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 .
DETAILED ACTION
Claim Status
Claims 1-5, 8, 12-14, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60 are currently pending. Claims 5, 8, 12, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54 have been amended. Claims 6-7, 9-11, 15-16, 18, 20-21, 23-26, 30-32, 35-36, 38-39, 41-45, 48-53, 55-59, 61-62 are canceled. Claims 1-5, 8, 12-14, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60 will be examined on the merits.
Priority
Acknowledgement is made of applicant’s claim for foreign priority based on an application filed on June 23, 2022. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement (IDS)
The information disclosure statement (IDS) submitted by Applicant is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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 (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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-4, 8, 12-14, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60 are rejected under 35 U.S.C. 103 as being unpatentable over Fisher et al. (WO 2021257788 A1; hereafter Fisher; PTO-892) in view of Zhang et al. (Published April 12, 2016; hereafter Zhang; PTO-892) and further view of Bryan et al. (Published February, 2006; hereafter Bryan; PTO-892) as evidenced by Salem-Bekhit et al. (Published November 23, 2021; hereafter Salem-Bekhit; PTO-892).
Fisher teaches that “the term “achromosomal dynamic system” or “ADAS” refers to a genome-free, non-replicating, enclosed membrane system comprising at least one membrane and having an interior volume suitable for containing a cargo (e.g., one or more of a nucleic acid, a plasmid, a polypeptide, a protein, an enzyme, an amino acid, a small molecule, a gene editing system, a hormone, an immune modulator, a carbohydrate, a lipid, an organic particle, an inorganic particle, or a ribonucleoprotein complex (RNP)), which is pertinent to claim 1, 27-28, 60. See for example, page 4; lines 25-30.
Fisher teaches ADAS can include a variety of additional components, including, for example, metabolic enzymes, targeting agents, cargo, bacterial secretion systems, and transporters, including combinations of the foregoing, which is pertinent to claim 27-28. See for example, page 5; lines 3-9.
Fisher teaches methods of delivering an ADAS, a method for delivering an ADAS to a target cell, the method comprising: (a) providing a composition comprising a plurality of ADAS; and (b) contacting the target cell with the composition of step (a). The target cell may be, e.g., an animal cell, a plant cell, or an insect cell, which is pertinent to claims 1, 34, 37, 40, 46-47, 60. See for example, page 29; lines 12-35.
Fisher teaches “ADAS may be derived from parent bacteria using any suitable method, e.g., genetic manipulation of the parent cell or exposure to a culture or condition that increases the likelihood of formation of bacterial minicells. Exemplary methods for making ADAS are those that disrupt the cell division machinery of the parent cell. In some embodiments, ADAS may comprise one or more endogenous or heterologous features of the parent cell surface, e.g., cell walls, cell wall modifications, flagella, or pilli, and/or one or more endogenous or heterologous features of the interior volume of the parent cell, e.g., nucleic acids, plasmids, proteins, small molecules, transcription machinery, or translation machinery. In other embodiments, ADAS may lack one or more features of the parent cell. ADAS may be loaded or otherwise modified with a feature not comprised by the parent cell, which is pertinent to claims 1, 8, 12, 54, 60. See for example, page 3; lines 30-35.
Fisher teaches “ADAS are minicells or modified minicells derived from a parent bacterial cell (e.g., a gram-negative or a gram-positive bacterial cell), which is pertinent to claim 22, 60. See for example, page 10; lines 12-15.
Fisher teaches “the ADAS (e.g., highly active ADAS) is made from a parent strain that is a human bacterium, such as a commensal human bacterium (e.g., E. coli, Staphylococcus sp., Bifidobacterium sp., Micrococcus sp., Lactobacillus sp., or Actinomyces sp.) or a pathogenic human bacterium (e.g., Escherichia coli EHEC, Salmonella typhimurium, Shigella fiexneri, Yersinia enterolitica, or Helicobacter pylori), or an extremophile”, which is pertinent to claim 22. See for example, page 23; lines 3-11; page 24-27; table 1; page 27; lines 8-27.
Fisher teaches “methods for manufacturing purified preparations of achromosomal dynamic active systems (ADAS), including highly active ADAS”, which is pertinent to claim 1. See for example, page 10; lines 27-36.
Fisher teaches “the preparation of step (a) is a pellet produced by a process comprising providing a supernatant of a culture comprising a plurality of ADAS and a plurality of parent bacterial cells,”, which is pertinent to claim 1. See for example, page 2; lines 24-29; page 6; lines 23-35.
Fisher teaches that a cargo may be any moiety disposed in the interior of an ADAS (e.g., encapsulated by the ADAS) or conjugated to the surface of the ADAS, which is pertinent to claims 27-29, 33. See for example, page 16; lines 11-14.
Fisher teaches “the bacterial secretion system is capable of exporting a cargo across the ADAS outer membrane into a target cell, such as an animal, fungal, bacterial, or plant cell, such as T3SS, T4SS, T3/T4SS, orT6SS”, which is pertinent to claims 27-28, 40, 46-47, 60. See for example, page 25; lines 19-25.
Fisher teaches that “the bacterial secretion system is a T3/4SS. A “T3/4SS” is a secretion system based on T3SS or T4SS, including hybrid systems as well as unmodified versions, which forms a protein tube between a bacterium (or ADAS) and a target cell, connecting the two and delivering one or more effectors. The target cell can be an animal, plant, fungi, or bacteria. In some embodiments a T3/4SS includes an effector, which may be a modified effector. Examples of T3SS systems include the Salmonella SPI-1 system, the EHEC coli ETT1 system, th e Xanthamonas Citri/Campestri T3SS system, and the Pseudomonas syringae T3SS system”, which is pertinent to claims 27-28. See for examples, page 25; lines 28-34.
Fisher teaches that “an ADAS provided by the invention comprising a bacterial secretion system comprises a T6SS. The T6SS, in its natural host, targets a bacterium and contains an effector that kills the bacteria. In certain particular embodiments, the T6SS is derived from P. putida K1-T6SS and, optionally, wherein the effector comprises the amino acid sequence of Tke2 (Accession AUZ59427.1), or a functional fragment thereof. In other embodiments, the T6SS, in its natural host, targets a fungi and contains an effector that kills fungi, e.g., the T6SS is derived from Serratia Marcescens and the effectors comprise the amino acid sequences of: Tfe1 (Genbank: SMDB11_RS05530) or Tfe2 (Genbank: SMDB11_RS05390), which is pertinent to claims 27-28, 60. See for example, page 20; lines 3-10.
However, Fisher does not teach constitutively express a type 1 pilus (Ti1P) as claim 1.
Fisher does not teach a modified fimS promoter that is operably linked to, and directs constitutive expression of, the components of the Ti1P as claim 2.
Fisher does not explicitly teach the components of the Ti1P are encoded by a fim operon as claim 3.
Fisher does not teach a mutation at a recombinase cleavage site that prevents recombination of the fimS promoter into an 'OFF' orientation, as claims 4, 17.
Zhang teaches “T1P are encoded by the fim operon; their expression is phase variable via inversion of fimS, a chromosomal DNA segment containing the fim promoter. This binary epigenetic switch results in bacteria switching between fimbriated and nonfimbriated states. Inversion is mediated by the FimB and FimE recombinases, whose genes are located immediately upstream of fimS and are found in most E. coli strains, which is pertinent to claims 1-3, 60.
Zhang teaches “comprehensive mutagenesis of the fimS promoter regulatory switch reveals novel regulation of type 1 pili in uropathogenic Escherichia coli”, which is pertinent to claims 1-4, 17, 60. See for example Figure 1.
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Zhang teaches “The percent of phase OFF reads was calculated for each mutation at each position, yielding a comprehensive map of changes in phase variation bias associated with mutations throughout fimS. Regions of fimS known to have large effects on phase variation when mutated were clearly identified, including the fim promoter transcriptional start site at position 349 and binding sites for fim recombinases at positions 36–72 and 343–376”, which is pertinent to claims 2-4, 17, 60. See for example, Fig. 1B; Figs. S2 and S3A.
Zhang teaches that the recombinases bind the fimS IRs [denoted “IR left” (IRL) and “IR right” (IRR)] during inversion, which is pertinent to claims 1-4, 17, 60.
Zhang teaches generation of fimS mutant strains, Locked-ON (LON) strains. The phase LON strains with the fimS (G398A) mutation were created by replacing genomic fimS in phase LON strains with the positive–negative selection cassette. The phase LON strains used were HZ215 and SLC-490. HZ215 harbored deletions in fimB, fimE, and fimX, whereas SLC-490 contains an inversion of IRL (fimS_ON; INV48-56; G to C mutation at position 398, C to G mutation at position 440 of fimS); both strains are unable to recombine at the fim switch, which is pertinent to claims 1-4, 8, 17, 60. See for example, Table S1 (strains).
Zhang also teaches HZ183–185 strain (fimS_ON (INV48-56, G398A), inversion of left inverted repeat, G to A mutation at position 398 in fimS, phase locked ON, which is pertinent to claims 1-4, 8, 17, 60. See for example, Table S1 (strains).
Zhang teaches “a negative selection system usable in unmodified E. coli clinical isolates enables the creation of markerless and scarless chromosomal mutant libraries, similar to genome editing mediated by CRISPR. Inclusion of sequence context flanking fimS enabled to discover a previously unknown pair of IRs (termed “UIRs” for 5′ UTR inverted repeats) that ensure high expression of fimA compared with other fim operon genes and may coordinate T1P expression with other pilus systems. Our results advance the high expression of fimA compared with other fim operon genes and may coordinate T1P expression with other pilus systems understanding of T1P regulation and provide a general method for studying other phase-variable and epigenetically regulated systems”, which is pertinent to claims 5, 54, 60.
Zhang teaches “T1P present a tip adhesin, FimH, that binds specifically to mannose, which is found on several glycosylated surface proteins, such as uroplakins and α1- and β3-integrins (4, 5), in the mammalian bladder. Binding to mannosylated proteins initiates a cascade of events including UPEC invasion of host tissues (2), formation of intracellular structures (6), and activation of the host immune response”, which is pertinent to claims 1, 60.
Zhang teaches that RNA structural probing on the fimA 5′ UTR., UIR mutations can affect fimA RNA structure, and these changes correlate well with in vivo phase and HA titer phenotypes, qRT-PCR of fim transcripts under ON induction. fimA transcript levels in all mutants (except G398C/C440G) were specifically reduced (∼2× lower; note log scale in Fig. 3B) compared with other fim transcripts. To verify that the low fimA transcript level was the primary defect, we overexpressed FimA using the fimS promoter (preserving the WT UIRs in trans) or the lacZ promoter (completely replacing the native fimA 5′ UTR, including the UIRs, in the plasmid-encoded fimA) in the G398A mutant. In both cases, supplying additional fimA transcript restored phase variation, MSHA, and MRHA titers to WT levels (Fig. 3C and Fig. S5C), implying that the UIRs act through fimA levels, which is pertinent to claims 1-4, 8, 17, 60. See for example, Figure 3. See figure below.
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Zhang teaches that the HA assay of the IR mutants G50A and C358T, and Wild-type strain (WT” refers to the parental UTI89 strain) under ON induction. Average log2 (HA titers), with SEs (y axis), for each mutant (x axis) are plotted using data from at least three independent experiments. Blue and orange bars represent HA titers performed without mannose and with 4% mannose added, respectively. (E) HA assay. Average log2 (HA titer), which is pertinent to claims 5, 54, 60. See for example, Figure S4. See Figure below.
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Zhang teaches that previous studies of T1P phase variation used in vitro assays, candidate gene approaches, and reporter fusions in nonpathogenic E. coli strains. Laboratory-adapted strains provide convenience in genetic manipulation, but, as mentioned above, regulation relevant to infection may differ in clinical isolates, which is pertinent to claims 1-4, 8, 17, 60.
However, neither Fisher nor Zhang teach the fim operon of E. coli CFT073 as claim 13.
Fisher and Zhang do not teach the preparation wherein the one or more heterologous nucleotide sequences comprise a sequence having at least 90% identity to the nucleotide sequence of SEQ ID NO: 1 as claim 14.
Bryan teaches that it is known that when CFT073 constitutively expresses type 1 fimbriae there is a decrease in motility but that mutants involved in motility (e.g., fliC, motB, and cheW) do not necessarily upregulate expression of type 1 fimbriae, which is pertinent to claims 13-14. See for example, Table 1.
Bryan teaches the ipuA and ipbA genes function in trans at the fim switch. No switching was observed, are fim OFF WAM2920 and fim ON WAM2921, controls in which all five recombinases are deleted. CFT073 fim switch “locked-on” and “locked-off” mutants previously isolated by Gunther et al. Also, for strains with fimBE deleted that started with fim in the on orientation, no switching to the off orientation was observed at any time, whether when the bacteria were taken directly from the urine or after the urine was plated onto LB plates and bacteria were grown overnight. See for example, Figures 2-5.
Bryan teaches Sequencing and annotation of the genome of CFT073 was described previously by Welch et al. In brief, GLIMMER was used to define open reading frames, and predicted proteins were searched against the database by using BLAST. A total of five fimBE-like recombinase genes were found in the genome of CFT073 (GenBank accession no. AEO14075). Aside from fimB and fimE, two were found at the region corresponding to 53′ of the E. coli K-12 genome near argW and were named ipuA and ipuB for integrase-like proteins in uropathogenic E. coli. The third is at the 7′ region next to the betABIT genes and was named ipbA for integrase-like protein at the betaine locus. Percent identity and similarity to the known fimBE recombinase genes of E. coli K12 (GenBank accession no. U00096) were determined by using BLASTp. Predicted protein sequences were aligned with the known sequences of FimB and FimE in E. coli K-12 using the ClustalW program in MacVector 7.2.2 (Accelrys Inc.) to identify the presence of the four catalytic amino acids known to be important for the lambda family of site-specific recombinases, which is pertinent to claim 14.
Bryan teaches the sequence GenBank accession no. AEO14075 (fim operon sequence from uropathogenic E. coli strain, CFT073), which is 100% identical to SEQ ID NO: 1, which is pertinent to claims 14. See Figure below and PTO-892 (NCBI – GenBank accession no. AEO14075).
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However, the expression of a type I pilus (T1P) in a parental bacterial cell and further production of ADAS is not taught by Fisher, Zhang and Bryan.
Salem-Bekhit teaches bacterial ghosts (BGs) are empty cell envelopes of nonliving evacuated bacterial cells. They are free from their cytoplasmic contents; however, they sustain their cellular 3D morphology and antigenic structures, counting on bioadhesive properties. Lately, they have been tested as an advanced drug delivery system (DDS) for different materials like DNA, peptides, or drugs, either single components or combinations. Different studies have revealed that, BG DDS were paid the greatest attention in recent years, which is pertinent to 1-5, 8, 12-14, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60.
Salem-Bekhit teaches that host colonization through bacterial adhesion to host surfaces is a crucial stage as it protects pathogens from mechanical clearance, conferring a notable advantage towards the endogenous microbiome. Accordingly, bacteria have displayed a diversity of molecular strategies allowing them to target and attach to host cells. The polymeric hair-like organelles known as pili are regarded as the first class of molecular structures involved in the adherence of bacteria to host cells. Via pyelonephritis-associated (P) pili at their surface, uropathogenic strains of E. coli (UPEC) colonize the urinary tract, resulting in kidney infections. Other UPEC strains have type I pili at their surface, which binds specifically to D-mannose receptors residing on the lining of the bladder. Additionally, another class of adhesive surface structures, type IV pili, are expressed by different Gram-negative bacteria, which is pertinent to 1-5, 8, 12-14, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60. See for example, Figure 4.
Salem-Bekhit teaches that foreign target antigens can be displayed on the surface of BGs as fusion protein with pili or with outer-membrane proteins. Furthermore, BGs can be loaded with active compounds, signifying ideal, target-oriented drug delivery vehicles. Ghosts have a sealed periplasmic compartment and the transfer of proteins into this space massively extends the capacity of BGs or recombinant BGs to function as transporters of foreign antigens, immunomodulators or other medications, which is pertinent to 1-5, 8, 12-14, 17, 19, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60.
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Therefore, it would have been obvious to one of ordinary skill in the art to combine the teachings of Fisher, Zhang and Bryan as evidenced by Salem-Bekhit, thereby arriving at the invention of claims 1-4, 8, 12-14, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60. Because Fisher teaches achromosomal dynamic system (ADAS) also known as minicells, which is a versatile system that can be used for delivery vectors capable of targeting cells and delivering biological agents, compositions containing such delivery vectors, and associated methods of delivering said vectors to cells. Moreover, both Zhang and Bryan teach uropathogenic E. coli fimS operon regulations, sequences and mechanisms to lock ON the expression (constitutive) of a type 1 pilus (TP1P), and discuss the E. coli fimS operon differences between pathogenic and laboratory strains. It would be very desirable and beneficial to combine the teachings of Fisher, Zhang and Bryan because as evidenced by Salem-Bekhit, the use of empty cell envelopes of nonliving evacuated bacterial cells prepared from bacterial parental cells (which are very similar to the concept of minicells/ADAS) associated with type I pili from UPEC strains would be very desirable as an advanced drug delivery system (DDS) for different materials like DNA, peptides, or drugs, either single components or combinations. Thus, one of skill in the art would know that type I pilus system from pathogenic E. coli bacteria, which has the best type I pili for delivering the target molecules to a host cell could be rewired into a domestic well-known laboratorial strain to produce a parental strain carrying the heterologous T1P. It would also be obvious to one skilled in the art to know that by rewiring a genetic circuitry in a bacterial strain, the expression levels of genes associated with T1P would have to be adjusted, for example by switching promoters, gene mutations, gene deletions and/or adopting the use of plasmids to achieve the level of gene expression for the new bacterial strain, it would have been obvious to substitute these known equivalents to one skilled in the art; see MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Therefore, claims 1-4, 8, 12-14, 22, 27-29, 33-34, 37, 40, 46-47, 54, 60 would have been prima facie obvious, absent evidence to the contrary.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements were known in the art (Ghosts cells; ADAS; uropathogenic E. coli FimS promoter, FimS operon, and regulatory system for production of fimbria (Type I pilus); advanced delivery system based on type I pilus, mutant strains; bacterial secretion system also used for delivery). In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
/PRICILA NMN HAUK TEODORO/Examiner, Art Unit 1645
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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