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
Applicant’s response dated 09/26/2025 is duly acknowledged.
Claims 18-20 (non-elected invention of Group II, with traverse) were previously canceled by applicants.
Claim 23 has been newly presented for examination.
Claims 1-17 and 21-23 (elected invention of Group I; directed to products in the form of “A genetically modified Clostridium strain…”, “Clostridium spore…” and “A composition comprising cells…”), as currently amended/presented, have been examined on their merits in this action hereinafter.
Priority
This application is a 371 of PCT/EP2020/087338 (filed on 12/18/2020), which claims domestic benefit from a US PRO 62/949,480 filed on 12/18/2019, and foreign priority from an European application EP 19217672.5 filed on the same date of 12/18/2019.
Objection to Specification - Withdrawn
In view of submission of amended specification on 09/26/2025, the objection to specification, as previously made (for embedded hyperlink) by the examiner, has been withdrawn.
Claim Rejections - 35 USC § 112 - Withdrawn
In view of amendments to instant claim 1 and 5, the 112b rejections as previously made by the examiner, have been withdrawn.
The following contains new grounds of objection/rejection necessitated by applicant’s current amendments to pending claims.
Claim Objections - Maintained
1. Claim 1 (as currently amended) is/remains objected to because of the following informalities: amended claim 1 recites the preamble limitations “…Clostridium strain characterized by…”, which should be amended to clarify, for instance “…Clostridium strain comprising…”, if appropriate. Appropriate correction is still suggested.
2. Claim 1 (as currently amended) is also objected to because of the following informalities: amended claim 1 recites the limitation in section (c), “a Clostridium metabolism gene”, wherein the biological name should be properly italicized as “Clostridium metabolism gene” in order to conform to the rest of the claim. Appropriate correction is required.
NOTE: 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.
Claim Rejections - 35 USC § 103 - New Grounds
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.
1. Claims 1-17, 21 and 22 (as currently amended) are/remain rejected under 35 U.S.C. 103 as being unpatentable over KUBIAK et al (2015; NPL cited in IDS dated 03/07/2024, citation no. 24) taken with BJOERNVAD et al (WO 2012/022777 A1; FOR previously made of record) and GONZALEZ et al (2010; NPL previously made of record).
Claim 1 (as currently amended) is directed to “A genetically modified Clostridium strain presenting characterized by:
(a) a sporulation phenotype that is inducible or repressible, wherein the sporulation phenotype is defined by a deletion, substitution, or insertion of a DNA sequence controlling expression of one or more Clostridium genes for Clostridium strain sporulation;
(b)
Clostridium haemolysis gene ; and
(c) one or additional genome modifications that inactivate or attenuate at least one Clostridium metabolism gene.”
Claim 8 is directed to “The genetically modified Clostridium strain according to claim 1, wherein the Clostridium strain is genetically modified to inactivate or attenuate at least one Clostridium gene for haemolysis, wherein the Sag operon is deleted.”
See also limitations of dependent claims 2-7, 9-17, 21 and 22 as currently presented (it is to be noted that none of the functional features recited in instant claim 1 require any specific nucleotide and/or amino acid sequence(s) per se).
Kubiak et al (2015), while reviewing the potential of clostridial spores as therapeutic delivery vehicles in tumor therapy (see Title, Abstract, entire section 3, Fig. 1, and Table 1), disclose the use of endospore forming Clostridium species, either on their own, or as a tumor delivery vehicle for anti-cancer drugs, because of the fact that intravenously (i.e. systemic administration) injected spores of these obligate anaerobes can exclusively germinate in the hypoxic/necrotic regions present in solid tumors and nowhere else in the body (see Abstract); wherein they disclose the mechanism of Clostridial-Directed Enzyme Prodrug Therapy (CDEPT) utilizing Clostridium sporogenes engineered spores as a delivery vector, wherein a nitroreductase gene (Prodrug Converting Enzyme, PCE) is expressed and integrated into the genome of C. sporogenes; wherein spores of the therapeutic strain (i.e. a composition comprising said strain) were prepared in commercial environments and injected (i.e. taken as in suspension form) into tumor-bearing animals; wherein after tumor colonization, a prodrug is delivered; wherein inside the tumor upon the spore germination, the expressed PCE subsequently converts the prodrug into a cytotoxic derivative killing or destroying the tumor or cancer cells (see schematic drawing, Fig. 1, for instance; and entire section 3.2); wherein the PCE can be used that comprise a tumor-specific antibody, and/or other suitable therapeutic modalities, for instances; wherein the PCE genes can be integrated (using allele-coupled exchange, ACE) into the clostridial genome itself (see section 4.4 on page 249, for instance) using pyrE locus, for instance that makes the integrated strains auxotrophic for uracil (i.e. cells lack metabolic pathway genes/enzymes for synthesizing uracil on their own, and need to be supplied exogenously for growth) and thus can be screened for growth on uracil phenotype for such recombinant cells, wherein once integrated into the clostridial genome, the therapeutic gene has advantage of being stably maintained, minimizing any risk of its loss, or of its dissemination by horizontal gene transfer (see section 4.4, 1st paragraph, for instance); wherein non-pathogenic clostridial delivery strains may be modified to express PCEs, antigens, or other therapeutic molecules that can be secreted into tumor environment in order to attract body’s defense mechanism and immunological anti-tumor response, for instance (see section 5.3 on page 251). They also disclose the art-known fact that Clostridium species are obligate, rod-shaped anaerobes and in common with the aerobic genus Bacillus, produce endospores in order to survive adversity (see section 3.1, 1st paragraph, for instance).
However, a genetically modified Clostridium strain having sporulation genes (see instant claims 3, 4, 12) under inducible or repressible promoter (for controlling expression of sporulation genes such as SpoOA SpaIIE, SpoIIAA, or SpoIIAB) has not been disclosed and/or taught by Kubiak et al, as discussed above.
Bjoernvad et al (2012) disclose conditional promoter inducible by factors such as stress such as low phosphorus conditions that control sporulation genes (albeit exemplified in another spore forming bacteria Bacillus species; see Title, Abstract, and Summary of the invention); wherein they disclose various types of conditional promoters that can be used (i.e. operationally linked) with sporulation genes in order to control their expression (see page 4, 2nd and 3rd paragraphs, for instance), examples of which are well known in the art such as tetracycline inducible promoter, xylose inducible promoters, or IPTG-inducible promoters, for instances; wherein the sporulation factors may be one of the stage II-III of sporulation, including SpoIIAC, SpoIIE, SpoIISB, SpoIIGB (see page 10, 2nd paragraph, for instance).
Thus, to a person of ordinary sill in the art, such modifications in the sporulation gene expression using various types of suitable conditional promoters for controlling expression of Clostridial sporulation phenotype or sporulation frequency would have been obvious to an artisan in the art, especially given the advantages of having appropriate control and/or regulation of the sporulation phenotype as may be desired for various downstream purposes including for preparations for therapeutic purposes as already eluded by the disclosure from Kubiak et al, as discussed above. Since, no specific criticality has been disclosed in the instant disclosure of record, and instant claim 1 as currently recited is generic for sporulation genes and for the type of conditional promoter per se, an artisan of ordinary skill in the art could reasonably employ any known conditional promoter for controlling the expression of sporulation genes of therapeutic Clostridium species, as disclosed by the combined teachings and/or suggestions from Kubiak et al when taken with disclosure from Bjoernvad et al. The limitations of claims 13-17, 21 and 22 would have been obvious to a person of ordinary skill in the art as Kubiak et al disclose spore preparations that can be injected in a subject in need and that have pharmacological properties for therapeutic/anti-cancer purposes disclosed.
However, the genetically modified Clostridium strain of claim 1, additionally having inactivated or attenuated “at least one Clostridium gene for haemolysis, wherein the Sag operon is deleted”, has not been specifically disclosed by the cited prior art references of Kubiak et al taken with Bjoernvad et al, as discussed above.
Gonzalez et al (2010), while teaching a post-translationally modified biotoxin from Clostridium botulinum (see Title, Abstract, and entire section of Introduction), disclose the fact that streptolysin S (SLS) is a well-known hemolytic/cytolytic, ribosomally encoded bacteriocin and virulence factor group A Streptococcus (GAS), which is used to characterize beta-hemolytic phenotype as one of the clinical diagnostic tools for this class which also includes bacteria from Clostridium species, and wherein SLS family gene clusters and clostridiolysin S gene clusters are defined by similar set of genes (see Introduction, right column on page 28220; and Figure 1 on page 28224), that are also shown to be functionally similar in terms of induction of hemolysis phenotype and thus virulence and/or pathogenic phenotypes known in Clostridiales (see Discussion on page 28228). They also disclose gene deletion/hemolytic complementation methods (such as SagA and ClosA gene clusters; see section “Experimental Procedures” on page 28221) in order to create Clostridium species mutants and/or variants lacking such hemolytic phenotypes (see entire section of Results starting on page 28223), which may be used as anti-infective strategy (i.e. to attenuate virulence of given Clostridium strains) and for other similar therapeutic purposes (see entire section of Discussion on page 28228). Although, Gonzalez et al do not directly disclose the use of Clostridium species as delivery vehicles for heterologous gene products in mammalian cells or subjects in need thereof, they do disclose the need and methods to attenuate such virulence factors including streptolysin S and Clostridolysin S by genetically altering and/or knocking out genes (such as SagA or ClosA related gene clusters) that are known to be responsible for their expression/production, and hemolytic phenotype and/or functions associated with them.
Thus, to an artisan of ordinary skill in the art, it would have been obvious to modify the Clostridium strains as disclosed by Kubiak et al taken with Bjoernvad et al such that said Clostridium strain that is designed to function as a therapeutic delivery vehicle for heterologous gene product, is (additionally) made less virulent by deleting the genes that are responsible for production of hemolytic components/enzymes, in order to be safer therapeutic delivery vector for clinical/tumor oncolysis purposes for instance, as already eluded in details by Kubiak et al, as discussed above (see Kubiak et al, section 5.1, page 250, 3rd paragraph, for instance). Since, the methods for genetic manipulations of Clostridium species sporulation genes have already been disclosed and/or known in the prior art as demonstrated by Gonzalez et al discussed above, unless evidence presented to the contrary on record, such genetic modifications in Clostridium strain(s) would have been obvious and/or fully contemplated by an artisan of ordinary skill in the art (at least as an anti-infective strategy, as already eluded by the disclosure of Gonzalez et al).
2. Claim 23 (newly recited) is rejected under 35 U.S.C. 103 as being unpatentable over KUBIAK et al (2015; NPL cited in IDS dated 03/07/2024, citation no. 24) taken with BJOERNVAD et al (WO 2012/022777 A1; FOR previously made of record) and GONZALEZ et al (2010; NPL previously made of record), as applied to claims 1-17, 21 and 22 above, and further in view of BANERJEE et al.( 2014; NPL cited as ref. [U] on PTO 892 form).
Claim 23 as newly presented has been reproduced as follows:
PNG
media_image1.png
93
674
media_image1.png
Greyscale
The detailed teachings and/or suggestions from Kubiak et al taken with Bjoernvad et al and Gonzalez et al as they pertain to claims 1-17, 21 and 22 as presented have been discussed above, and further relies upon in the same manner hereinafter.
However, the genetically modified Clostridium strain, wherein “the inducible or repressible DNA promoter sequence is a lactose dependent promoter…” (instant claim 23) has not been specifically disclosed by the cited prior art references of Kubiak et al taken with Bjoernvad et al and Gonzalez et al, as discussed above.
Banerjee et al (2014) disclose lactose-inducible system for metabolic engineering of Clostridium strains, in particular Clostridium ljungdahlii (see Title, Abstract, and Introduction on page 2410); wherein they disclose the fact that the lactose-inducible regulator and promoter system for gene expression bgaR-PbgaL sequence (see page 2410, right column, for instance. And cited references therein) can be engineered into various strains of Clostridium, and can provide effective control for lactose-dependent expression of a diversity of genes introduced downstream of the PgaL sequence; which they successfully cloned using suitable plasmid vector and demonstrated controlled expression of metabolic genes encoding, for instance aldehyde/alcohol dehydrogenase AdhE1 gene (see Abstract), demonstrating the fact that such lactose-dependent promoter system will be useful for desired metabolic engineering of various Clostridium strains.
Thus, to an artisan of ordinary skill in the art, such modification in the genetically engineered Clostridium strains as to incorporate lactose-inducible or lactose-dependent control of expression of sporulation genes as disclosed by the combined teachings from Kubiak et al taken with Bjoernvad et al and Gonzalez et al, would have been obvious and/or fully contemplated, at least for the benefit of superior expression and control of downstream genes under the PgaL promoter sequence as specifically taught and demonstrated for a 30-fold increase of expression over wild-type strain (see Abstract on page 2410; Figures 2-3 on page 2412), albeit using adhE1 gene expression in Clostridium ljungdahlii strain. Since, the methods for genetic manipulations of Clostridium species sporulation genes have already been disclosed and/or known in the prior art as demonstrated by Gonzalez et al discussed above, such genetic modifications in desired Clostridium strain(s) would have been obvious and/or fully contemplated by an artisan of ordinary skill in the art, unless evidence and/or data provided on record to the contrary (which is currently lacking on record). Thus, the invention as currently claimed fails to distinguish itself over the combined teachings and/or suggestions from the cited prior art references of record as discussed above.
It is also noted to applicants that the scope of the showing must be commensurate with the scope of claims to consider evidence probative of superior or unexpected results, for example. In re Dill, 202 USPQ 805 (CCPA, 1979), In re Lindner 173 USPQ 356 (CCPA 1972), In re Hyson, 172 USPQ 399 (CCPA 1972), In re Boesch, 205 USPQ 215, (CCPA 1980), In re Grasselli, 218 USPQ 769 (Fed. Cir. 1983), In re Clemens, 206 USPQ 289 (CCPA 1980). It should be clear that the probative value of the data is not commensurate in scope with the degree of protection sought by the claims (see instant claim 1, for instance).
Thus, the claim as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the invention as claimed.
As per MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. In re American Academy of Science Tech Center, F.3d, 2004 WL 1067528 (Fed. Cir. May 13, 2004)(The USPTO uses a different standard for construing claims than that used by district courts; during examination the USPTO must give claims their broadest reasonable interpretation.). This means that the words of the claim must be given their plain meaning unless applicant has provided a clear definition in the specification. In re Zletz, 893 F.2d 319, 321, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989).
Examiner’s Response to Arguments
Applicant’s arguments with respect to claims 1-17, 21 and 22 as they pertain to the 103(a) rejection of record (see REM dated 09/26/2025, pages 8-13) have been considered but are moot because of the new grounds of objections/rejections made in this office action, as discussed above in details.
Conclusion
NO claims are currently allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 SATYENDRA K. SINGH whose telephone number is (571)272-8790. The examiner can normally be reached M-F 8:00- 5:00.
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, LOUISE W HUMPHREY can be reached at 571-272-5543. 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.
SATYENDRA K. SINGH
Primary Examiner
Art Unit 1657
/SATYENDRA K SINGH/Primary Examiner, Art Unit 1657