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 .
Claim Status
The amended claim set filed on 30 December 2025 is acknowledged. Claims 1 and 3-29 are currently pending. Of those, claims 3-4 are amended. Claim 29 is new, and claims 12-28 are withdrawn. Claim 2 is cancelled. Claims 1, 3-11, and 29 will be examined on the merits herein.
Response to Amendment
The Applicants’ arguments filed 30 December 2025 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 30 June 2025 will be referred to “NFOA”.
Objection(s) and Rejection(s) Withdrawn
The objection to claim 4 is withdrawn in view of the amendments to the claim.
The rejection of claim 1 under 35 U.S.C. 112(a) is withdrawn in view of Applicant’s arguments pointing to locations in the specification that collectively support the limitation (Remarks, pg. 9).
The rejection of claims 1 and 3-11 under 35 U.S.C. 103 is withdrawn in view of the statement of Common Ownership under 35 U.S.C. 102(b)(2)(C), stating that the instant application and PCT/US2019/048396 (published as WO 2020/046982 A1) were owned by the same owner no later than the effective filing date of the instant invention.
The provisional nonstatutory double patenting rejection over copending application 17/272,199 in view of WO 2020/046982 A1 is withdrawn because WO 2020/046982 A1 no longer qualifies as prior art.
Rejection(s) Maintained
Double Patenting
Response to Arguments
Applicant has requested that this rejection be held in abeyance (Remarks, pg. 11). The applicant is reminded that a complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer. Such a response is required even when the nonstatutory double patenting rejection is provisional. See MPEP 804.I.B.1.
The following rejections have been amended to reflect the claim amendments.
18/566497
Claims 1 and 3-11 remain provisionally rejected and claim 29 is newly rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-4, and 6-17 of copending Application No. 18/566,497 (‘497) in view of Pósfai (2006, Science) as evidenced by Bonhivers (1998, Biochimie). This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, the ‘497 claims teach a bacterial minicell derived from a genome reduced bacterium having a reduced number of expressed genes (‘497 claim 1), wherein the reduced number of expressed genes comprises a reduction of at least about 1.0% of genes (‘497 claim 11), wherein the bacterial minicell comprises a recombinant protein on the surface of the minicell (‘497 claims 3-4) and the recombinant protein is an antigen on the surface of a membrane (‘497 claim 6). The ‘497 claims teach that the bacterial minicell induces an enhanced immune response against the antigen when administered to a subject as compares to an immune response that would have been induced in the subject by a minicell derived from a bacterium of the same strain that has a full complement of expressed genes (‘497 claim 7) and that reducing and/or eliminating expression of one or more genes yields the enhanced immune response (‘497 claim 8).
Regarding instant claims 3 and 29, the ‘497 claims teach that the bacterium is a Gram-negative bacterium, optionally a member of the Enterobacteriaceae (‘497 claim 9).
Regarding instant claim 4, the ‘497 claims teach that the bacterium may be an E. coli or Salmonella bacterium (‘497 claim 10).
Regarding instant claim 5, the ‘497 claims teach that the reduced number of expressed genes may comprise a reduction of at least about 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, 10%, 11%, 12%, 13%, 14%, 15%, or greater than 15% of genes (‘497 claim 11).
Regarding instant claim 6, the ‘497 claims teach that the reduced number of expressed genes may comprise a reduction of at least about 2.4%, 15.9%, or 29.7% (‘497 claim 12).
Regarding instant claims 7-8, the ‘497 claims teach that the bacterium comprises an autotransporter (AT) expression vector encoding the antigen, wherein the expression on the surface is provided by the AT expression vector (‘497 claims 13-14).
Regarding instant claim 9, the ‘497 claims teach that the autotransporter expression vector may comprise a codon optimized sequence encoding the antigen (‘497 claim 15).
Regarding instant claim 10, the ‘497 claims teach that the AT expression vector may comprise a monomeric autotransporter vector or a trimeric autotransporter vector (‘497 claim 16).
Regarding instant claim 11, the ‘497 claims teach that the antigen may be derived from a microbe (‘497 claim 17).
However, the ‘497 claims do not teach a bacterium modified to have a reduction of one or more genes that encode proteins expressed on the surface of the bacterium, wherein the reduction of one or more genes that encode proteins expressed on the surface of the bacterium refers to reduced expression of one or more genes in the genome of the bacterium, as in instant claim 1.
Regarding instant claims 1 and 5-6, Pósfai teaches reduced-genome Escherichia coli strains that decrease redundancy in the genome and remove unwanted or unnecessary functions in order to increase metabolic efficiency (pg. 1044, paragraph bridging left and center columns). Genes that were deleted to create these strains include those encoding proteins expressed on the surface of the bacterium, such as fhuA (Table S4), an outer membrane protein that acts as a receptor for phages (as is evidenced by Bonhivers, Abstract). Genome reduction had beneficial results in several strains; MDS42, which comprises a reduction of 15.9% of genes (704 genes deleted/ 4,434 total genes in MG1655 * 100%) compared to the parent strain MG1655, has a significantly higher electroporation efficiency and had accurate propagation of recombinant genes and plasmids known to be unstable in other bacteria strains, while also maintaining stable growth and protein production (Table 1 and Abstract).
Therefore, it would have been prima facie obvious, to a person of ordinary skill in the art, to use the genome reduced E.coli strain MDS42, taught by Pósfai, as the parent cell in order to produce the bacterial minicell taught by the ‘497 claims, thereby arriving at the claimed invention. The person of ordinary skill in the art would have been motivated to make the modification because the genome reduced E. coli of Pósfai have been able to take up and propagate vectors, including those that are unstable in other strains. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because the genome reduced cells of Pósfai are able to take up vectors and express recombinant genes as well as commercial strains, so one would expect the successful expression of an antigen and successful incorporation of genetic modifications to produce the minicells, as described by the ‘497 claims. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
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 (i.e., genome reduced bacteria and bacteria derivatives, antigens expressed on a bacterial membrane, and autotransporter expression vectors) were known in the art. 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.
17/924,963
Claims 1 and 3-11 remain provisionally rejected and claim 29 is newly rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5-7, and 9-13 of copending Application No. 17/924,963 (‘963) in view of Pósfai (2006, Science) as evidenced by Bonhivers (1998, Biochimie). This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, the ‘963 claims teach a modified bacterium or derivative thereof having a reduced number of expressed genes, wherein the reduced number of expressed genes comprises a reduction of at least about 1.0% of genes (‘963 claim 7), and comprising a viral antigen, wherein the viral antigen is expressed on a surface of a membrane or derivative thereof, wherein the bacterium induces an enhanced immune response against the viral antigen when administered to a subject as compared to an immune response that would have been induced in the subject by a bacterium of the same strain that has a full complement of expressed genes (‘963 claim 1).
Regarding instant claims 3 and 29, the ‘963 claims teach that the bacterium may be a Gram-negative bacterium, optionally a member of the Enterobacteriaceae (‘963 claim 5).
Regarding instant claim 4, the ‘963 claims teach that the bacterium may be E. coli (‘963 claim 6).
Regarding instant claims 5-6, the ‘963 claims teach that the reduced number of expressed genes may comprise a reduction of at least about 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, 10%, 11%, 12%, 13%, 14%, 15%, or greater than 15% of genes (‘963 claim 7).
Regarding instant claims 7-8, the ’963 claims teach that the modified bacterium may comprise an autotransporter (AT) expression vector encoding the antigen, wherein the expression on the surface is provided by the AT expression vector (‘963 claims 9-11).
Regarding instant claim 9, the ‘963 claims teach that the autotransporter expression vector may comprise a codon optimized sequence encoding the antigen (‘963 claim 12).
Regarding instant claim 10, the ‘963 claims teach that the AT expression vector may comprise a monomeric autotransporter vector or a trimeric autotransporter vector (‘963 claim 13).
Regarding instant claim 11, the ‘963 claims teach that the antigen is a viral antigen, i.e., derived from a microbe (‘963 claims 1-3).
However, the ‘963 claims do not teach a bacterium modified to have a reduction of one or more genes that encode proteins expressed on the surface of the bacterium, wherein the reduction of one or more genes that encode proteins expressed on the surface of the bacterium refers to reduced expression of one or more genes in the genome of the bacterium, as in instant claim 1.
The teachings of Pósfai as evidenced by Bonhivers with respect to instant claims 1 and 5-6 are set forth in the double patenting rejection over copending application 18/566,497 above (para. 22).
Therefore, it would have been prima facie obvious, to a person of ordinary skill in the art, to modify the modified bacterium or derivative thereof as taught by the ‘963 claims by using the genome reduced E. coli strain MDS42 taught by Pósfai as the genome reduced host bacterium expressing the antigen encoded by the autotransporter expression vector taught by the ‘963 claims, thereby arriving at the claimed invention. The person of ordinary skill in the art would have been motivated to make the modification because the genome reduced E. coli of Pósfai have been able to take up and propagate vectors, including those that are unstable in other strains. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because the ‘963 claims teach that the bacterium has a reduced number of expressed genes and the genome reduced cells of Pósfai are able to take up vectors and express recombinant genes as well as commercial strains, so one would expect the successful expression of the viral antigen. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
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 (i.e., genome reduced bacteria and bacteria derivatives, antigens expressed on a bacterial membrane, and autotransporter expression vectors) were known in the art. 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.
New Rejection(s)
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 3-8, 10-11, and 29 are newly rejected under 35 U.S.C. 103 as being unpatentable over Pósfai et al. (2006, Science; herein “Pósfai”) as evidenced by Bonhivers et al. (1998, Biochimie; herein “Bonhivers”) in view of Hjelm et al. (2014, Appl. Environ. Microbiol.; herein “Hjelm”).
Regarding claims 1, 3-6, and 29, Pósfai teaches reduced-genome Escherichia coli strains that decrease redundancy in the genome and remove unwanted or unnecessary functions in order to increase metabolic efficiency (pg. 1044, paragraph bridging left and center columns). Genes that were deleted to create these strains include those encoding proteins expressed on the surface of the bacterium, such as fhuA (Table S4), an outer membrane protein that acts as a receptor for phages (as is evidenced by Bonhivers, Abstract). Genome reduction had beneficial results in several strains; MDS42, which comprises a reduction of 15.9% of genes (704 genes deleted/ 4,434 total genes in MG1655 * 100%) compared to the parent strain MG1655, has a significantly higher electroporation efficiency and had accurate propagation of recombinant genes and plasmids known to be unstable in other bacteria strains, while also maintaining stable growth and protein production (Table 1 and Abstract).
However, Pósfai does not teach a modified bacterium comprising an antigen on a surface of a membrane or derivative thereof, wherein the bacterium induces an enhanced immune response against the antigen when administered to a subject, and wherein the reduced expression of one or more genes yields the enhanced immunogenicity, as in claim 1, an antigen is put on the surface of the bacterium by expression of the cell itself, as in claim 7, an autotransporter expression vector encoding the antigen, wherein the expression on the surface is provided by the autotransporter expression vector, as in claim 8, wherein the autotransporter expression vector comprises a monomeric autotransporter vector or a trimeric autotransporter vector, as in claim 10, or an antigen derived from a microbe, as in claim 11.
Regarding claims 1, 3-4, 11, and 29, Hjelm teaches a modified E. coli (a gram-negative bacterium and member of the family Enterobacteriaceae) expressing the Mycobacterium tuberculosis antigen ESAT6 on its surface (Abstract).
Regarding claims 7-8 and 10, Hjelm teaches that the ESAT6 antigen was expressed by the E. coli from the pHbpD(p15A)-ESAT6 vector encoding the monomeric hemoglobin protease autotransporter (Hbp), which displays the ESAT6 antigen on the cell surface (Abstract and pg. 727, left col., para. 2 and 4).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to combine the genome-reduced E. coli taught by Pósfai with the HbpD autotransporter vector encoding the ESAT6 antigen taught by Hjelm, thereby arriving at the invention of claims 1, 3-8, 10-11, and 29. The person of ordinary skill in the art would have been motivated to make the modification because the genome reduced E. coli of Pósfai are more metabolically efficient than other E. coli strains and the HbpD expression system of Hjelm successfully expresses heterologous antigens on the E. coli cell surface. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Hjelm suggests that autotransporter expression vectors may be used to express an antigen on the surface of bacterial membranes in order to elicit an immune response (Abstract). Additionally, because the genome reduced cells of Pósfai are able to take up vectors and express recombinant genes as well as commercial strains, one would expect the successful expression of an antigen. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
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 (i.e., genome reduced bacteria, antigens expressed on a bacterial membrane, and autotransporter expression vectors) were known in the art. 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.
Claims 1, 3-11, and 29 are newly rejected under 35 U.S.C. 103 as being unpatentable over Pósfai (2006, Science) as evidenced by Bonhivers (1998, Biochimie) in view of Hjelm (2014, Appl. Environ. Microbiol.) as applied to claims 1, 3-8, 10-11, and 29 above, and further in view of Mauro (2018, BioDrugs).
The combination of Pósfai and Hjelm is set forth in para. 39-45 above and teaches all limitations of claims 1, 3-8, 10-11, and 29.
However, the combination of Pósfai and Hjelm does not teach a codon optimized sequence encoding an antigen, as in claim 9.
Regarding claim 9, Mauro teaches that codon optimization is routinely used in therapeutic applications of protein expression and increases protein expression by up to more than 1000-fold (pg. 72, left col., para. 4). Mauro also teaches that codon optimization is used to overcome the bias in codon usage that differs between different organisms that can affect translation efficiency (pg. 72, right col., para. 3 – pg. 73, right col., para. 1).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the E. coli produced by the combination of Pósfai and Hjelm by codon optimizing the ESAT6 nucleotide sequence encoded by the pHbpD vector, thereby arriving at the invention of claims 1, 3-11, and 29. The person of ordinary skill in the art would have been motivated to make the modification because Mauro teaches that codon optimization of heterologous genes increased the efficiency of protein expression. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Mauro teaches that codon optimization is used in various types of host cells and expression systems and that codon optimization tools are known in the art. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
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 (i.e., genome reduced bacteria, antigens expressed on a bacterial membrane, autotransporter expression vectors, and codon optimization) were known in the art. 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.
Double Patenting
17/272,199
Claims 1, 3-11, and 29 are newly provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 and 7-11 of copending Application No. 17/272,199 ('199) in view of Mauro (2018, BioDrugs) and Pósfai (2006, Science) as evidenced by Bonhivers (1998, Biochimie). This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, the ‘199 claims teach a modified bacterium, or a derivative thereof, comprising a heterologous antigen expressed on a surface of a membrane of the bacterium (‘199 claim 1). The ‘199 claims also teach that the modified bacterium may comprise a mutation, wherein said mutation is deletion of genes (i.e., reduced expression) that blunt the immune response (i.e., wherein the reduced expression of one or more genes yields enhanced immunogenicity), said mutation is directed to multiple mutations in several genes that affect the immune response or the presentation of antigens in or on the bacteria (i.e., the bacterium is modified to have a reduction of one or more genes that encode proteins expressed on the surface of the bacterium and refers to reduced expression of one or more genes in the genome of the bacterium), or said mutation is directed to large scale mutations or deletions such that the bacteria have a substantially reduced set of genes, up to the limits of bacterial cell viability (‘199 claim 5).
Regarding instant claim 3, the ‘199 claims teach that the bacterium may be a Gram-negative bacterium (‘199 claim 2).
Regarding instant claims 4 and 29, the ‘199 claims teach that the bacterium may be a Salmonella or E. coli (‘199 claims 3-4), members of the Enterobacteriaceae.
Regarding instant claims 7-8, the ‘199 claims teach that the modified bacterium comprises an autotransporter (AT) expression vector encoding a heterologous antigen (‘199 claims 1 and 7).
Regarding instant claim 10, the ‘199 claims teach that the AT expression vector comprises an expression cassette with a monomeric autotransporter or a trimeric transporter (‘199 claim 8).
Regarding instant claim 11, the ‘199 claims teach that the antigen is derived from a microbe (‘199 claims 9-11).
However, the ‘199 claims do not teach a modified bacterium having a reduction of at least about 1.0% of genes, as in instant claim 1, a reduction of at least about 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, 10%, 11%, 12%, 13%, 14%, 15%, or greater than 15%, as in instant claim 5, a reduction of at least about 2.4%, 15.9%, or 29.7%, as in instant claim 6, an autotransporter expression vector comprising a codon optimized sequence encoding the antigen, as in instant claim 9.
Regarding claim 9, Mauro teaches that codon optimization is routinely used in therapeutic applications of protein expression and increases protein expression by up to more than 1000-fold (pg. 72, left col., para. 4). Mauro also teaches that codon optimization is used to overcome the bias in codon usage that differs between different organisms that can affect translation efficiency (pg. 72, right col., para. 3 – pg. 73, right col., para. 1).
Regarding claims 1, 3-6, and 29, Pósfai teaches reduced-genome Escherichia coli strains that decrease redundancy in the genome and remove unwanted or unnecessary functions in order to increase metabolic efficiency (pg. 1044, paragraph bridging left and center columns). Genes that were deleted to create these strains include those encoding proteins expressed on the surface of the bacterium, such as fhuA (Table S4), an outer membrane protein that acts as a receptor for phages (as is evidenced by Bonhivers, Abstract). Genome reduction had beneficial results in several strains; MDS42, which comprises a reduction of 15.9% of genes (704 genes deleted/ 4,434 total genes in MG1655 * 100%) compared to the parent strain MG1655, has a significantly higher electroporation efficiency and had accurate propagation of recombinant genes and plasmids known to be unstable in other bacteria strains, while also maintaining stable growth and protein production (Table 1 and Abstract).
Therefore, it would have been prima facie obvious, to a person of ordinary skill in the art, to modify the autotransporter expression vector encoding an antigen taught by the ‘199 claims to use a codon optimized sequence for the antigen, as taught by Mauro, and combine the resulting autotransporter expression vector with the genome reduced MDS42 strain of E. coli taught by Pósfai, thereby arriving at the claimed invention. The person of ordinary skill in the art would have been motivated to make the modification because the ‘199 claims teach that the modified bacterium may have a reduced set of genes, and the genome reduced E. coli of Pósfai have been able to take up and propagate vectors, including those that are unstable in other strains. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because the genome reduced cells of Pósfai are able to take up vectors and express recombinant genes as well as commercial strains, one would expect the successful expression of an antigen. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
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 (i.e., genome reduced bacteria, antigens expressed on a bacterial membrane, and autotransporter expression vectors) were known in the art. 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.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/DANIEL E KOLKER/Supervisory Patent Examiner, Art Unit 1645