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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-11 in the reply filed on 02/06/2026 is acknowledged.
Priority
The instant application filed on 10/06/2023 claims priority to U.S. Provisional Application 63/413,880 filed on 10/06/2022. PRO 63/413,880 finds support for the instantly claimed invention; therefore, the effective filing date for the instant application is 10/06/2022.
Information Disclosure Statement
No Information Disclosure Statement (IDS) has been filed in this Application. Applicant is reminded that each individual associated with the filing and prosecution of a patent application has a duty of candor and good faith in dealing with the U.S. Patent and Trademark Office, which includes a duty to disclose to the Office all information known to that individual to be material to patentability (see 37 C.F.R. § 1.56).
Specification
The disclosure is objected to because of the following informalities:
“Escherichia coli” and “E. coli” throughout the specification should be italicized.
“Cancer cells” in [0003], first sentence should not be capitalized.
“Pseudomonas putida” and “P. putida” throughout the specification should be italicized.
“E-coli” in [0023] should be “E. coli”.
“2x1010 CFU/day” in [0024] and [0042] should be “2x1010 CFU/day”.
“1011 CFU/ml” in [0024] and [0039] should be “1011 CFU/ml”.
“1.0x109 colony-forming units (CFU)/ml” in [0025] should be “1.0x109 colony-forming units (CFU)/ml”.
“(106, 108, and 1010 CFU/100 µl)” in [0027] should be “(106, 108, and 1010 CFU/100 µl)”.
“Examiner” in [0029] should be “examined”.
“106 MC38” in [0032] should be “106 MC38”.
“(1010/100 µl)” in [0033], [0039], and [0040] should be “(1010/100 µl)”.
“(mm3)” in [0033] should be “(mm3)”.
“1010” in [0043] should be “1010”.
Appropriate correction is required.
Claim Objections
Claims 2, 3, 8, and 9 are objected to because of the following informalities: all bacterial names should be italicized. For instance, Escherichia coli should be Escherichia coli, E. coli should be E. coli, and Pseudomonas putida should be Pseudomonas putida. Appropriate correction is required. This is an objection, not a rejection, because these appear to be typographical errors.
Claims 2 and 8 are objected to because they recite the abbreviation rMETase and abbreviations should be completely recited upon first use. This is an objection, not a rejection, because rMETase is defined in the instant specification as recombinant methioninase (see, e.g., instant specification, [0003]).
Claim Rejections - 35 USC § 112(b), Indefiniteness
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.
Claims 1-11 are rejected under 35 U.S.C. 112(b) 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.
Claims 1, 6-7, and 11 recite the term “effective amount”; however, this is a relative term which renders the claim indefinite. The phrase “effective amount” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The instant specification states “The disclosed composition may include the E. coli JM109 in safe amounts, or the amounts considered safe for administration to humans. Such an amount can be determined clinically and can be optimized through clinical studies. For example, a tolerability study demonstrated that up to 2×1010 CFU/day of E. coli JM109-rMETase is tolerable” (see, e.g., instant specification, [0024]); however, this amount of E. coli JM109-rMETase is not correlated to an effective amount to release methioninase in the gut of a subject. Furthermore, the instant specification teaches E. coli JM109-rMETase (1010 CFU/100µl) that was tested to determine efficacy against M38 (i.e., colon cancer) in mice (see, e.g., instant specification [0033], [0039], [0043] & Figures 2A-2B); however, again, this is not correlated to an effective amount of E. coli JM109-rMETase to release methioninase in the gut of a subject. Moreover, although the claim provides the function to be achieved, more than one effect can be implied from the specification. Additionally, the instant specification does not teach what is considered an effective amount for each function claimed and generically teaches the amount of bacteria without correlating this amount to the amount of methioninase released within the gut of a subject (see, e.g., MPEP 2173.05(c)(III)). Therefore, the instant specification lack a standard for measuring the degree intended and one of ordinary skill in the art would not readily understand how to determine whether or not an amount is effective (see, e.g., MPEP 2173.05(n)). For the purposes of applying prior art, the Examiner has interpreted “effective amount” to be any amount that releases methioninase or decreases cancer growth.
Claims 4 and 10 recite “…at least in an amount sufficient for treating or controlling growth of a cancer in a subject”; however, this amount is described functionally and the instant specification only teaches the activity of rMETase (i.e., 39.7 U/ml and 7.9 U/ml) in a colon cancer mouse model (see, e.g., instant specification, [0039]), not the physical amount of rMETase. Based on this, it is unclear if rMETase activity, as taught in the instant specification, is the same as the amount of rMETase or the amount of bacteria administered, as recited in the claimed invention. Based on the teachings in the instant specification, one of ordinary skill in the art would not readily understand if rMETase activity is the same as the amount of rMETase. Therefore, the use of functional language in these claims fails to provide a clear-cut indication of the scope of the subject matter embraced by the claim and thus is indefinite (see, e.g., MPEP2173.05 (g)).
Claims 2-5 and 8-10 are included in this rejection for depending on rejected independent claims 1 and 7, and failing to rectify the noted deficiencies.
Claim Rejections - 35 USC § 112(a), Written Description
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.
Claims 1-11 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Independent claims 1 and 7 recite “…in an effective amount to release recombinant methioninase in a gut of the subject.” Claims 4 and 10 recite “…wherein the recombinant methioninase is released at least in an amount sufficient for treating or controlling growth of a cancer in the subject.” Claims 6 and 11 recite “wherein the effective amount of the composition is sufficient to allow for gut colonization.” These amount of the bacterial strains and the amount of recombinant methioninase are described functionally (i.e., by what they do instead of what they are), and there is no description of these amounts in the instant specification, as discussed below.
The instant specification describes the tolerability of E. coli JM109-rMETase and specifically shows that 2x1010 CFU/day of E. coli JM109-rMETase is tolerable (see, e.g., instant Specification, [0024]). Furthermore, the instant specification describes 1011 and 1010 CFU/ml and of E. coli JM109-rMETase to result in 39.7 U/ml and 7.9 U/ml of rMETase activity, respectively (see, e.g., instant Specification, [0039]). The instant specification describes that 2x1010 CFU/day of E. coli JM109-rMETase inhibited MC-38 tumor growth in C57BL6 mice (see, e.g., instant specification, [0042]). The instant specification describes that E. coli JM109-rMETase at 1010CFU/ml is well tolerated in nude mice (see, e.g., instant specification [0043]).
With regards to the written description set forth in the instant specification pertaining to “recombinant methioninase producing bacterial strains in an effective amount to release recombinant methioninase in a gut of the subject” (claims 1 and 7), there are several distinct issues with this:
First, “effective amount” is not sufficiently described in the instant specification. The instant specification teaches “The disclosed composition may include the E. coli JM109 in safe amounts, or the amounts considered safe for administration to humans. Such an amount can be determined clinically and can be optimized through clinical studies. For example, a tolerability study demonstrated that up to 2×1010 CFU/day of E. coli JM109-rMETase is tolerable. In a separate study, it was found that E. coli JM109-rMETase (1011 CFU/ml), after exposure to Isopropyl β- d-1-thiogalactopyranoside (IPTG), had rMETase activity of 39.7 U/ml, which is about one-tenth of the rMETase usually used for mice (500 U/ml)” (see, e.g., instant specification, [0024]). Based on this this, the effective amount can be optimized and invites one to experiment to determine the effective amount of E. coli JM109-rMETase. Furthermore, the instant specification does not provide guidance, nor does the instant specification distinguish between the effective amount of E. coli JM109-rMETase needed to treat cancer versus colonize the gut of a subject. Based on the teachings in the instant specification, the amount of E. coli JM109-rMETase can be experimented with and optimized in order to determine effective amount(s) of E. coli JM109-rMETase that can treat cancer and colonize the gut. Overall, the instant specification does not sufficiently describe what an effective amount of E. coli JM109-rMETase is for treating cancer versus colonizing the gut; however the instant specification teaches that this amount can be optimized through experimentation. Moreover, the amounts of E. coli JM109-rMETase provided in the instant specification at [0024] pertain to tolerability of E. coli JM109-rMETase and not for treating cancer, as claimed.
Secondly, Applicant does not show in their examples, nor does Applicant sufficiently describe in the instant specification, the amount of the recombinant methioninase producing bacterial strain effective to generate or produce methioninase in the gut of the subject. Applicant provides examples showing that E. coli JM109-rMETase at 1010CFU/100µl was administered orally to mice with colon cancer (see, e.g., instant specification, [0033]) and Applicant teaches that the amount of methioninase was measured in stool samples (see, e.g., instant specification, [0034]-[0036]), however, this does not teach the physical amount of rMETase that is released within the gut of a subject. Furthermore, Applicant does not provide any guidance in the instant specification pertaining to whether or not the amount of rMETase in stool samples is correlated to the amount of rMETase in the gut. Based on this, Applicant generically teaches the amount of E. coli JM109-rMETase administered, but does not correlate this to the amount of rMETase released within the gut; therefore, the instant specification does not sufficiently teach an effective amount of E. coli JM109-rMETase for release of recombinant methioninase within the gut of a subject. Furthermore, based on the teachings set forth in the instant specification, the amount of E. coli JM109-rMETase administered for tolerability studies (see, e.g., instant specification, [0038]) and treatment of colon (see, e.g., instant specification, [0042]) and breast cancer (see, e.g., instant specification, [0043]) is not correlated to the amount of recombinant methioninase released in the gut.
Thirdly, the instant specification only describes two amounts of E. coli JM109-rMETase (1011 and 1010 CFU/ml) that were tested to measure the amount of methioninase activity within the gut of a subject (see, e.g., instant Specification, [0039]). However, this does not set forth a representative number of species for the claimed genus, wherein the genus is an effective amount of E. coli JM109-rMETase to release recombinant methioninase in a gut of the subject. Applicant is broadly claiming all effective amounts of E. coli JM109-rMETase that release recombinant methioninase in a gut of a subject; however, Applicant only teaches two E. coli JM109-rMETase concentrations (i.e., 1011 and 1010 CFU/ml) (see, e.g., instant Specification, [0039]), which is not sufficient for the claimed genus (see, e.g., MPEP 2163(II)(3)(ii)). Applicant’s disclosure of only two concentrations of E. coli JM109-rMETase that release methioninase does not reflect variation within the genus because there could be lower and/or higher concentrations of E. coli JM109-rMETase that result in methioninase release. Therefore, Applicant has not provided a representative number of species for an effective amount of E. coli JM109-rMETase to release rMETase in a gut of the subject. Additionally, as discussed above, the instant specification does not provide support or guidance that there is a correlation between the amount of E. coli JM109-rMETase and the amount of rMETase released within the gut.
With regards to the written description set forth in the instant specification pertaining to “…wherein the recombinant methioninase is released at least in an amount sufficient for treating or controlling growth of a cancer in the subject” (claims 4 and 10), there are several distinct issues with this:
First, the instant specification describes the amount of E. coli JM109-rMETase (1011 and 1010 CFU/ml) that was administered to C57BL6 mice (see, e.g., instant specification, [0038]); however, the instant specification measured rMETase activity produced from these concentrations of administered E. coli JM109-rMETase (see, e.g., instant specification, [0039]), but the instant specification does not teach the physical amount of rMETase that was released in the gut of the subject, as claimed (see 112(b) rejection above regarding this). Additionally, as discussed above, Applicant is measuring rMETase activity in stool samples, which does not actually give a representation of the amount of rMETase in the gut of a subject.
Secondly, Applicant tests one concentration of E. coli JM109-rMETase (i.e., 1010 CFU/100 µl) within mouse models of colon cancer, which results in only one activity/amount of rMETase being tested for treating colon cancer. This does not reflect variation within the genus because there could be other recombinant methioninase concentrations sufficient for treating colon cancer in a subject. Therefore, Applicant does not set forth a representative number of species for a sufficient amount of methioninase released for treating or controlling growth of a cancer in a subject. Applicant is broadly claiming an effective amount of E. coli JM109-rMETase; however, Applicant sets forth only one E. coli JM109-rMETase concentration, which is not sufficient for the claimed genus. Additionally, as discussed above, the instant specification does not provide guidance that the amount of E. coli JM109-rMETase is correlated to the amount of rMETase released. Moreover, the instant specification describes administration of E. coli JM109-rMETase to determine efficacy against 4T1 (i.e., mammary gland cancer; breast cancer cell line) in mice (see, e.g., instant specification, [0043]); however, the instant specification does not provide guidance on what amount(s) of E. coli JM109-rMETase are required to release rMETase in order to treat 4T1 tumors in mice.
With regards to the written description set forth in the instant specification pertaining to “…wherein the effective amount of the composition is sufficient to allow gut colonization” (claims 6 and 11), the instant specification does not teach any concentration of E. coli JM109-rMETase concentration that is sufficient to allow gut colonization. Furthermore, the instant specification lacks written description, guidance, and concentrations pertaining to gut colonization by E. coli JM109-rMETase. Therefore, the instant specification does not set forth a representative number of species for the claimed genus.
Claim Rejections - 35 USC § 112(a), Enablement
Claims 1-11 are rejected under 35 U.S.C. 112(a) as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
In re Wands (858 F2d, 721, 727, 8 USPQ 2d 1400, 1404 (Fed Cir. 1988)), the issue of
enablement in molecular biology was considered. It was held that the following factors should be considered to determine whether the claimed invention would require the skilled artisan undue
experimentation:
1) Amount of experimentation necessary;
2) Amount of direction or guidance presented;
3) Presence or absence of working examples;
4) Nature of the invention;
5) State of the prior art;
6) Relative skill of those in the art;
7) Predictability or unpredictability of the art; and
8) Breadth of the claims.
Independent claim 1 recites:
A method for treating cancer in a subject in need thereof, the method comprising: administering, orally, to a subject, a composition comprising recombinant methioninase producing bacterial strains in an effective amount to release recombinant methioninase in a gut of the subject.
Nature of the invention: The invention is directed towards a method of treating cancer through administration of recombinant methioninase producing bacterial strains.
Breadth of the claims: As claimed, the method of treating cancer consists of orally administering all recombinant methioninase producing bacterial strains (dosage is not claimed).
Amount of direction or guidance presented: The instant specification teaches “a method for treating cancer in a subject in need thereof, the method comprising administering, orally, to a subject, a composition comprising recombinant methioninase producing bacterial strains in an effective amount to release recombinant methioninase in a gut of the subject. The bacterial strains comprise E. coli bacteria having cloned rMETase gene from Pseudomonas putida using plasmid pATG3131. The E. coli bacteria comprise the E. coli JM109 strain. The recombinant methioninase enzyme is released at least in an amount sufficient for treating or controlling growth of a cancer in the subject. The cancer is colon cancer, breast cancer, or any other cancer. The effective amount of the composition is sufficient to allow gut colonization” (see, e.g., instant specification, [0009]). Moreover, the instant specification teaches “The use of E-Coli JM109 is only provided as an example and any such organism can be incorporated into the disclosed composition without departing from the scope of the present invention” (see, e.g., instant specification, [0023]). Therefore, the instant specifications teaches E. coli JM109 as the strain for production of recombinant methioninase, but goes on to state that theoretically the strain for production of recombinant methioninase can be any microorganism.
Presence or absence of working examples: The instant application provides examples showing that E. coli JM109 is tolerable at concentrations up to 2x1010 CFU/day (see, e.g., instant specification, [0024]), and that E. coli JM109-rMETase is tolerable at 106, 108, and 1010 CFU/day (see, e.g., instant specification, [0038]). Furthermore, the instant specification teaches that E. coli JM109-rMETase significantly inhibits MC-38 tumor growth in C57BL6 mice at a concentration of 1010/100 µl (see, e.g., instant specification, [0039]). Additionally, the instant specification teaches that E. coli JM109-rMETase significantly suppressed the growth of 4T1 tumors compared to control treated mice (see, e.g., instant specification, [0043]). Therefore, Applicant only provides working examples in the instant specification for E. coli JM109-rMETase as the recombinant methioninase producing bacterial strain, and there is no extrapolation in the instant specification for how other bacterial strain(s) expressing rMETase would be generated and used to treat cancers, such as colon cancer and breast cancer.
Based on the Applicant’s disclosure, the Applicant would not be enabled for all recombinant methioninase producing bacterial strains because the Applicant only reduces to practice the administration of E. coli JM109-rMETase for treatment of colon cancer and breast cancer. There is no guidance on treatment of these cancer types, or other types of cancers, with other types of recombinant methioninase producing bacterial strains. Based on this, Applicant would not be enabled for all recombinant methioninase producing bacterial strains, as Applicant only reduced to practice E. coli JM109-rMETase.
State of the prior art: The prior art does not teach oral administration of E. coli JM109-rMETase for treatment of cancer; however, the prior art does teach production of rMETase by Han (US 2019/0153421; Date of Publication: May 23, 2019), wherein Han teaches “Recombinant L-methionine α-deamino-γ-mercaptopurine lyase (methioninase, METase) [EC 4.4.1.11] from Pseudomonas putida has been previously cloned and was produced in Escherichia coli (AntiCancer, Inc., San Diego, Calif.). The rMETase is a homotetrameric PLP enzyme of 172-kDa molecular mass” (see, e.g., Han, [0033]). Therefore, Han teaches the same method of producing an E. coli strain that expresses rMETase, but does not teach oral administration of the E. coli strain, and instead teaches administration of the rMETase produced by the E. coli strain for the treatment of cancer (see, e.g., Han, [0038]). Similarly, Akita (US Patent No. 6,475,767; Date of Publication: November 5, 2000) teaches methods of producing and cultivating and rMETase expression strain by cloning the rMETase gene into E. coli host strains (see, e.g., Akita, “Cultivation of rMETase Expression Strain”, col 2, lines 50-65). Therefore, like Han, Akita teaches producing rMETase by cloning the rMETase gene into E. coli. Overall, the prior art does not teach orally administering an E. coli strain that is expressing rMETase for cancer treatment; however, the art does teach generating an E. coli strain for expression of rMETase, wherein the rMETase is administered for cancer treatment. Furthermore, the prior art does not teach generation of other bacterial strains that are engineered to recombinantly express rMETase from Pseudomonas putida and wherein these engineered bacterial strains are orally administered for treatment of cancer.
Relative skill of those in the art: Based on the state of the prior art, the relative skill of those in the art pertaining to generation of bacterial strains that are engineered to recombinantly express rMETase from Pseudomonas putida and wherein these engineered bacterial strains are administered for treatment of cancer is low.
Predictability or unpredictability of the art: The level of unpredictability within the art is high, as there are many types of bacterial strains that can be engineered to recombinantly express rMETase from Pseudomonas putida; however, it is unpredictable as to whether or not these engineered strains will actually result in treatment of cancer. Moreover, the prior art of Han and Akita, as discussed above, primarily centers around expression of rMETase from engineered E. coli strains; however, it is unpredictable as to whether or not other engineered bacterial strains will result in expression of rMETase, like E. coli. Furthermore, the prior art teaches administration of the produced rMETase enzyme to treat cancer (see, e.g., Han, abstract); however, the prior art does not teach administration of the E. coli strain that is expressing rMETase; therefore, it is unpredictable how other bacterial strains that are engineered to express rMETase would be tolerated in vivo following oral administration, especially since other bacterial strains may be toxic. Further, the specification does not contemplate how cancer(s) can be treated through administration of engineered bacteria expressing rMETase, wherein the engineered bacteria are bacteria other than E. coli. Therefore, the level of unpredictability in within the art is high.
Amount of experimentation necessary: Since there are many bacterial species, in general and which can be genetically engineered to express rMETase, one of ordinary skill in the art would have undue experimentation in order to produce an engineered bacterial strain expressing rMETase that can be orally administered to treat cancer. Moreover, one of ordinary skill it the art would have undue experimentation in order to determine whether or not the engineered bacterial strain is tolerated in vivo following oral administration. Therefore, the amount of experimentation is high.
Claim Rejections - 35 USC § 103, Obviousness
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, 6-7, and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Han (US 2019/0153421; Date of Publication: May 23, 2019) in view of Chiang (Metabolic engineering of probiotic Escherichia coli for cytolytic therapy of tumors; 2021) and Martinson (Escherichia coli Residency in the Gut of Healthy Human Adults; 2020).
Han’s general disclosure relates to “A composition and method for lowing serum and plasma levels of methionine by oral administration” (see, e.g., Han, abstract), and “methods for treatment of cancer, including malignant melanoma, by oral administration of the methioninase composition” (see, e.g., Han, abstract). Moreover, Han discloses methods of producing recombinant methioninase (rMETase) from Pseudomonas putida in Escherichia coli (see, e.g., Han, [0033]). Additionally, Han discloses that “Administration of rMETase by intra-peritoneal injection (“ip-rMETase”) inhibits tumor growth in a patient-derived orthotopic xenograft (“PDOX”) model of a BRAF-V600E mutant melanoma. When the efficacy of rMETase in combination with a first-line melanoma drug, temozolomide (TEM), combination therapy of TEM, first line therapy, and rMETase is significantly more efficacious than any of these monotherapies. Additionally, rMETase if efficacious against Ewing's sarcoma in a PDOX model, wherein rMETase effectively reduced tumor growth compared to untreated control mice. Serum and tumor MET levels were lower in the rMETase group, versus controls” (see, e.g., Han, [0021]).
Regarding claims 1 and 7 pertaining to the recombinant methioninase producing bacterial strain, Han teaches “Recombinant L-methionine α-deamino-γ-mercaptopurine lyase (methioninase, METase) [EC 4.4.1.11] from Pseudomonas putida has been previously cloned and was produced in Escherichia coli (AntiCancer, Inc., San Diego, Calif.). The rMETase is a homotetrameric PLP enzyme of 172-kDa molecular mass” (see, e.g., Han, [0033]).
Regarding claim 1 pertaining to treating cancer in a subject in need thereof, Han teaches that “An excessive requirement for methionine appears to be a metabolic defect in cancer, and the only known such metabolic defect shared by cells across most types of cancer cells. This elevated methionine (“MET”) use by cancer cells is termed “methionine dependence (“MET dependence”). It has been previously shown that growth of cancer cells can be selectively arrested by methionine deprivation, such as with recombinant methioninase (“r-METase”)” (see, e.g., Han, [0004]). Moreover, Han teaches “Targeting MET by administration of recombinant methioninase (“rMETase”) can arrest the growth of cancer cells in vitro and in vivo, presumably by decreasing MEI concentration in the tumor interstitial microenvironment” (see, e.g., Han, [0006]). Additionally, Han teaches that “Orally administered rMETase is significantly more effective at inhibiting melanoma tumor growth than intraperitoneal rMETase” (see, e.g., Han, [0038]).
However, Han does not teach: oral administration of the bacterial strain in an effective amount to release recombinant methioninase into the gut of a subject (claims 1 and 7); or wherein the effective amount of the composition is sufficient to allow gut colonization (claims 6 and 11).
Chiang’s general disclosure relates to bacteria-mediated delivery of therapeutic proteins to tumors for cancer treatment (see, e.g., Chiang, abstract). Moreover, Chiang discloses that E. coli can be genetically engineered to deliver “a variety of bioactive payloads, notably involving prodrugs-concerted enzymes, short hairpin RNA, cytokines, antigens, antibodies, and bacterial toxins” to cancerous sites for treatment (see, e.g., Chiang, Introduction, pg. 1). Furthermore, Chiang teaches that these engineered bacteria “target tumors where they reside, replicate, and continuously produce the payloads on site. It enables in situ delivery of the produced bioactive molecules to tumor site, which improves the therapeutic efficacy” (see, e.g., Chiang, Introduction, pg. 1). Additionally, Chiang discloses multiple examples of engineered E. coli strains that have been developed to deliver recombinantly expressed proteins to tumor microenvironments in order to eradicate cancer cells (see, e.g., Chiang, Introduction, pgs. 1-2).
Regarding claims 1 and 7 pertaining to administration of a bacterial strain for recombinant expression of proteins, Chiang teaches that tumor-seeking bacteria, such as E. coli, can be engineered to synthesize a variety of therapeutic agents, wherein the engineered bacteria “target tumors where they reside, replicate, and continuously produce the payloads on site. It enables in situ delivery of the produced bioactive molecules to tumor site, which improves the therapeutic efficacy” (see, e.g., Chiang, Introduction, pg. 1). Moreover, Chiang teaches that tumor-targeting bacteria have been genetically instructed to deliver a variety of bioactive payloads, such as prodrug-converted enzymes (see, e.g., Chiang, Introduction, pg. 1). Furthermore, Chiang teaches engineering E. coli Nissle for expression of azurin, a cytotoxic protein that induces cancer cell apoptosis, for treatment of colorectal cancer (see, e.g., Chiang, Introduction, pg. 2). Chiang also teaches engineering E. coli Nissle for expression of hemolysin E for treatment of colorectal cancer (see, e.g., Chiang, Introduction, pg. 2). Overall, Chiang’s teachings show that bacteria, such as E. coli, can engineered as carriers to express and deliver different “bioactive payloads” to tumor sites for cancer treatment.
Martinson’s general disclosure relates to colonization of E. coli within the gut and that repeated exposure to E. coli may promote colonization of E. coli within the gut (see, e.g., Martinson, “Exposure Versus Colonization”, pg. 2). Moreover, Martinson teaches that “E. coli is a species of almost exclusively nonpathogenic bacteria. In cross-sectional studies of human adults, E. coli is a member of the intestinal microbiome of over 90% of individuals” (see, e.g., Martinson, Introduction, pg. 2). Additionally, Martinson discloses at some E. coli serotypes more stably colonize the gut than others (see, e.g., Martinson, “Temporal E. coli Dynamics in the Pre-PCR Era”, pg. 3).
Regarding claims 1, 6-7, and 11 pertaining to oral administration of an effective amount of E. coli and E. coli gut colonization, Martinson teaches that oral ingestion of E. coli at a concentration of 109 to 1010 CFU twice daily was capable of colonizing the gut of some volunteers (see, e.g., Martinson, “Exposure Versus Colonization”, pg. 2). Please refer to Examiner’s interpretation of the phrase “effective amount” in the 112(b) rejection above.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce Han’s recombinant methioninase producing E. coli strain, wherein the E. coli strain can be administered orally for recombinant production of anti-cancer proteins within subjects with cancer, as taught by Chiang. One would have been motivated to do so because Chiang teaches tumor-seeking bacteria, such as E. coli, can be engineered to synthesize a variety of therapeutic agents, wherein the engineered bacteria “target tumors where they reside, replicate, and continuously produce the payloads on site. It enables in situ delivery of the produced bioactive molecules to tumor site, which improves the therapeutic efficacy” (see, e.g., Chiang, Introduction, pg. 1). Additionally, Chiang teaches that tumor-targeting bacteria have been genetically instructed to deliver a variety of bioactive payloads, such as prodrug-converted enzymes (see, e.g., Chiang, Introduction, pg. 1). Furthermore, Martinson teaches that E. coli can be orally ingested at a concentration of 109 to 1010 CFU twice daily and that this concentration of E. coli is capable of gut colonization in some individuals (see, e.g., Martinson, “Exposure Versus Colonization”, pg. 2). Moreover, Han teaches cloning rMETase from Pseudomonas putida in E. coli in order to recombinantly express rMETase (see, e.g., Han, [0033]). Additionally, Han teaches that rMETase can be used to arrest the growth of cancer cells through methionine deprivation (see, e.g., Han, [0004]). Additionally, Han teaches “When compared with ip-rMETase, oral rMETase (“o-rMETase”) is significantly more effective as an anticancer agent than ip-rMETase, provided administration of the o-rMETase is accompanied by pyridoxal-L-phosphate (“PLP”) in drinking water” (see, e.g., Han, [0025]). Han also teaches “Orally administered rMETase is significantly more effective at inhibiting melanoma tumor growth than intraperitoneal rMETase” (see, e.g., Han, [0038]). Therefore, based on the teachings of Han, Chiang, and Martinson, it would have been obvious to orally administer an engineered E. coli strain recombinantly expressing rMETase from Pseudomonas putida in order to treat cancer in a subject. One would have expected success because Han and Chiang both teach methods of treating cancers through expression of recombinant proteins produced by engineered E. coli strains, and Martinson teaches colonization of E. coli strains.
Claims 2-3 and 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Han, Chiang, and Martinson as applied to claims 1, 6-7, and 11 above, and further in view of Akita (US Patent No. 6,475,767; Date of Publication: November 5, 2002).
The teachings of Han, Chiang, and Martinson, herein referred to as modified-Han-Chiang-Martinson are discussed above as it pertains to orally administering recombinant methioninase producing E. coli to treat cancer in subjects in need thereof.
Regarding claims 2 and 8 pertaining to the E. coli bacterial strain, modified-Han-Chiang-Martinson teaches “Recombinant L-methionine α-deamino-γ-mercaptopurine lyase (methioninase, METase) [EC 4.4.1.11] from Pseudomonas putida has been previously cloned and was produced in Escherichia coli (AntiCancer, Inc., San Diego, Calif.). The rMETase is a homotetrameric PLP enzyme of 172-kDa molecular mass” (see, e.g., Han, [0033]).
However, modified-Han-Chiang-Martinson does not teach: plasmid pATG3131 (claims 2 and 8); or an E. coli JM109 strain (claim 3 and 9).
Akita’s general disclosure relates to a process of producing L-methionine γ-lyase crystals (see, e.g., Akita, abstract). Moreover, Akita discloses “Recently, it was found that L-methionine .gamma.-lyase has an antitumor activity (WO94/11535). In the past, L-methionine .gamma.-lyase could be obtained in very small quantity from Pseudomonas. putida. However, recent development of recombinant DNA technology provides a possibility of its large quantity production (Inoue, H. et al., J. Biochem. 117, 1120-1125 (1995))” (see, e.g., Akita, “Background Art”, col 1, lines 25-31). Additionally, Akita discloses methods of producing and cultivating and rMETase expression strain by cloning the rMETase gene into E. coli host strains (see, e.g., Akita, “Cultivation of rMETase Expression Strain”, col 2, lines 50-65).
Regarding claims 2 and 8 pertaining to plasmid pATG3131, Akita teaches “rMETase(-ATG) of LMGL/T-vector was inserted in downstream of the initiation codon of plasmid pATG3131 which contained trc promoter, SD sequence, initiation codon (ATG), 5SrrnBT.sub.1 T.sub.2 terminator and tetracycline resistant gene” (see, e.g., Akita, col 8, lines 13-17).
Regarding claims 3 and 9 pertaining to E. coli JM109, Akita teaches E. coli JM109 as a suitable host cell for expression of rMETase (see, e.g., Akita, col 4, “Reference Example 1”, lines 46-47).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce modified-Han-Chiang-Martinson’s recombinant methioninase producing bacterial strain, wherein the bacterial strain contains the plasmid pATG3131 and is expressed within E. coli JM109, as taught by Akita. One would have been motivated to do so because Akita teaches that the JM109 E. coli strain is a suitable host cell for rMETase expression (see, e.g., Akita, col 2, lines 60-65 & Reference Example 1). Moreover, Akita teaches that the pATG3131 plasmid contains a trc promoter, SD sequence, at ATG initiation codon, 5SrrnBT1T2 terminator, and tetracycline resistant gene (see, e.g., Akita, Example 4, col 8, lines 13-16), and that this plasmid can be cloned into E. coli JM109 (see, e.g., Akita, Example 4, col 8, lines 25-27). Moreover, modified-Han-Chiang-Martinson teaches “Recombinant L-methionine α-deamino-γ-mercaptopurine lyase (methioninase, METase) [EC 4.4.1.11] from Pseudomonas putida has been previously cloned and was produced in Escherichia coli (AntiCancer, Inc., San Diego, Calif.)” (see, e.g., Han, [0033]). Therefore, based on the teachings of modified-Han-Chiang-Martinson and Akita, one would have been motivated to use the E. coli JM109 strain and pATG3131 plasmid to recombinant produce rMETase. One would have expected success because modified-Han-Chiang-Martinson and Akita both teach rMETase expression in E. coli strains.
Claims 4-5 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Han, Chiang, and Martinson as applied to claims 1, 6-7, and 11 above, and further in view of Park (Efficacy of oral recombinant methioninase combined with oxaliplatinum and 5-fluorouracil on primary colon cancer in a patient-derived orthotopic xenograft mouse model; 2019).
The teachings of Han, Chiang, and Martinson, herein referred to as modified-Han-Chiang-Martinson are discussed above as it pertains to orally administering recombinant methioninase producing E. coli to treat cancer in subjects in need thereof.
Regarding claims 4 and 10 pertaining to the recombinant methioninase, modified-Han-Chiang-Martinson teaches “Recombinant L-methionine α-deamino-γ-mercaptopurine lyase (methioninase, METase) [EC 4.4.1.11] from Pseudomonas putida has been previously cloned and was produced in Escherichia coli (AntiCancer, Inc., San Diego, Calif.). The rMETase is a homotetrameric PLP enzyme of 172-kDa molecular mass” (see, e.g., Han, [0033]).
However, modified-Han-Chiang-Martinson does not teach: an amount sufficient for treating growth of a cancer in the subject (claims 4 and 10); or wherein the cancer is colon cancer (claim 5);
Park’s general disclosure relates to determining “the efficacy of oral recombinant methioninase (o-rMETase) on a colon cancer primary tumor using a patient-derived orthotopic xenograft (PDOX) nude mouse model” (see, e.g., Park, abstract). Moreover, Park discloses that rMETase “targets MET-dependence/addiction of cancer and can inhibit the growth of cancer cells in vitro and in vivo” (see, e.g., Park, Introduction, pg. 306) and that oral rMETase is significantly more effective than intraperitoneal injection of rMETase (see, e.g., Park, Introduction, pg. 307). Furthermore, Park discloses that oral rMETase is effective at inhibiting colon cancer tumor growth in a colon cancer PDOX model, compared to the untreated control group (see, e.g., Park, Section 3.2, pg. 308).
Regarding claims 4 and 10 pertaining to the amount of methioninase to treat growth of a cancer in the subject, Park teaches that oral methioninase (o-rMETase) was administered to a subject wherein “100 units/day of o-rMETase by gavage for 2 weeks” (see, e.g., Park, Section 2.5, pg. 307). Furthermore, Park teaches that o-METase at this concentration is effective at inhibiting tumor growth and reducing tumor volume compared to untreated controls (see, e.g., Park, Section 3.2, pg. 308 & Figure 3, pg. 309).
Regarding claim 5 pertaining to the cancer type, Park teaches that rMETase is effective at treating colon cancer (see, e.g., Park, Abstract & Section 3.2, pg. 308 & Figure 3, pg. 309).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to administer modified-Han-Chiang-Martinson’s recombinant methioninase producing bacterial strain, wherein the methioninase is produced in an amount for treatment of colon cancer, as taught by Park. One would have been motivated to do so because Park teaches that o-rMETase treatment at 100 units/day results is effective at inhibiting colon cancer tumor growth and reducing tumor volume in a colon cancer PDOX model, compared to untreated controls (see, e.g., Park, Section 3.2, pg. 308). Moreover, modified-Han-Chiang-Martinson teaches methods of producing recombinant methioninase (rMETase) from Pseudomonas putida in Escherichia coli (see, e.g., Han, [0033]). Additionally, modified-Han-Chiang-Martinson teaches that orally administered rMETase is more effective as an anticancer agent than intraperitoneal administered rMETase (see, e.g., Han, [0025). Furthermore, modified-Han-Chiang-Martinson teaches that E. coli can be orally administered to humans and that E. coli at a concentration of 109 to 1010 CFU twice daily was capable of colonizing the gut of some volunteers (see, e.g., Martinson, “Exposure Versus Colonization”, pg. 2). Therefore, one of ordinary skill in the art would understand that if engineered E. coli expressing rMETase is administered at a concentration of 109 to 1010 CFU twice daily, as taught by modified-Han-Chiang-Martinson, that the amount of rMETase produced can be measured, and that if this amount is at or above 100 units of rMETase then it can be used to treat colon cancer, as taught by Park. Therefore, based on the teachings of modified-Han-Chiang-Martinson and Park, it would be obvious to administer an engineered E. coli strain expressing rMETase within the gut of a subject, wherein the amount of rMETase produced by the engineered E. coli strain is at or above 100 units/day, and wherein the rMETase is administered for colon cancer treatment. One would have expected success because modified-Han-Chiang-Martinson and Park all teach production of rMETase and administration of rMETase for cancer treatment.
Conclusion
Claims 1-11 are rejected.
No claims are allowed.
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/NATALIE IANNUZO/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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