequence identity to the sequence encoding the BDNF signal peptide comprised in SEQ ID NO: 7 (SEQ ID NO: 30). Hempstead further discloses the signal sequences of the approximately 18 amino acid residues found at the N-terminus of native BDNF (see paragraph [0082]).
Regarding claim 78, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Alonso et. al. discloses a recombinant nucleic acid construct that has 100% sequence similarity to the sequence encoding the propeptide and mature protein of human IGF1 comprised in SEQ ID NO: 7 in the instant application.
Regarding claim 81, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Alonso teaches a nucleotide sequence that is substantially homologous to the nucleotide sequence of the invention can typically be isolated from a producer organism of the polypeptide of the invention based on the information contained in said nucleotide sequence, or it is constructed based on the DNA sequence described above (see paragraph [0064]).
Regarding claims 82-83, the teachings of Guler-Gane, Alonso, and Hempstead as applied to claim 55 are discussed above.
Alonso and Hempstead together teach nucleic acid construct sequences that have 100% sequence similarity to the SEQ ID: NO 28, SEQ ID NO: 29, and SEQ ID NO: 30 all of which together make up SEQ ID NO: 7. It is noted that instant SEQ ID NO: 8 is the RNA sequence that corresponds to the DNA sequence of SEQ ID NO: 7.
See the alignment below, wherein Qy is SEQ ID NO: 7 and Db is SEQ ID NO: 8.
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591
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Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the composition of Guler-Gane with Alonso’s construct encoding the IGF1 protein and Hempstead’s heterologous BDNF signal peptide to arrive at the instant claims with a reasonable expectation of success. There is a reasonable expectation of success because Alonso teaches that it is possible to fuse IGF1 to a heterologous signal sequence, and therefore an ordinary artisan would be motivated to try any heterologous signal sequence including a signal sequence from BDNF. One would have been motivated to substitute Guler-Gane’s SEAP protein and CD33 signal peptide with Alonso’s IGF1 protein and Hempstead’s BDNF signal peptide because Alonso teaches that IGF1 has therapeutic benefits for diseases such as cirrhosis and that a heterologous signal peptide can be fused to IGF1 to facilitate transport into the endoplasmic reticulum, and facilitate secretion from cells, and because Hempstead teaches the pro-domains may comprise a signal sequence which characteristically includes a stretch of hydrophobic amino acid residues that facilitates transport into the ER and facilitates secretions from cells, and the signal sequences found at the N-terminus of BDNF (SEQ ID NO: 93) constitute suitable signal sequences (paragraph 0080). As instant SEQ ID NO: 8 is the RNA sequence that corresponds to the DNA sequence of SEQ ID NO: 7, since Alonso and Hempstead teach nucleic acid construct sequences that have 100% sequence similarity to the SEQ ID: NO 28, SEQ ID NO: 29, and SEQ ID NO: 30 all of which are comprised within SEQ ID NO: 7, it would be obvious that the sequences of Alonso and Hempstead would also have 100% sequence similarity to instant SEQ ID NO: 8.
Accordingly, the limitations of claims 82-83 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Response to Arguments
Applicant's arguments, filed 05/28/2026 have been fully considered and are partially persuasive regarding claim 58, which recites “wherein the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein” and therefore the unexpected results and arguments cited by Applicant in the response regarding this limitation are found persuasive for claim 58. Therefore, the rejection has been withdrawn for claim 58 and will remain objected to as being dependent on a rejected base claim. However, the rejection remains for claims 55,56,59-61,64 and 77-83 which do not require the limitation of the quantity of the secreted protein to be higher than the quantity of secreted protein using a signal peptide homologous to the protein for Applicant’s arguments and unexpected results.
Applicant argues on page 2 that the cited references provide no motivation to select BDNF signal peptide and that the present application demonstrates that even highly optimized and commercially successful secretion signal peptides are not functionally interchangeable in the context of IGF-1 secretion, and that the dramatic secretion enhancement achieved by the BDNF signal peptide was highly surprising and unexpected result which could not have been reasonably predicted by a person of ordinary skill in the art. Applicant argues on page 3 that Alonso not only does not mention BDNF but directs the skilled artisan toward a specific set of signal peptides for use with IGF-1 (gelsolin, albumin, fibrinogen, among others, the signal peptides from tissue plasminogen activator, insulin, and neuron growth factor, and therefore a person of ordinary skill following Alonso would have tried these signal peptides, not BDNF. Applicant argues the Office citing In re Susi is inapposite and does not authorize the examine to ignore an affirmative, specific recommendation made by the very reference relied upon for motivation, as Alonso’s enumerated list is not a list of preferred embodiments among many equals but is the specific answer to the question of which signal peptides are suitable for use with IGF-1, and that answer does not include BDNF. Applicant argues they tested two of Alonso’s specific recommendations: the insulin signal peptide (Cpd.10) and the NGF signal peptide (Cpd. 13) and as shown in Fig 22 both decrease IGF-1 secretion relative to the native IGF-1 signal peptide and therefore Alonso’s own recommended signal peptides fail, which transforms Alonso from a neutral reference into one that affirmatively steers the skilled artisan towards choices that do not work and away from BDNF.
This is not found persuasive because Guler-Gane provides motivation for further exploration regarding the potential posed by utilizing heterologous signal peptides from highly secreted proteins to improve protein yields as being attractive (by replacing the signal peptide the level of expression of the protein can be modified. Indeed, this has shown to be the case in a number of studies, where replacement of the native signal peptides with those from proteins that are known to secrete at high levels can significantly improve secreted levels, and the potential posed by utilizing heterologous signal peptides from highly secreted proteins to improve protein yields is an attractive one (page 2, bottom)). Also, Alonso provides the suggestion of using IGF1 with a heterologous signal sequence (it is possible to include a polynucleotide encoding the IGF1 fused to a heterologous signal sequence that is synthetically derived or isolated from another gene that directs the protein into the endoplasmic reticulum from which it is discharged to the appropriate destination [0058]), with Hempstead teaching suitable BDNF signal peptides. Therefore, since Hempstead teaches the signal sequence facilitates transport into the endoplasmic reticulum, and facilitates the secretion from cells [0080] and that BDNF signal peptides are suitable, which is the same desire as the signal peptides of Alonso, there would be a reasonable expectation of success and sufficient motivation. Regardless of whether there are other equally obvious heterologous signal peptides to be used, the use of the BDNF signal peptide is not any less obvious. Regarding Applicant’s argument about the suggested signal peptides of Alonso, this is not found persuasive because the rejection is made under 103 and does not need to exemplify all embodiments, only suggest. In addition, there is no requirement recited in claim 55 and those claims that depend on claim 55, other than claim 58, that the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein.
Applicant argues on page 4 they designed and tested 20 different IGF-1 constructs incorporating distinct signal peptides (Table 1 of spec), including 3 signal peptides currently in use for commercial therapeutic antibody and recombinant protein manufacturing in CHO cell systems (Cpd. 3, Cpd. 6 and Cpd. 7) and that these signal peptide sequence represent the state of the art in recombinant protein secretion engineering, and that under the Examiner’s theory that heterologous signal peptides from highly-secreted proteins predictably improve protein yields, Cpd. 3,6 and 7 should have been among the strongest candidates. However, they did not outperform the native IGF-1 signal peptide. Figs 17 and 19 show Cpd. 3,7 and 7 failed to significantly improve IGF-1 secretion, and the only construct the produced a dramatic, consistent and multi-cell-line improvement was Cpd. 4 which encodes the BDNF signal peptide. Applicant argues this data is fatal to the rejection as it directly refutes the Examiner’s foundational premise that if signal peptide substitution from a highly-secreted protein predictably improves yields, then the most widely used industrial signal peptides should have worked, and they did not. It also eliminates the basis of any reasonable expectation of success, as if industrially optimized signal peptides specifically designed for mammalian cell secretion fail, no basis exists for predicting that a neurotrophin signal peptide (BDNF) would succeed dramatically.
This is not found persuasive. The instant claims are directed to a product (a composition…) and "the patentability of apparatus or composition claims depends on the claimed structure, not on the use or purpose of that structure." Catalina Mktg. Int'l, Inc. v. Coolsavings.com, Inc., 289 F.3d 801,809 (Fed. Cir. 2002). Note: MPEP 2111.02. All of the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention. Note: MPEP 2143 KSR International Co. v. Teleflex Inc., 550 US 398, 82 USPQ 2d 1385 (2007).
Most of the claims do not recite or require any particular function. Claims 58 and 61 do recite a wherein clause reciting that the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein. Therefore, the above arguments are not found persuasive other than for claim 58 as the other claims do not require that the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein. I
Applicant argues on pages 5-6 that the scientific literature confirms signal peptide selection is unpredictable, citing Owji et al., and also pointing to Guler-Gane that CD33 signal peptide alone failed to drive SEAP secretion, but adding 2 alanine residues significantly improved it. This 2 aa addition, an 11% change to an 18-residue signal peptide produced a qualitative functional transformation. If signal peptide performance were predictable from general hydrophobicity or known behavior in one context a 2 alanine addition should produce on a proportionate, marginal change, however it transformed a non-functional construct into a working one. Applicant argues on page 6 that the present invention discloses not merely that the BDNF signal peptide outperforms other signal peptides with IGF-1 but the reason it does so: a specific local hydrophobicity architecture characterized by a “ladder-like” sliding-window hydrophobicity profile. Applicant evaluated local hydrophobicity profiles for all 20 tested signal peptides which revealed that signal peptides producing significantly enhanced IGF-1 secretion (positive examples Cpd. 4 and 14-20) exhibited a characteristic pattern: high local hydrophobicity scores in early windows with a gradual, ladder-like decrease in later windows, and signal peptides failing to improve secretion (negative examples Cpd. 1-3,5-13) lacked this pattern, and no prior art reference teaches, describes or suggests this biophysical correlation. Applicant states this was evaluated for IGF-1 but also for EPO, insulin, IL-10 and IL-4 confirming local hydrophobicity architecture rather than a protein-specific or context-specific artifact, is the operative principle. Unmodified IGF-2 signal peptide (Cpd. 8) cloaking the ladder-like profile produced only 80% of IGF-1 native SP secretion, while a modified IGF-2 signal peptide (Cpd.22) engineered to exhibit the ladder-like profile through targeted substitutions and deletions achieved 560% of native SP secretion, and Applicant argues no prior art reference teaches or suggests this local hydrophobicity architecture, and a skilled artisan relying on the references would have no basis for predicting that the BDNF signal peptide specifically or the ladder-like local hydrophobicity profile generally would produce the observed dramatic enhancement of IGF-1 secretion. Applicant argues on page 8 that there is no reasonable expectation of success, citing Bayer Schering Pharma AG v. Barr Laboratories, Inc. and Unigene Laboratories, Inc. v. Apotex. Inc. Owji confirms unpredictability as a matter of scientific consensus; the failure of industrially validated signal peptides in Applicant’s own experiments provides direct experimental confirmation that unpredictability and failure of Alonso’s own recommended signal peptides (insulin SP, NGF SP) demonstrates that following the art’s specific guidance leads to failure not success.
This is not found persuasive other than for claim 58, because as previously argued, other than claim 58, the other claims do not require that the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein.
Applicant argues unexpected results on pages 8-9 in that the secretion level of IGF-1 expressed from the instant claimed recombinant RNA construct in claim 55 is 3.1-6.1 times higher than the secretion level of IGF-1 expressed from a corresponding construct comprising the native IGF-1 signal peptide (compare Cpd.1 and Cpd.4 in Figures 17,19,20 and Example 1). Figure 18 shows Cpd. 4 is more potent in inducing secretion compared to Cpd. 1 representing a qualitatively distinct advantage beyond mere secretion quantity enhancement. Applicant argues these results are unexpected for 3 reasons: the signal peptides Alonso recommended for use with IGF-1, the insulin signal peptide (Cpd. 10) and the NGF signal peptide (Cpd. 13) do not improve IGF-1 secretion and decrease it relative to native IGF-1 signal peptide (compare Cpd. 1, 10 and 13 in Fig 22 and Example 1). The closest prior art’s explicit recommendations fail and the claimed invention succeeds dramatically. The industrially validated signal peptides proven to drive high-yield secretion in CHO-based manufacturing (Cpds. 3.6 and 7) failed to improve IGF-1 secretion, and based on the Examiner’s logic that heterologous signal peptides from highly-secreted proteins improve yields, these should have been the best candidates, but they were not. Last, the improved potency (EC50, Fig. 18) and confirmed in vivo efficacy represent advantages entirely unpredictable in the cited art. Applicant states that unexpected in vivo potency of the construct was confirmed in a published follow-on animal study directed to the same BDNF signal peptide comprising IGF-1 and reported that the BDNF signal peptide comprising IGF-1 construct demonstrated 16-fold higher potency compared to a corresponding construct comprising the endogenous IGF-1 signal peptide in a relevant animal model, and this 16-fold in vivo potency advantage goes substantially beyond the already impressive 3.1-6.1 fold secretion improvement observed in the in vitro cell studies of the instant application, and that the benefit of BDNF signal peptide is not an in vitro artifact but translated to in vivo settings. Applicant notes this published data could be submitted as additional evidence by way of a Declaration should the Examiner require further substantiation thereof. Applicant cites on page 10 pertaining to the Examiner’s argument that the unexpected results data are not commensurate in scope with the claims, In re Clemens. The relevant variable here is the BDNF signal peptide, not the identity range of the IGF-1 coding sequence. The secretion enhancement is attributable to the BDNF signal peptide and downstream mature protein sequence does not affect signal peptide function. 85-100% identity variant of IGF-1 retains the same protein fold, mature protein identity and same secretory pathway requirements and therefore the unexpected results are fully commensurate in scope with the claims. Applicant notes on page 11 that the BDNF signal peptide mediated secretion enhancement was confirmed across multiple heterologous proteins with no sequence identity to IGF-1 (EPO, insulin, IL-10 and IL-4), and if the BDNF signal peptide can dramatically enhance secretion of proteins bearing no sequence identity to IGF-1, minor sequence variations within 85-100% of IGF-1 identity range are irrelevant to the secretion phenotype.
While these unexpected results and arguments are found persuasive for claim 58 which recites the limitation that the quantity of the secreted protein is higher than the quantity of the secreted protein using a signal peptide homologous to the protein, and therefore the unexpected results and arguments provided by Applicant above are commensurate in scope with the claims, it is not found persuasive for claim 55 and the other claims which recite no such limitation. Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In re Clemens, 622 F.2d 1029, 1036, 206 USPQ 289, 296 (CCPA 1980). See also In re Peterson, 315 F.3d 1325, 1329-31, 65 USPQ2d 1379, 1382-85 (Fed. Cir. 2003); In re Grasselli, 713 F.2d 731, 741, 218 USPQ 769, 777 (Fed. Cir. 1983) Note: MPEP 716.02(d).” In re Hill, 284 F.2d 955, 128 USPQ 197 (CCPA 1960).
For these reasons, the 103 rejection is maintained for claims 55,56,59-61,64-69,73,75-84.
Claims 65,66 and 73 are rejected under 35 U.S.C. 103 as being unpatentable over Guler-Gane, et al. (PLOS ONE, Vol 11 No 5, 19 May 2016), Alonso et. al. (US 2012/0093775; Published: Apr. 19,2012; Effectively filed: Mar. 26, 2010) and Hempstead et. al. (US 2008/0025978 Al; Published: Jan. 31, 2008; Effectively filed: Jul. 27, 2007) as applied to claim 55 above, and further in view of Jani and Fuchs (Journal of Visualized Experiments, Vol 61, 26 March 2012).
Regarding claims 65-66, Guler-Gane, Hempstead, and Alonso teach all of the elements of the current invention for claim 55 as stated above.
Guler-Gane, Alonso, and Hempstead do not teach that the composition comprises the recombinant RNA construct, wherein the recombinant RNA construct is a recombinant messenger RNA (mRNA) construct, and wherein the recombinant RNA construct further comprises an anti-reverse cap analog (ARCA) and/or an internal ribosome entry site (IRES) at the 5' end.
Jani and Fuchs teach a composition comprising a recombinant RNA construct (page 1, abstract, paragraphs 1 and 2), including a recombinant RNA construct encoding the naturally secreted protein Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc) (pages 1-3, protocol steps 1-5; page 8, Discussion, paragraph 4), and a recombinant RNA that comprises an antireverse cap analog (ARCA) (pages 1-2, protocol steps 1; page 8, Discussion, paragraph 2). Jani and Fuchs teach that recombinant mRNA constructs are useful in applications that require large amounts of high-quality RNA, such as RNA structure and function studies, RNA vaccine development, and transfection and expression experiments (page 1, abstract, paragraphs 1 and 2; pages 7-8, Discussion, paragraphs 1-2). Jani and Fuchs also teach that the 5’ cap is essential for RNA stability and efficient translation, and that use of ARCA yields “functionally active capped RNA suitable for transfection or other applications” (page 1, abstract, paragraph 3). Additionally, use of a composition that comprises ARCA, “ensures incorporation of the cap in the correct orientation” as taught by Jani and Fuchs (page 8, Discussion, paragraph 2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the compositions of Guler-Gane, Alonso and Hempstead to incorporate the teachings of Jani and Fuchs and produce a recombinant mRNA construct that further comprises an anti-reverse cap analog to encode the heterologous signal peptide of BDNF operably linked to the IGF1 protein. One of ordinary skill in the art would have been motivated to do so based on the advantages of using recombinant mRNA constructs and ARCA, as taught by Jani and Fuchs above. Further, as Jani and Fuchs report a composition comprising recombinant RNA constructs, that further comprises ARCA, encoding proteins with signal peptides, there is a reasonable expectation that Jani and Fuchs’ composition could be successfully applied to the expression constructs of Guler-Gane, Alonso and Hempstead, which also encode proteins with signal peptides.
Regarding claim 73, Guler-Gane, Alonso, and Hempstead teach all of the elements of the current invention for claim 55 as stated above.
Guler-Gane, Alonso, and Hempstead do not teach a method of synthesizing the composition of claim 55, wherein the method comprises synthesizing a recombinant RNA construct in vitro.
Jani and Fuchs teach an in vitro transcription method for the synthesis of RNA transcripts (page 1, abstract, paragraphs 1 and 2) and applies this method to the synthesis of mRNA encoding the naturally secreted proteins Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc) (pages 1-3, protocol steps 1-5; page 8, Discussion, paragraph 4). Jani and Fuchs teach that in vitro transcription methods are useful to generate recombinant mRNA constructs for applications that require large amounts of high-quality RNA, such as RNA structure and function studies, RNA vaccine development, and transfection and expression experiments (page 1, abstract, paragraphs 1 and 2; pages 7-8, Discussion, paragraphs 1-2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the compositions of Guler-Gane, Alonso and Hempstead to incorporate the teachings of Jani and Fuchs and use their in vitro method to synthesize a recombinant RNA construct that encodes the BDNF signal peptide operably linked to the IGF1 protein. One of ordinary skill in the art would have been motivated to do so based on the advantages of using in vitro transcription methods, as taught by Jani and Fuchs above. Further, as Jani and Fuchs synthesize recombinant RNAs that encode proteins with signal peptides, and state that, “the method described in this paper can be used to transcribe, cap and transfect any desired mRNA” (page 8, Discussion, paragraph 4), there is a reasonable expectation that Jani and Fuchs’ method could be successfully applied to the expression constructs of Guler-Gane, Alonso and Hempstead.
Response to Arguments
Applicant's arguments filed 05/28/2026 have been fully considered but they are not persuasive.
Applicant argues on page 11 that as claims 65,66 and 73 depend from claim 55, they are not obvious over Guler-Gane, Hempstead, and Alonso and Jani and Fuchs for at least the reasons that claim 55 is not obvious, and because the combination of Guler-Gane, Hempstead, Alonso and Jani and Fuchs does not teach or suggest all of the limitations of claim 55.
This is not found persuasive. No new arguments are made, and the examiner has responded to the arguments pertaining to claim 55 in the response above, and therefore the response provided by the examiner to the rejection of claim 55 also pertains to the rejection of the dependent claims and the rejection is maintained.
Claims 67 and 68 are rejected under 35 U.S.C. 103 as being unpatentable over Guler-Gane, et al. (PLOS ONE, Vol 11 No 5, 19 May 2016), Alonso et. al. (US 2012/0093775; Published: Apr. 19,2012; Effectively filed: Mar. 26, 2010) and Hempstead et. al. (US 2008/0025978 Al; Published: Jan. 31, 2008; Effectively filed: Jul. 27, 2007), as applied to claim 55 above, and further in view of Holtkamp, et al. (Blood, Vol 108 No 13, 15 December 2006).
Regarding claims 67 and 68, Guler-Gane, Hempstead, and Alonso teach all of the elements of the current invention for claim 55 as stated above.
Guler-Gane does not teach that the recombinant RNA construct, wherein the recombinant RNA construct further comprises a polyA tail at the 3’end and that the polyA tail is 120 bp in length.
Holtkamp teaches a recombinant RNA construct encoding eGFP and eGFP variant markers, wherein the recombinant RNA construct further comprises a polyA tail at the 3’end and that the polyA tail is 120 bp in length (page 4010, Figure 1; page 4013, section “Poly(A) tail length has an impact on translational efficiency” and Figure SA-C). Holtkamp teaches that a recombinant RNA construct with a 120 bp polyA tail results in higher protein levels compared to proteins expressed from an RNA construct with a shorter tail, and RNA constructs with longer tails did not significantly affect expression (page 4013, section “Poly(A) tail length has an impact on translational efficiency”). Further, Holtkamp teaches that a 120 bp polyA tail “can be achieved by encoding the poly(A) tract in the template vector rather than attaching it by enzymatic polyadenylation” (page 4015, column 1, paragraph 3).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Guler-Gane, Alonso, and Hempstead to incorporate the teachings of Holtkamp and use an RNA construct with a defined and uniform 120 bp polyA tail at the 3’end to encode the BDNF signal peptide operably linked to the IGF1 mature protein. One of ordinary skill in the art would have been motivated to do so based on the advantages of using an RNA construct with a 120 bp polyA tail, as taught by Holtkamp above. Further, as Holtkamp synthesize recombinant RNAs with a defined and uniform 120 bp polyA tail by encoding the polyA tract in the DNA template vector, there is a reasonable expectation that it could be successfully applied to the expression construct of Guler-Gane, which is also a DNA-based vector.
Response to Arguments
Applicant's arguments filed 05/28/2026 have been fully considered but they are not persuasive.
Applicant argues on page 12 that as claims 67 and 68 depend from claim 55, they are not obvious over Guler-Gane, Hempstead, and Alonso and Holtkamp for at least the reasons that claim 55 is not obvious, and because the combination of Guler-Gane, Hempstead, Alonso and Holtkamp does not teach or suggest all of the limitations of claim 55.
This is not found persuasive. No new arguments are made, and the examiner has responded to the arguments pertaining to claim 55 in the response above, and therefore the response provided by the examiner to the rejection of claim 55 also pertains to the rejection of the dependent claims and the rejection is maintained.
Claim 69 is rejected under 35 U.S.C. 103 as being unpatentable over Guler-Gane, et al. (PLOS ONE, Vol 11 No 5, 19 May 2016), Alonso et. al. (US 2012/0093775; Published: Apr. 19,2012; Effectively filed: Mar. 26, 2010) and Hempstead et. al. (US 2008/0025978 Al; Published: Jan. 31, 2008; Effectively filed: Jul. 27, 2007) as applied to claim 55 above, and further in view of Kotaoka et al. (US9314529B2, published 19 April 2016).
Regarding claim 69, Guler-Gane, Hempstead, and Alonso teach all of the elements of the current invention for claim 55 as stated above.
Guler-Gane does not teach a pharmaceutical composition comprising the composition of claim 55 and pharmaceutically acceptable excipient, carrier, or diluent.
Kotaoka teaches a nucleic acid delivery composition (column 31, claim 1), a carrier composition (column 33, claim 4), and a pharmaceutical composition used for nucleic acid therapy, comprising the nucleic acid delivery composition according or the carrier composition (column 36, claims 6 and 8). Kataoka teaches that any nucleic acid can be used with their compositions, and that “examples of nucleic acid include DNA, RNA, naturally-occurring or non-naturally-occurring nucleic acid analogues (such as peptide nucleic acids), altered nucleic acids and modified nucleic acids, and any of these may be used. In addition, the nucleic acid may be a single-stranded nucleic acid or double-stranded nucleic acid, and there are no restrictions on the presence or absence of a protein encoding function or other functions” (column 14, lines 27- 36). Kataoka also teaches that their compositions have low cytotoxicity, and high transfection and gene expression efficiency (abstract).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Guler-Gane, Alonso, and Hempstead to incorporate the teachings of Kotaoka and use a pharmaceutical composition with a pharmaceutically accepted carrier comprising the nucleic acid expression vector that encodes the BDNF signal peptide linked to the IGF1 mature protein. One of ordinary skill in the art would have been motivated to do so based on the advantages of using the compositions of Kotaoka, as they teach above. Further, as Kotaoka teach that the composition is not dependent on the type of nucleic acid or the encoded protein(s), there is a reasonable expectation that it could be successfully applied to the expression constructs of Guler-Gane.
Response to Arguments
Applicant's arguments filed 05/28/2026 have been fully considered but they are not persuasive.
Applicant argues on page 13 that as claim 69 depends from claim 55, claim 69 is not obvious over Guler-Gane, Hempstead, and Alonso and Kotaoka for at least the reasons that claim 55 is not obvious, and because the combination of Guler-Gane, Hempstead, Alonso and Kotaoka does not teach or suggest all of the limitations of claim 55.
This is not found persuasive. No new arguments are made, and the examiner has responded to the arguments pertaining to claim 55 in the response above, and therefore the response provided by the examiner to the rejection of claim 55 also pertains to the rejection of the dependent claims and the rejection is maintained.
Claims 75,76 and 84 are rejected under 35 U.S.C. 103 as being unpatentable over Guler-Gane, et al. (PLOS ONE, Vol 11 No 5, 19 May 2016), Alonso et. al. (US 2012/0093775; Published: Apr. 19,2012; Effectively filed: Mar. 26, 2010) and Hempstead et. al. (US 2008/0025978 Al; Published: Jan. 31, 2008; Effectively filed: Jul. 27, 2007) as applied to claim 55 above, and further in view of Andries et. al. (Journal of Controlled Release, Vol 217, pages 337-344, 10 November 2015).
Regarding claim 75, 76 and 84, Guler-Gane, Alonso, and Hempstead teach all of the elements of the current invention for claim 55 as stated above.
Guler-Gane, Alonso, and Hempstead do not teach a recombinant RNA construct wherein one or more uridines are chemically modified N1-methylpseudouridine-5'- Triphosphate or wherein the recombinant RNA construct comprises a sequence with at least 85% sequence identity to SEQ ID NO: 8 and wherein the RNA construct comprises one or more chemically modified uridines.
Alonso teaches a polynucleotide composed of ribonucleotides and/or deoxyribonucleotides including both single-stranded and double-stranded polynucleotides as well as modified polynucleotides (methylated, protected and the like) [0051].
Andries further teaches that mRNAs containing the N1-methylpseudouridine modification provide higher gene expression and reduced immunogenicity (Abstract, Fig. 2, Fig. 3, Fig. 5).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the compositions of Guler-Gane, Alonso, and Hempstead by incorporating the modified polynucleotide N1-methylpseudouridine modification of Andries. One of ordinary skill in the art would have been motivated to do so based on the teaching of Andries that such a modification will have the benefit of higher mRNA gene expression and reduced immunogenicity.
Accordingly, the limitations of claims 75,76 and 84 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Response to Arguments
Applicant's arguments filed 05/28/2026 have been fully considered but they are not persuasive.
Applicant argues on page 13 that as claims 75-76 depend from claim 55, they are not obvious over Guler-Gane, Hempstead, and Alonso and Andries for at least the reasons that claim 55 is not obvious, and because the combination of Guler-Gane, Hempstead, Alonso and Andries does not teach or suggest all of the limitations of claim 55.
This is not found persuasive. No new arguments are made, and the examiner has responded to the arguments pertaining to claim 55 in the response above, and therefore the response provided by the examiner to the rejection of claim 55 also pertains to the rejection of the dependent claims and the rejection is maintained.
Conclusion
Claims 55,56,59-61,64-69,73 and 75-84 are rejected.
Claim 58 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE L SULLIVAN whose telephone number is (703)756-4671. The examiner can normally be reached Monday-Friday, 7:30-3:30 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram R Shukla can be reached at 571-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/ Primary Examiner, Art Unit 1636
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