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 2-3, 16, 19-20 have been canceled. Claims 1, 4-6, 9, 15-17 are still at issue and are present for examination.
Claims 7-8, 10-14, and 18 remain withdrawn as drawn to non-elected invention. Regarding rejoinder of some of dependent claims with the elected invention, applicant must rest assured that once allowable subject matter is identified, rejoinder of some of said dependent claims will be seriously considered by the examiner.
Applicants' arguments filed on 3/23/26, have been fully considered and are deemed to be persuasive to overcome some of the rejections previously applied. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 17 is 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. Claim 17 depends from canceled claim 16 and is therefore improper.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1, 5-6, 15 and 17 remain rejected under 35 U.S.C. 103 as being unpatentable over Fuenzalida et al., “Fuenzalida” (US2020/0165635, 5/2020, cited previously) in view of Ting et al., “Ting” (US2018/0203017, 7/2018, cited previously), according to previous office action.
In response to the last office action, applicant provided no specific explanations and simply amended the claims back to what was presented on 2/8/24, which was examined and rejected previously (see the office action prepared after applicant’s pre-appeal request of 10/4/24, currently of record). Therefore, the 103 rejection is repeated here from the office action of 10/4/24, as following:
As mentioned previously, Fuenzalida teaches (see [0006] and claims (see claim 19) “an in vitro method for enriching eukaryotic cells which are modified by homologous recombination, comprising
(a) subjecting a population of eukaryotic cells (transformed with a composition of matter (see claim 1) comprising a mixture of at least two different nucleic acid molecules, each nucleic acid molecule comprising at least one nucleotide sequence encoding a selection marker indicating homologous recombination when integrated in the sequence of interest comprised in a eukaryotic cell and at least one nucleotide sequence encoding a selection marker indicating heterologous recombination when not integrated in the sequence of interest comprised in said eukaryotic cell, wherein the selection markers when being expressed are optically discriminable, e.g. in FACS or any fluorescence guided capture, and wherein the nucleotide sequence encoding a selection marker indicating homologous recombination in a eukaryotic cell is flanked 5′ and 3′ by nucleotide sequences that are homologous to nucleotide sequences of a nucleic acid sequence of interest comprised by the eukaryotic cell, each of the at least two different nucleic acid molecules comprising a different nucleotide sequence encoding (1) a selection marker indicating homologous recombination in said eukaryotic cell and as a means for selecting said marker indicating heterologous recombination and separating transformed cells expressing said selection marker indicating heterologous recombination in said eukaryotic cell; and (2) a second marker for selecting heterologous recombination is said cell;
(b) subjecting the non-separated cells to means for selecting for said marker indicating homologous recombination in order to enrich transformed cells comprising said homologous recombination; optionally further comprising,
(c) subjecting said enriched cells to sequencing; optionally further comprising
(d) removing the nucleotide sequence encoding said marker indicating homologous recombination.
In claim 18, one of the selection markers is recited to be iLOV (which is not selectable antibiotic resistance marker).
In paragraph [0038], Fuenzalida further discloses that in a preferred embodiment the nucleic acid molecule of the invention comprises a chemical resistance selection marker may be HPRT1 and (such selection marker is not a selectable antibiotic resistance marker), see instant claim 6. And in [0039], Fuenzalida states that it is envisioned herein that the chemical resistance selection marker is associated or not associated with the selection marker indicating homologous recombination. Accordingly, the chemical resistance selection marker may be associated with the selection marker indicating homologous recombination via a linking element (i.e., a linker), e.g., P2A, T2A, E2A, F2A or and internal ribosome entry site (IRES), T2A being preferred.
In [0077-0080], Fuenzalida discloses that in another preferred embodiment the invention provides an in vitro method for producing eukaryotic cells comprising a modification in its genome introduced by homologous recombination, comprising
(a) subjecting a population of cells transformed with a nucleic acid molecule of the invention or a composition of the invention to means for selecting for said marker indicating heterologous recombination and separate transformed cells expressing said selection marker indicating heterologous recombination in said eukaryotic cell;
(b) subjecting the non-separated cells to means for selecting for said marker indicating homologous recombination in order to enrich transformed cells (which inherently comprises screening for cells expressing fivefold higher fusion titers than randomly transformants (see also 112 second rejection above)).In addition, in [0037], Fuenzalida recites: “The nucleotide sequence encoding a selection marker indicating homologous recombination may be removed by excision or recombination or cleavage after depositing a modification into the genome. The removal of the nucleotide sequence encoding a selection marker indicating homologous recombination may be performed by the use of a recombinase, transposase, RNA guided nuclease or nuclease. The excision, recombination or cleavage of the nucleotide sequence encoding a selection marker indicating homologous recombination may be induced by the expression of a recombinase, transposase, RNA guided nuclease or nuclease. Such enzyme can be delivered by electroporation or transfection of a double stranded DNA, transfection of a pre transcribed mRNA or pre translated protein” and,
(c) sequencing said enriched transformed cells in order to determine whether said enriched transformed cells comprise the desired modification.
Finally, in [0076] of Fuenzalida, it is recited that in a further preferred embodiment of the invention, the in vitro method for enriching eukaryotic cells which are modified by homologous recombination further comprises removing the nucleotide sequence encoding said marker indicating homologous recombination. Said marker indicating homologous recombination is preferably removed by excision. Fuenzalida neither specifically teaches an enterokinase cleavage site “DDDDK” nor utilizes Pichia pastoris as a host in its method.
Ting et al., teaches about polypeptide systems (and DNA encoding them) for detecting protein-protein interactions, prior to this invention. In claim1 parts (a)-(b), Ting recites a component of its system as following : (a) a nucleic acid system comprising a first nucleic acid comprising, in order from 5′ to 3′: a) a nucleotide sequence encoding a first, light-activated fusion polypeptide comprising, in order from amino terminus to carboxyl terminus: i) a transmembrane domain; ii) a first member of a protein interaction pair; iii) a LOV-domain light-activated polypeptide (see also [0542], wherein iLOV is explicitly mentioned); and iv) a proteolytically cleavable linker; etc. and (b) an insertion site for DNA encoding the polypeptide of interest.
In [0241], Ting mentions that an example of a protease cleavage site that can be included in a proteolytically cleavable linker is an enterokinase cleavage site, e.g., DDDDK, where cleavage occurs after the lysine residue, implying that the linker is longer than the cleavage site and hence, such proteolytically cleavable linker (or DNA encoding it) inherently has “a peptide linker” and a cleavage site. In [0342], Ting further teaches that its system can be introduced in Pichia pastoris and many other types of Pichia, many yeasts etc.
Before the effective filing date of this application, it would have been obvious to one of ordinary skill in the art to start with the method of Fuenzalida and depending on the desired recombinant protein of interest, employ the P. pastoris host cell of Ting instead of a eukaryotic host of Fuenzalida and employ LOV or iLOV markers of Ting (or DNA encoding them) together with a linker encoding “DDDDK” of Ting (or DNA encoding them).
One of ordinary skill in the art is motivated in substituting the eukaryotic host of Fuenzalida with a less expensive and faster-growing host of Ting, namely P. pastoris., utilizing a variety of fluorescent markers, see [0059], including iLOV thought by both Fuenzalida and Ting. This is because P. pastoris of Ting, despite being a relatively simple cell, is highly popular host for recombinant protein expression and allows for appropriate folding (in the endoplasmic reticulum) and secretion of recombinant proteins to the external environment of the cell. Moreover, in the P. pastoris expression system due to its limited production of endogenous secretory proteins, the purification of recombinant protein is easy, resulting in less expensive protein-production costs, rendering this invention obvious.
Finally, one of ordinary skill in the art has a reasonable expectation of success in substituting the eukaryotic host cell and linkers of Fuenzalida in the method Fuenzalida with those of Ting’s because, the prior art as evidenced by Boettner (J. Biotechnol., 99, 51-62, 2002, cited in the IDS) was fully established as how to transfect/transform P. pastoris cells, ferment them and obtain recombinant proteins therefrom, before the effective filing of this application.
Applicant is reminded that Boettner reference is not a part of this rejection and is merely cited to show the level of knowledge of one of ordinary skill in the art, before the effective filing of this application.
Allowable Subject Matter
Claim 4 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 is because a method for isolating recombinants produced from a host comprising creating a DNA sequence encoding a fusion protein by combining a DNA sequence encoding an iLOV protein (reporter protein) with a DNA sequence encoding a peptide linker and a cleavage site for enterokinase protease and a DNA sequence encoding an epidermicin-NI01 protein, wherein the peptide linker DNA sequence is between the iLOV protein DNA sequence and the epidermicin-NI01 encoding DNA sequence;
introducing the DNA sequence encoding the fusion protein into a host, the host comprising P. pastoris, to form transformants;
identifying and isolating from the transformants, using fluorescence detection, at least one recombinant which expresses the epidermicin-NI101 protein; and
isolating said epidermicin-NI01 from the fusion protein produced by the at least one recombinant by cleaving the iLOV protein and linker sequences from the target protein is free of prior at. Further, the prior art fails to suggest utilizing iLOV reporter protein (or DNA encoding it) in P. pastoris for recombinant expression of epidermicin-NI101 DNA sequence and isolating expression product of said DNA sequence, as specifically claims. Hence said method is also non-obvious.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARYAM MONSHIPOURI whose telephone number is (571)272-0932. The examiner can normally be reached full-flex.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melenie L Gordon can be reached on 571-272-8037. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MARYAM MONSHIPOURI/Primary Examiner, Art Unit 1651
Prosecution Insights