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 .
Notice of Pre-AIA or AIA Status
DETAILED ACTION
Status of the Claims
Claim 16, and 19-21 are cancelled. Claims 22-25 are new. Claims 1-15, 17-18 and 22-25 are pending and under examination.
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 .
Priority
This application is a national stage entry of PCT/EP2022/074095 filed on 8/30/2022, which claims priority from European applications EP22169108.2 filed on 4/20/2022 and EP21193811.3 filed on 8/30/2021.
Information Disclosure Statement
The information disclosure statement filed on 02/29/2024 has been considered by the examiner.
Claim Objections
Claims 11, 12, and 14 are objected to for containing periods in the claim (e.g. a., b., c., d.) where applicant can easily consider using notations such as a), b), c) or d). Generally, only one period is allowed at the end of the claim unless being used as a decimal point or other pertinent reason.
Claim 11 is objected to for “Inducing”, “Extracting” and “Isolating”, which should be lower case as “inducing”, “extracting” and “isolating”.
Claim 12 is objected to because it starts out separating ways to induce SlyB expression in the host cell using “-“, but then after the second recitation of “-“ provides for a list of different ways to cause the induction only separated by commas. Applicant should either continue with the “-“ notations for each different way or else, they can have each different type of induction in the group separated by either commas or semicolons.
Claim 25 is objected to for missing a “further” between “SlyB nanodisc” and “comprises” as “at least one macromolecule” is an addition to the nanodisc.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-10 and 22-24 rejected under 35 U.S.C. 101 because the claim is to a product of nature that is indicated as “isolated SlyB nanodisc” in the claim. However, the claim provides for the naturally occurring structure of a SlyB nanodomain as characterized by Janssens et al (Nature, December 2023, volume 626, pages 617-625). Janssens teaches that SlyB encapsulates outer membrane proteins (polypeptides) in stress-induced lipid nanodomains (title and abstract). Figure 4 teaches the lipid nanodomains that are formed with two SlyB proteins (tan color) surrounding phospholipid bilayer (blue color), lipid anchor (pink) with BamA outer membrane protein (a macromolecule) in the lipid bilayer (green), and Lipopolysaccharides around the outer portion of the SlyB proteins of the structure (in yellow). The figure legend of figure 4 provides that there is SlyB protomer (page 622). Jannsens was using cryo-EM structures in order to characterize the natural structure (page 621). Part e of figure 4 shows one LPS per one SlyB protomer (1:1 ratio). The first column on page 622 provides for BamA being enclosed in the lumen and Sly B oligomer. Note that figure 4 shows the shape of a disc for the nanodomain. Additionally, see part h of Figure 5 with how the nanodomains would occur in the lipid outer membrane of the cell. Janssens teaches conserved domains of SlyB protomer in gram negative bacteria (page 622). Since Janssens provides the structure of the claims and having SlyB and LPS, it would be immunogenic. Janssens teaches the structures in a cell membrane, and thus, are comprised in a cell that could be considered a host cell. Regarding claim 24, endogenous expression of SlyB can be affected naturally in a cell as are other proteins to reduce or raise it. Note that isolation here is not changing the natural structure or natural composition of the nanodomain. Additionally, teachings of Plesa et al (Res Microbiol, 2006, volume 157, pages 582-592) teach SlyB as a lipoprotein in the bacteria Burkholderia multivorans (abstract) and that SlyB mutants were identified (abstract). Figure 1 of Plesa provides for SlyB sequences from different bacteria. In regards to the size of the nanodiscs, Liu et al (Bioactive Materials, 2022, volume 14, pages 169-181) teaches that outer membrane vesicles of gram negative bacteria usually range from 20-250 nm (section 2.1) but also provides some vesicles from E coli were 15-100 nm (section 2.1). As outer membrane vesicles naturally occur and are capable of carrying components of the outer membrane, the SlyB nanodomains will be part of such vesicles.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-15, 17, 18 and 22-25 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 SlyB proteins of gram-negative bacteria, does not reasonably provide enablement for all the numerous proteins that the claims cover based on applicant’s broad definitions in the specification and in view of the protein also having to function in the nanodisc structure. 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 and use the invention commensurate in scope with these claims. Further below, it is noted that the definitions provided for SlyB oligomers and proteins by applicant extend beyond the sequences and types of variants that are offered in the specification for SlyB proteins for use in their invention.
Listov et al (Nat Rev Mol Cell Biol, Feb 1, 2025) teaches designing complex protein structures is challenging and is ongoing (abstract). Listov teaches in outlook that methods for designing proteins from scratch are limited and there are many challenges. Thus, making new proteins is a very challenging endeavor for those in the art.
The instant specification is toward SlyB and provides for conserved SlyB proteins. It does not teach proteins outside the scope of these for use as the oligomers that form the belt of the nanodisc, however, applicant provides a broad amount of alterations and for variants for the sequences it provides. Applicant’s specification allows for (see pages 26 and 27):
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and additionally in regards to SlyB proteins:
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The phrases of “SlyB proteins comprising amino acid sequences….”, “at least 60%, .... amino acid identity”, and “further SlyB mutant or variant sequence thereof” allows for many varying amino acid sequences and sequence additions, which would lead to different functional polypeptide sequences. Thus, it is not clear what the meets and bounds of the sequences are when applicant refers to SlyB oligomers and SlyB proteins in the claims. Claims 2 and 13 still allow for open language “SlyB proteins comprise” as well as “or a bacterial homologue with at least 80% identity…” where bacterial homologue is not specific to a functional sequence that applicant sees at their invention. Again, this leads to unclear scope of the claim. Thus, as the claims in light of the specification allow for many variations in sequence which would lead to substantial variations in protein function, the metes and bounds of the claimed invention is not clear. Applicant may provide a more defined limitation into the independent claims regarding sequences and if using % identities clarify the claim for those percent identities to allow for the necessary SlyB functions.
One of skill in the art is a biochemist.
As the art recognizes the difficulty with making new proteins and the specification does not teach one of skill in the art all the proteins that the claims would encompass based on broad definitions of the specification, one of skill in the art would have undue experimentation in order to make all such proteins and test them for the appropriate function for the nanodiscs as not all of them will be useful for that purpose based on numerous possible functions. Therefore, applicant does have enablement for the SlyB proteins with the sequences it discloses, but does not have enablement for the numerous variations of proteins covered by claims based on applicant’s definitions of what SlyB oligomers and proteins can encompass.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-15, 17, 18 and 22-25 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.
Claim 8 is indefinite for “molecular weight” in regards to the SlyB nanodisc-macromolecular complex. For one, there are multiple types of molecular weights such as Number average, weight average, Z-average and viscosity average and without an indication of what molecular weight is being referred to, it is unclear how to read the metes and bounds of this limitation. Secondly, the complex is made up of different molecules including SlyB protomer, lipids of the lipid bilayer, lipid anchor, saccharolipids, various types of macromolecules that could be nucleic acid, protein or others and so different types of molecular weights can apply to each part. Without providing how the molecular weight of the entire complex is calculated to one value, it is unclear how to read this limitation. For the purpose of compact prosecution, if the prior art teaches such a complex with components of or near to that of the applicant’s claims, it will be consider capable of having such a molecular weight.
Claim 2 recites the limitation "the SlyB proteins" in the claim with a first recitation being “two or more SlyB proteins”. There is insufficient antecedent basis for this limitation in the claim. Applicant may amend the claim to say “the two or more SlyB proteins”.
Claim 11 recites the limitation "the host cell culture" in the claim with a first recitation being “a host cell culture”. There is insufficient antecedent basis for this limitation in the claim. Applicant may amend the claim to have part a say “inducing SlyB expression in a host cell of a host cell culture”. As cells can exist in an organism or on a surface and not in culture, it cannot be presumed that the host cell of part a is in culture as the claim is stated.
Claims 12-15 are rejected as being dependent on an indefinite claim.
Claims 11, 14 and 15 recite the limitation "the isolated SlyB nanodisc particles" or “the SlyB nanodisc particles” in the claims with a first recitation in claim 11 being “one or more SlyB nanodisc particles”. There is insufficient antecedent basis for this limitation in the claim. Applicant may amend the claim to indicate these as “the one or more SlyB nanodisc particles”.
Claims 18 recites the limitation "the macromolecule" in the claim with dependence to claims 17 and 1 that have not introduced “macromolecule”. There is insufficient antecedent basis for this limitation in the claim.
Claims 1, 2, 11, and 13 are indefinite for the lack of clarity in SlyB protomer (protein, oligomer), which is a major portion of the SlyB nanodisc, and what proteins, the limitations actually cover. Applicant’s specification allows for (see pages 26 and 27):
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and additionally in regards to SlyB proteins:
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The phrases of “SlyB proteins comprising amino acid sequences….”, “at least 60%, .... amino acid identity”, and “further SlyB mutant or variant sequence thereof” allows for many varying amino acid sequences and sequence additions, which would lead to different functional polypeptide sequences. Thus, it is not clear what the meets and bounds of the sequences are when applicant refers to SlyB oligomers and SlyB proteins in the claims. Claims 2 and 13 still allow for open language “SlyB proteins comprise” as well as “or a bacterial homologue with at least 80% identity…” where bacterial homologue is not specific to a functional sequence that applicant sees at their invention. Again, this leads to unclear scope of the claim. Thus, as the claims in light of the specification allow for many variations in sequence which would lead to substantial variations in protein function, the metes and bounds of the claimed invention is not clear. Applicant may provide a more defined limitation into the independent claims regarding sequences and if using % identities clarify the claim for those percent identities to allow for the necessary SlyB functions. For the purpose of compact prosecution, prior art that reasonably reads on the structural features of the nanodisc will read on the claim since many variants are allowed.
Claims 3-10, 12, 14-15, 17-18, and 22-25 are rejected as being dependent on indefinite claims.
Claim Rejections – 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-12, 15 and 23 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al (Chemical Communications, June 2017, volume 53, pages 7569-7572, in applicant’s IDS) as evidenced by Janssens et al (Nature, December 2023, volume 626, pages 617-625).
Chen teaches multi-functional bacterial outer membrane vesicles and provides for E coli (title and abstract). Chen teaches “isolated” outer membrane vesicles that contain SlyB protein (figure 1). Chen teaches using PCR amplification of SlyB gene and introduction into a vector that can be overexpressed in cells (second column of page 7569). Chen teaches “Overexpression of either SlyB or SlyB-Nluc in whole-cell lysates and the membrane fraction was first demonstrated by Western blot (Fig. S1, ESI†). After collecting the resulting OMVs by ultracentrifugation, the presence of these proteins in OMVs was also confirmed by Western blot” (first column of page 7570). Chen teaches an average diameter of intact vesicles of 41 +/- 2 nm (39-43 nm) (first column, page 7571). Thus, vesicles can be below 40 nm in size. Chen teaches encapsulation of Nluc (a protein) inside OMVs with SlyB (this is within the lipid bilayer) (page 7571). Below Jannsens evidences the structure of the SlyB nanodomains/nanodiscs that form due to SlyB in the cell’s membrane. The SlyB-Nluc is a transgenic protein, and thus, is not a natural protein to the cell it is incorporated into making it heterologous. Figure 2 of Chen provides for the overexpression confirmation.
Janssens evidences the SlyB nanodomain (abstract). Janssens evidences that SlyB encapsulates outer membrane proteins (polypeptides) in stress-induced lipid nanodomains (title and abstract). Figure 4 evidences the lipid nanodomains that are formed with two SlyB proteins (tan color) surrounding phospholipid bilayer (blue color), lipid anchor (pink) with BamA outer membrane protein in the lipid bilayer (green), and Lipopolysaccharides around the outer portion of the SlyB proteins of the structure (in yellow). The figure legend of figure 4 provides that there is SlyB protomer (page 622). Jannsens was using cryo-EM structures in order to characterize the natural structure (page 621). Part e of figure 4 shows one LPS per one SlyB protomer (1:1 ratio). The first column on page 622 provides for BamA being enclosed in the lumen and Sly B oligomer. Note that figure 4 shows the shape of a disc for the nanodomain. Additionally, see part h of Figure 5 with how the nanodomains would occur in the lipid outer membrane of the cell. Janssens evidences conserved domains of SlyB protomer in gram negative bacteria (page 622). Since Janssens provides the structure of the claims and having SlyB and LPS, it would be immunogenic. Janssens evidences the structures in a cell membrane, and thus, are comprised in a cell that could be considered a host cell. Janssens also makes evident that outer membrane proteins of the cell will get incorporated into the nanodomains.
Thus, when overexpressing SlyB protein in bacterial cells, these nanostructures will form and when the nanovesicles are harvested, they will be isolated from the cell as evidenced by Jannsens. Before, cell production of nanovesicles, the nanodiscs will be part of the cell (comprised in the host cell).
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.
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 (i.e., changing from AIA to pre-AIA ) 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 14, 17, 18, 22, and 25 in addition to claims 1 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al (Chemical Communications, June 2017, volume 53, pages 7569-7572, in applicant’s IDS) and Fischer US 20200108133A1.
Chen’s teachings are provided above. Chen also recognizes its OMVs for antigen binding (abstract) and that liposomes are frequently used for therapy and diagnosis as they are compatible for drug delivery and biosensing (page 7569). Here, Chen also teaches they have applications in vaccines. Thus, OMVs are seen as having utilities for drug/vaccine delivery to subjects.
Chen does not teach mixing isolated SlyB nanodisc particles with a macromolecule to allow encapsulation of the macromolecule with the SlyB nanodisc, below 20 nm, or the method of claim 17 for immunizing a subject.
Fischer teaches antigenic combinations for immunizing a host from infection (abstract). Fischer provides for a nanodisc structure with scaffold proteins as a belt structure, lipids/lipid bilayer, and LPS (lipopolysaccharide) (Figure 3 and paragraph 7) that is similar to the structure of Chen as evidenced by Janssens. Figure 3 of Fischer teaches combining the IgIC with the nanodisc structure which leads to IgIC being put into the lipid bilayer of the nanodisc structure (the lumen of the structure). Fischer teaches administering an effective amount of the immunogenic composition (paragraphs 361-362). Fischer teaches protein antigens (paragraph 204). Fischer teaches 5 to 25 nm or 3 to 6 nm for the nanolipoprotein with discoidal shape (paragraph 237).
One of ordinary skill in the art before the time of filing would have utilized lipopolysaccharide discoidal protein lipid bilayer containing SlyB by combined teachings of Chen and Fischer for the delivery of immunogenic compositions like antigens as both references recognize these types of protein-lipid nanosystems for that purpose of vaccine and drug delivery. Thus, there was a reasonable expectation of success in combining the teachings of the references to provide for SlyB nanodiscs and using them for successfully delivering vaccine antigens to subjects for immunization/vaccination. Fischer also allows for sizes of less than 20 nm as well as the mixing/combining step to include the antigen into the lipid bilayer of the nanodisc carrier.
Claims 13 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al (Chemical Communications, June 2017, volume 53, pages 7569-7572, in applicant’s IDS) and Fischer US 20200108133A1 and Meuskens et al (Front Cell Infect Microbiol, 2017, volume 7, claims 1-13).
Chen and Fischer teaches the claims as discussed above.
Chen and Fischer does not teach using endogenous SlyB deficient cells for the overexpression/expression.
Meuskens teaches new strains for improved expression of outer membrane proteins (title and abstract). Meuskens teaches using deletion mutants of E coli designed for overexpression of outer membrane proteins (abstract). Meuskens teaches “These strains harbor deletions of four genes encoding abundant β-barrel proteins in the outer membrane (OmpA, OmpC, OmpF, and LamB), both single and in all combinations of double, triple, and quadruple knock-outs. The sequences encoding these outer membrane proteins were deleted completely, leaving only a minimal scar sequence, thus preventing the possibility of genetic reversion. (abstract). Meuskens teaches “As surface exposed molecules, outer membrane β-barrel proteins are also potential drug and vaccine targets” (abstract). Meuskens teaches “As the amount of competing OMPs is low, heterologous OMPs can be purified efficiently and simply with e.g., ion exchange chromatography, without the need to introduce affinity tags, which might compromise protein function. This applies even to transmembrane β-barrel proteins of eukaryotic origin, some of which have been produced in bacteria (page 11).
As SlyB is an outer membrane protein, one of ordinary skill in the art before the time of filing would also consider knocking it out in Chen in view of Fischer in order to improve overexpression of the recombinant form based on the teachings of Meuskens. There would be a reasonable expectation of success in making endogenous SlyB deficient cells and utilizing those cells for the overexpression of SlyB and other outer membrane proteins and getting improved overexpression particularly to use for isolation.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARK V STEVENS whose telephone number is (571)270-7080. The examiner can normally be reached M-F 9:00 am to 6:00 pm EST.
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/MARK V STEVENS/Primary Examiner, Art Unit 1613
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