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 .
Claims 11, 14, 30 have been canceled. Claims 1-10, 12, 13, 15-29, 31-42 remain pending.
Applicant's arguments filed 5-26-26 have been fully considered but they are not persuasive.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Preliminary Information
SEQ ID NO: 1 is an amino acid sequence encoding wild-type human Factor VII precursor protein (pg 5 description of Fig. 1) and was well known in the art as NP 000122.1 published in Thim (“Amino acid sequence and posttranslational modifications of human factor VIIa from plasma and transfected baby hamster kidney cells”, Biochemistry 27 (20), 7785-7793, 1988) (see NP000122.1 ).
SEQ ID NO: 2 is a wild-type mRNA encoding the human FVII precursor protein of SEQ ID NO: 1 (pg 5, description of Fig. 1) and was well-known in the art as EU557239.1 described by Masroori (“High-level expression of functional recombinant human coagulation factor VII in insect cells”, Biotechnol. Lett. 32 (6), 803-809, 2010) (see EU557239).
SEQ ID NO: 3 and 4 are mRNA encoding the human FVII precursor protein of SEQ ID NO: 1 that have been codon optimized for expression in humans; both encode the human FVII of SEQ ID NO: 1 (pg 5, description of Fig. 2). SEQ ID NO: 3 (1401 nt) is 86% identical to SEQ ID NO: 4 (1401 nt):
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SEQ ID NO: 11 (claim 27) is the amino acid sequence of a fusion protein comprising the precursor FVII protein of SEQ ID NO: 1 and the albumin protein of SEQ ID NO: 5 (pg 37).
SEQ ID NO: 12 (claim 27) is the amino acid sequence of a fusion protein comprising the precursor FVII protein of SEQ ID NO: 1 and the albumin protein of SEQ ID NO: 7 (pg 37).
SEQ ID NO: 13 (3177 nt) is a nucleic acid sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 13 are equivalent to nucleotides 1-1401 of SEQ ID NO: 3; nucleotides 1402-3177 are equivalent to SEQ ID NO: 6 (pg 37).
SEQ ID NO: 14 (3213 nt) is a nucleotide sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 14 are equivalent to SEQ ID NO: 3; nucleotides 1402-3213 are equivalent to SEQ IDNO: 8 (pg 37).
SEQ ID NO: 15 is a nucleic acid sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 15 are equivalent to nucleotides 1-1401 of SEQ ID NO: 4; nucleotides 1402-? are equivalent to SEQ ID NO: 6 (pg 37).
SEQ ID NO: 16 is a nucleotide sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 16 are equivalent to SEQ ID NO: 4; nucleotides 1402-? are equivalent to SEQ IDNO: 8 (pg 37).
SEQ ID NO: 17 is a nucleic acid sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 17 are equivalent to nucleotides 1-1401 of SEQ ID NO: 2 (wild-type, well-known mRNA encoding FVII); nucleotides 1402-? are equivalent to SEQ ID NO: 6 (pg 37).
SEQ ID NO: 18 is a nucleotide sequence encoding an FVII-albumin fusion protein; nucleotides 1-1401 of SEQ ID NO: 18 are equivalent to SEQ ID NO: 2 (wild-type, well-known mRNA encoding FVII); nucleotides 1402-? are equivalent to SEQ IDNO: 8 (pg 37).
SEQ ID NO: 22 (10784 nt) is an FVII expression vector (Table 5, pg 111). Nucleotides 2382-3782 and 5389-6789 of SEQ ID NO: 22 are two hFVII open reading frames that are equivalent to SEQ ID NO: 3.
The specification does not teach the functions of the nucleic acids of SEQ ID NO: 23, 24, or 25; however, SEQ ID NO: 3 is equivalent to nucleotides 2046-3446 of SEQ ID NO: 23 (3968 nt), nucleotides 1056-2456 of SEQ ID NO: 24 (2996 nt), and nucleotides 2046-3446 and 5053-6453 of SEQ ID NO: 25 (6993 nt).
Response to comments
Applicants say SEQ ID NO: 23 equivalent to nucleotides 337-4304 of SEQ ID NO: 22 in the first transcription unit. The meaning of this is indecipherable, and the function of SEQ ID NO: 23 cannot be determined.
Applicants say SEQ ID NO: 24 equivalent to nucleotides 4334-7429 of SEQ ID NO: 22 in the 2nd transcription unit. The meaning of this is indecipherable, and the function of SEQ ID NO: 24 cannot be determined.
Applicants say SEQ ID NO: 25 equivalent to nucleotides 337-7329 of SEQ ID NO: 22 spanning the first and second transcription unit. The meaning of this is indecipherable, and the function of SEQ ID NO: 25 cannot be determined.
It is assumed SEQ ID NOs: 22-25 are limited to fusion protein embodiments.
Claim Objections/Interpretations
SEQ ID NO: 3 or 4 is at least 95% identical to SEQ ID NO: 3 or 4, so saying it twice in claim 1 is redundant. Claim 1 does not clearly set forth the structure/function of the device. The metes and bounds of a “cell-containing compartment” cannot be determined and appear to be extraneous because the device contains cells, i.e. the device is the “compartment”. The metes and bounds of a “foreign body response (FBR)” cannot be determined. The “means for mitigating the foreign body response (FBR) when the device is implanted into the subject” cannot be determined. The phrase “the subject” lacks antecedent basis. The term “RPE” should be spelled out before being abbreviated. Claim 1 encompasses RPEs in culture media because the cells in solution are an “implantable device”, and the media is a “cell-containing compartment”. The solution used for implantation is pH appropriate for cell growth which “mitigates” any FBR. Nothing else is required in claim 1 beyond RPEs in cell culture. Accordingly, claim 1 can be written more simply, accurately, and succinctly as ---A composition comprising isolated mammalian retinal pigmented cell (RPE) comprising an exogenous nucleic acid sequence encoding human Factor VII (FVII), wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4---.
Claim 2 can be written more clearly as ---wherein the exogenous nucleic acid sequence encoding FVII is operably linked to a promoter comprising the nucleic acid sequence of SEQ ID NO: 10 or 21---.
Claim 3 can be written more clearly as ---wherein the exogenous nucleic acid sequence encoding FVII comprises the nucleotide sequence of SEQ ID NO: 3 and is operably linked to a promoter comprising the nucleic acid sequence of SEQ ID NO: 10 or 21---.
Claim 7 can be written more clearly as ---wherein the exogenous nucleic acid sequence comprises the nucleotide sequence of SEQ ID NO: 22--- [which is a plasmid comprising SEQ ID NO: 3].
Claim 8 requires reconsideration and clarification. The sequence may be integrated into the genome of the cell or it may be episomal, but it is unclear how the phrases “an extrachromosomal expression vector” or “is integrated into at least one chromosomal location in the RPE cell” further limits the structure/function of the exogenous nucleic acid sequence.
It is unclear when/how RPEs are “derived from” ARPE-19 cells as required in claim 9. Assuming ARPE-19 is an RPE cell line, the RPEs are either ARPE-19 cells or they are not. Claim 9 can be written more accurately as ---wherein the RPE cell is an ARPE-19 cell---. This assumes the metes and bounds of an ARPE-19 cell line are well-known.
Claim 10 is redundant given the changes suggested above and can be canceled.
Claim 24 is inaccurate because SEQ ID NO: 11 and 12 encode fusion proteins comprising h FVII and albumin; they are not FVII proteins as claimed.
SEQ ID NO: 17 and 18 in claims 5, 12, 37, 38 encode FVII-albumin fusion proteins and contain wild-type sequences encoding FVII that are not “at least 95% identical to SEQ ID NO: 3 or 4” as required in claims 1 or 12.
It is assumed SEQ ID NOs: 23-25 in claims 6, 12, 40-42 are limited to fusion proteins containing codon optimized sequences.
Election/Restrictions
The Groups have been modified in view of the major restructuring of the claims in the amendment filed 5-26-26. New Groups have been added.
Embodiments relating to codon optimized sequences encoding non-fusion proteins (SEQ ID NO: 3 or 4), sequences encoding fusion proteins containing only wild-type sequences (SEQ ID NO: 17 and 18), and sequences encoding fusion proteins containing codon optimized sequences (SEQ ID NO: 19-21, 23-25) have been separated.
The “implantable device” in Groups I-III is being treated as RPEs in cell culture for reasons set forth above under “Claim objections/Interpretations”.
The RPEs encapsulated by a polymer in claims 18-22, Groups VII-IX, are being separated from the RPEs in culture because they are related as intermediate-final products that are patentably distinct. Claims 15-17 have been added to Groups VII-IX because they are limited to a polymer that encapsulates RPE cells which is not required in claim 1. Claim 24 is limited to a fusion protein comprising FVII-albumin and has been
Group I, claims 1-3, 7-10, drawn to an implantable device comprising RPEs that express an isolated nucleic acid sequence that is codon optimized for expression of human factor VII and is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4; and cells comprising the nucleic acid sequence (non-fusion proteins). Group I is for SEQ ID NO: 3 and 4 and the plasmid of SEQ ID NO: 22 (which contains SEQ ID NO: 3).
Group II, claim 4, 5, 24, drawn to an implantable device comprising RPEs that contain a nucleic acid sequence encoding a fusion protein comprising a human factor VII precursor and albumin, wherein the sequence encoding human factor VII precursor is a wild-type nucleic acid sequence. SEQ ID NO: 17 and 18 in claim 5 do not comprise an isolated nucleic acid sequence that is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4 as required in claim 1 because they comprise the a wild-type nucleic acid sequence that is NOT at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4. Therefore, SEQ ID NO: 17 and 18 embodiments are not part of Group I; Group II is for SEQ ID NO: 17 and 18.
Group III, claims 4-6, 24 drawn to an implantable device comprising RPEs that contain a nucleic acid sequence encoding a fusion protein comprising a human factor VII precursor and albumin, wherein the sequence encoding human factor VII precursor is codon optimized. Group III is for SEQ ID NOs: 13-16, 23-25.
Group IV, claims 12, 13, 25-27, 29, 31, 32, 39, drawn to an isolated nucleic acid sequence that is codon optimized for expression of human factor VII and is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4; and cells comprising the nucleic acid sequence. Group I is for SEQ ID NO: 3 and 4 and the plasmid of SEQ ID NO: 22 (which contains SEQ ID NO: 3).
Group V, claims 12, 37, 38 drawn to a nucleic acid sequence encoding a fusion protein comprising a human factor VII precursor and albumin, wherein the sequence encoding human factor VII precursor is a wild-type nucleic acid sequence. SEQ ID NO: 17 and 18 in claim 5 do not comprise an isolated nucleic acid sequence that is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4 as required in claim 1 because they comprise the a wild-type nucleic acid sequence that is NOT at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4. Therefore, SEQ ID NO: 17 and 18 embodiments are not part of Group IV; Group V is for SEQ ID NO: 17 and 18.
Group VI, claims 12, 28, 33-36, 40-41, drawn to a nucleic acid sequence encoding a fusion protein comprising a human factor VII precursor and albumin, wherein the sequence encoding human factor VII precursor is codon optimized. Group VI is for SEQ ID NOs: 13-16, 23-25.
Group VII-IX, claims 15-22, drawn to a hydrogel capsule with compartments and polymers comprising an implantable device. Groups VII, VIII, and IX are materially distinct and separate based on the RPEs containing the nucleic acid sequences in Group I, II, and III.
Group X-XII, claim 23, drawn to a method of treatment using the device of claim 14. Groups X, XI, and XII are materially distinct and separate based on the RPEs containing the nucleic acid sequences in Group I, II, and III.
Applicants elected Group III, previously claims 14-17, drawn to an implantable device comprising RPE cells and nucleic acid encoding FVII, on 5-26-26 without traverse in response to the second restriction requirement, and applicants wish to limit the search to any sequence that is codon optimized for expression of human factor VII precursor and at least 95% identical to SEQ ID NO: 3 or 4. First, SEQ ID NO: 17 and 18 are not limited to codon optimized sequences for expressing human FVII precursor, so they have been removed from Group III and moved into group V. Second, SEQ ID NO: 13-18, 23-25 are limited to fusion proteins which have been removed from Group III and moved into Group II, III, V, VI, et al.. The elected subject matter is now Group I, and will only be examined as it relates to RPEs containing a nucleic acid sequence encoding human factor VII precursor and at least 95% identical to SEQ ID NO: 3 or 4. SEQ ID NO: 13-18, 23-25 will not be considered or examined.
Claims 4-6, 12, 13, 15-29, 31-42 have been withdrawn.
Claims 1-3, 7-10 are being examined as they relate to isolated RPEs comprising a nucleic acid sequence that is codon optimized for expression of human factor VII precursor and at least 95% identical to SEQ ID NO: 3 or 4.
Claims 1-3, 7-10 are not being examined as they relate to RPEs comprising a nucleic acid sequence encoding a FVII-albumin fusion protein (whether they are codon optimized or otherwise).
Claims 1-3, 7-10 are not being examined as they relate to RPEs encapsulated in a polymer as required in claims 15-22 (Groups VII-IX).
Claims 1-3, 7-10 are not being examined as they relate to using RPEs comprising the nucleic acid sequence for treatment in a subject as require in claim 23 (Group X-XII).
Claim 24 will not be examined because SEQ ID NO: 11 and 12 are fusion proteins.
Claim Rejections - 35 USC § 112
Written Description
Claims 1-3, 7-10 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.
A) The specification lacks written description for any implantable device comprising any “cell-containing compartment” comprising a RPE cell and any “means for mitigating” a “foreign body response (FBR)” comprising a sequence encoding FVII that is at least 95% identical to SEQ ID NO: 3, 4 as required in claim 1 other than a composition comprising isolated mammalian retinal pigmented cell (RPE) comprising a nucleic acid sequence encoding human Factor VII (FVII), wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4.
Claim 1 is drawn to “An implantable device comprising at least one cell-containing compartment which comprises an engineered RPE cell and at least one means for mitigating the foreign body response (FBR) when the device is implanted into the subject , wherein the engineered RPE cell is capable of expressing and secreting a factor VII (FVII) protein, wherein the engineered RPE cell and comprises an exogenous nucleotide sequence comprising a coding sequence for the FVII protein, wherein the coding sequence comprises a precursor FVII coding sequence selected from the group consisting of:(i) SEQ ID NO:3,(ii) a nucleotide sequence that is at least 95% identical to SEQ ID NO:3,(iii) SEQ ID NO:4, and(iv) a nucleotide sequence that is at least 95% identical to SEQ ID NO:4”.
The metes and bounds of a “cell-containing compartment” cannot be determined (see 112/2nd), but polymer embodiments are not under consideration (Groups VII-IX above). The metes and bounds of a “means for mitigating” a “foreign body response (FBR)” cannot be determined (see 112/2nd). The claims encompass any species of RPEs and putting them into any species of subject. The specification is limited to culturing mammalian RPEs in media. The specification does not correlate culture media to any other non-encapsulating polymer or “implantable device” as broadly encompassed by claim 1. The specification does not teach any “means for mitigating” FBR (whatever that is) other than a pH balanced culture media. The specification does not correlate mammalian RPE cells to RPEs of any invertebrate, fish, amphibian, reptile, or bird as broadly encompassed by claim 1. The specification does not correlate implanting RPE cells into a mammal to implanting them into any “subject” that is a bacteria, invertebrate, fish, amphibian, reptile, or bird as broadly encompassed by claim 1. Accordingly, claim 1 lacks written description other than a composition comprising isolated mammalian retinal pigmented cell (RPE) comprising a nucleic acid sequence encoding human Factor VII (FVII), wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4.
Enablement
Claims 1-3, 7-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a composition comprising isolated mammalian retinal pigmented cell (RPE) comprising a nucleic acid sequence encoding human Factor VII (FVII), wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4 does not reasonably provide enablement for the claims as written. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make/use the invention commensurate in scope with these claims.
A) The specification does not enable making/using any implantable device comprising any “cell-containing compartment” comprising a RPE cell and any “means for mitigating” a “foreign body response (FBR)” comprising a sequence encoding FVII that is at least 95% identical to SEQ ID NO: 3, 4 as required in claim 1 other than a composition comprising an isolated mammalian retinal pigmented cell (RPE) comprising a nucleic acid sequence encoding human Factor VII (FVII), wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4.
Claim 1 is recited above. Claim 1 is not under consideration as it relates to RPEs encapsulated in a polymer as required in claims 15-22.
The metes and bounds of a “cell-containing compartment” cannot be determined (see 112/2nd), but polymer embodiments are not under consideration (Groups VII-IX above). The metes and bounds of a “means for mitigating” a “foreign body response (FBR)” cannot be determined (see 112/2nd). The claims encompass any species of RPEs and putting them into any species of subject. The specification is limited to culturing mammalian RPEs in media. The specification does not correlate culture media to any other non-encapsulating polymer or “implantable device” as broadly encompassed by claim 1. The specification does not teach any “means for mitigating” FBR (whatever that is) other than a pH balanced culture media. The specification does not correlate mammalian RPE cells to RPEs of any invertebrate, fish, amphibian, reptile, or bird as broadly encompassed by claim 1. The specification does not correlate implanting RPE cells into a mammal to implanting them into any “subject” that is a bacteria, invertebrate, fish, amphibian, reptile, or bird as broadly encompassed by claim 1. Given the lack of guidance in the specification taken with the art at the time of filing, it would have required those of skill undue experimentation to determine how to make/use any implantable non-encapsulated device as broadly encompassed by claim 1 other than a composition comprising isolated mammalian RPE comprising a nucleic acid sequence encoding human FVII, wherein the nucleic acid sequence is at least 95% identical to the nucleotide sequence of SEQ ID NO: 3 or 4.
Indefiniteness
Claims 1-3, 7-10 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.
A) Claim 1 does not clearly set forth the structure/function of the device. The metes and bounds of a “cell-containing compartment” cannot be determined and appear to be extraneous because the device is the “compartment”. The metes and bounds of a “foreign body response (FBR)” cannot be determined. The “means for mitigating the foreign body response (FBR) when the device is implanted into the subject” cannot be determined. The phrase “the subject” lacks antecedent basis. The solution used for implantation is pH appropriate for cell growth which “mitigates” any FBR. But it is unclear what else is required in claim 1 beyond RPEs in cell culture. It is unclear how the phrases further limit the RPEs in cell culture or what the metes and bounds of the phrases mean. Therefore, those of skill would not be able to determine when they were infringing on the claims.
Claim Rejections - 35 USC § 103
A) Claims 1, 8-10 are rejected under 35 U.S.C. 103 as being unpatentable over Carmona (20200263196) in view of SEQ ID NO: 1433 described by Bancel (US 20130259924).
The effective filing date of Carmona is 9-27-17, the filing date of provisional application 62563877, which is prior to applicants’ effective filing date of 3-27-19.
Carmona taught isolated mammalian retinal pigmented epithelial (RPE) cells comprising an exogenous nucleic acid sequence encoding Factor VII (FVII) (para 11, 39, 45). The cells in culture medium are an “implantable device” with a “cell-containing compartment” and a means for mitigating the foreign body response (FBR) when the device is implanted into the subject” because the medium is pH balanced and does not evoke an immune response in a subject (and because the phrases are indefinite).
Carmona did not teach the FVII was encoded by a nucleic acid sequence that is at least 95% identical to SEQ ID NO: 3 or 4 as required in claim 1.
However, SEQ ID NO: 1433 of Bancel encoded FVII and was at least 95% identical to SEQ ID NO: 3:
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(pg 45, Table 6, Target No: 142).
Thus, it would have been obvious to those of ordinary skill in the art at the time of filing to make isolated mammalian RPEs comprising an exogenous nucleic acid sequence encoding FVII as described by Carmona using the sequence of Bancel. Those of ordinary skill in the art at the time of filing would have been motivated to replace the exogenous sequence encoding FVII of Carmona with the exogenous sequence encoding FVII described by Bancel because the sequence of Bancel are codon optimized open reading frames (pg 36-37, para 228).
The exogenous nucleic acid is in a plasmid (Carmona para 499) which is extrachromosomal as required in claim 8.
Carmona used ARPE-19 cells (Para 499) as required in claim 9.
The RPEs in culture are the composition of claim 10.
Thus, Applicants' claimed invention as a whole is prima facie obvious in the absence of evidence to the contrary.
B) Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Carmona (20200263196) in view of SEQ ID NO: 1433 described by Bancel (US 20130259924) as applied to claims 1, 8-10 and further in view of BI770945 (2001).
The combined teachings of Carmona and Bancel taught isolated mammalian RPE cells comprising an exogenous nucleic acid sequence encoding Factor VII (FVII) that is at least 95% identical to SEQ ID NO: 3 for reasons set forth above.
The combined teachings of Carmona and Bancel did not teach the sequence was operably linked to a promoter that had the sequence of SEQ ID NO: 10 or 21 as required in claim 2.
However, Carmona taught the sequence was operably linked to a promoter (para 5, 72, 119) and the promoter of SEQ ID NO: 10 was known as shown in BI770945:
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Thus, it would have been obvious to those of ordinary skill in the art at the time of filing to make RPEs expressing FVII as described by the combined teachings of Carmona and Bancel using the promoter of BI770945. Those of ordinary skill in the art at the time of filing would have been motivated to use the promoter to functionally express FVII in the RPEs.
Thus, Applicants' claimed invention as a whole is prima facie obvious in the absence of evidence to the contrary.
It is assumed claim 3 is limited to using a nucleic acid sequence encoding FVII that is 100% identical to SEQ ID NO: 3.
It is assumed that claim 7 is limited to a plasmid comprising a nucleic acid sequence comprising SEQ ID NO: 22 which contains the nucleotide sequence of SEQ ID NO: 3.
The art at the time of filing did not reasonably teach or suggest a nucleic acid sequence encoding FVII that is 100% identical to SEQ ID NO: 3 as required in claims 3 or 7.
Conclusion
No claim is allowed.
Inquiry concerning this communication or earlier communications from the examiner should be directed to Michael C. Wilson who can normally be reached at the office on Monday through Friday from 9:30 am to 6:00 pm at 571-272-0738.
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Michael C. Wilson
/MICHAEL C WILSON/
Primary Examiner, Art Unit 1638
Prosecution Insights