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 .
Priority
Acknowledgement is made that the instant application is a National Stage of International application No. PCT/US2021/057716 (filed 11/02/2021), which claims the benefits of US Provisional Application No. 63/108,629.
Claim Objections
Claims 5 and 17 are objected to because of the following informalities:
Regarding claim 5: Claim 5 recites "wherein the removing..." the word "the" appearing prior to the word "removing" should be removed in this sentence.
Regarding claim 17: Claim 17 recites "the anion-exchange chromatography is a polystyrene/divinyl benzene resin". The word "is" should be corrected to the word "uses".
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 20, and 23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 1: Claim 1 recites the limitation "the AAV particles" in lines 5 and 6. There is insufficient antecedent basis for this limitation in the claim. The limitation should be corrected to “the rAAV particles”.
Regarding claim 20: Claim 20 recites the limitation "the elute" in lines 3, 6, 9, and 10. There is insufficient antecedent basis for this limitation in the claim.
Regarding claim 23: Claim 23 recites wherein the removal step (i.e. anion exchange chromatography) allows the composition of the providing step (i.e. the initial composition) to have a greater quantity of therapeutically effective rAAV particles… It is unclear how performing anion exchange chromatography would increase the amount of therapeutically effective rAAV particles in the initial composition. For the purpose of compact prosecution, the claim will be interpreted as stating the composition obtained after performing anion exchange chromatography has a greater concentration of therapeutically effective rAAV particles. Note: it is not possible to increase the quantity of rAAVs, only the concentration.
Additionally, as written, it is unclear what the quantity of therapeutically effective rAAV particles is greater than in the phrase “having a greater quantity of therapeutically effective rAAV particles”.
Appropriate corrections is required.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 5, 22, 23, 26-28, and 33-35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Fiedler et al (WO2018128688A1).
Fiedler et al discloses a method of purifying AAVs comprising an anion exchange chromatography (AEX) step and a zonal ultracentrifugation (ZUC) step (See Fig. 1). In some embodiments the AAVs of Fiedler et al are rAAVs (See ¶0059). The method of Fiedler et al removes empty capsids. Fiedler et al discloses a feature of AAV vector generation in cell culture is the formation of an excess of "empty" capsids, which lack the vector genome or have truncated or incomplete vector DNA (See ¶006-007). Such empty capsids are unable to provide a therapeutic benefit associated with transgene production (See ¶006). The ZUC step of Fiedler et al uses a sucrose gradient (See claim 1). In exemplary embodiments, 61%...95%, 96%, 97%, 98%, 99%, or 100% of AAV particles in the fraction obtained from the sugar gradient are full AAV capsids (See ¶0027). The AAVs of Fiedler et al are transfected with repcap plasmids (See ¶001478). In exemplary embodiments, Fiedler et al uses AAV8 adenoviruses with VP1, VP2, or VP3 capsids (See ¶116).
Regarding claims 1 and 21: Fiedler et al discloses a method of purifying rAAVs comprising steps of AEX and ZUC which reads on a method of purifying therapeutically effective recombinant adeno virus particles comprising the steps of providing a composition, removing a first portion from the composition by anion-exchange chromatography and removing a second portion from the composition by zonal ultracentrifugation. AAV production inherently produces a composition with impurities, such as empty capsids (reads on therapeutically ineffective rAAV particles), comprising impurities having a net charge different from the AAV particles and a portion of impurities having a density different from AAV particles. Furthermore, AEX is a method of separation based on charge, thus AEX inherently removes impurities having a net charge different from the AAV particles. Zonal centrifugation is a method of separation based on density, thus ZUC inherently separates impurities having a density different from the AAV particles. Additionally, Fiedler et al discloses in some embodiments the fraction obtained from ZUC has 100% full AAV capsids which reads on yielding a composition that is substantially devoid of AAV production impurities and substantially devoid of therapeutically ineffective rAAV particles.
Regarding claims 5 and 22: Following the discussion of claims 1 and 21 above, Fiedler et al discloses a method of purifying rAAVs comprising removing a first portion of impurities by AEX. AEX is used to separate impurities with a different charge than the full rAAVs. Thus, in the method of Fiedler et al, removing the first portion from the composition by AEX allow for the removal of the second portion from the composition by ZUC.
Regarding claim 23: Following the discussion of claim 21 above, Fiedler et al discloses a method of purifying rAAVs comprising removing a first portion of impurities by AEX. AEX removes empty capsids which have a different charge from the full capsids and concentrates the sample. Thus in the method of Fiedler et al, the AEX step (reads on removal step) results in a composition with a greater concentration of full capsids (AEX) which can then be processed by ZUC.
Regarding claims 26 and 27: Following the discussion of claim 21 above, Fiedler et al discloses that in some embodiments the fraction obtained from ZUC has 100% full AAV capsids which reads on the composition after AEX and ZUC is at least 95% pure from therapeutically ineffective rAAV particles and free from any detectable therapeutically ineffective rAAV particles.
Regarding claim 28: Following the discussion of claim 21 above, Fiedler et al discloses an rAAV production step of transfecting rAAVs with a repcap plasmid (reads on capsids associated with Rep proteins). Fiedler et al further discloses methods for removing empty capsids (reads on therapeutically ineffective rAAV particles). Thus, the empty capsids of Fiedler et al comprise capsids associated with Rep proteins.
Regarding claim 33: Following the discussion of claim 21 above, Fiedler et al discloses empty capsids which lack the vector genome which reads on the therapeutically ineffective rAAV particles comprise capsids devoid of a vector genome.
Regarding claim 34: Following the discussion of claim 21 above, Fiedler et al discloses empty capsids with truncated or incomplete vector DNA which reads on the therapeutically ineffective rAAV particles comprise capsids with vector genomes having one or more sizes that are insufficient for cells infected by the capsids to generate therapeutically effective nucleotide sequences.
Regarding claim 35: Following the discussion of claim 35 above, Fiedler et al discloses empty capsids with truncated or incomplete vector DNA. In situations where a cell is infected by the empty capsid of Fiedler et al and a full capsid of Fiedler et al, the presence of the empty capsid would inherently reduce the expression of an element by the cell compared to a cell infected under the same condition with only full capsids because there would be fewer full capsids within the cell that are capable of expressing the element. i.e. if two cells are infected under the same conditions with the same number of rAAVs but one cell has 50% full capsids and 50% empty capsids whereas the other cell has 100% full capsids, the cell comprising only full capsids would inherently express more of the element encoded by the rAAV because there are more capsids capable of expressing the element.
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-5, 21-23, 25-28, and 33-35 are rejected under 35 U.S.C. 103 as being unpatentable over Fiedler et al (WO2018128688A1).
The teachings of Fiedler et al are set forth above.
Fiedler et al anticipates claims 1, 5, 21-23, 26-28, and 33-35.
Regarding claims 2-4: Following the discussion of claim 1 above Fiedler discloses a method of purifying rAAV particles comprising steps of AEX and ZUC. In some embodiments, the method of Fiedler et al produces a composition with 100% full capsids.
The definition of AAV production impurities provided in the specification of the instant application encompasses ineffective rAAV, aggregates of the rAAV particles, extrinsic high molecular weight DNA, small nucleotides, proteins, buffer components, etc. Given that Fiedler et al teach recovering the fraction in an elution buffer, it is not clear that the composition of Fiedler et al after AEX and ZUC is at least 95%, 99%, or 99+% pure from AAV production impurities, including buffer components.
However, it would have been prima facie obvious, to one of ordinary skill in the art, before the effective filing date to optimize the type of AEX resin used or the length of time for which ZUC is performed in order to achieve a composition which is 95% or 99% pure from AAV production impurities. Additionally, it would have been prima facie obvious to include a filtration method following the ZUC step in order to remove buffer components to achieve a composition that is 99+% pure from AAV production impurities. Where the general conditions of a claim are disclosed in the prior art it is not inventive to discover the optimum or workable ranges by routine experimentation. See MPEP2144.05(II).
Regarding claim 25: Following the discussion of claim 21 above, Fiedler et al discloses a method of purifying rAAVs comprising an AEX step which reads on a removal step. AEX inherently removes therapeutically ineffective particles with charges different from the therapeutically effective particles.
Fiedler et al does not disclose AEX removes at least 50% of the therapeutically ineffective rAAV particles from the composition.
Although Fiedler et al does not disclose the AEX step removes 50% of therapeutically ineffective rAAV particles from the composition, it would have been prima facie obvious, to one of ordinary skill in the art, before the effective filing date, to optimize the type of AEX resin used in order to achieve removal of 50% of therapeutically ineffective rAAV particles. Where the general conditions of a claim are disclosed in the prior art it is not inventive to discover the optimum or workable ranges by routine experimentation. See MPEP2144.05(II).
Claims 1-5, 17, 18, 21-23, 25-28, and 33-35 are rejected under 35 U.S.C. 103 as being unpatentable over Fiedler et al (WO2018128688A1) in view of Zatirakha et al (Journal of Chromatography A, 2014).
The teachings of Fiedler et al are set forth above.
Fiedler et al anticipates claims 1, 5, 21-23, 26-28, and 33-35 and renders claims 2-4 and 25 obvious.
Regarding claims 17 and 18: Following the discussion of claim 1 above, Fiedler et al discloses a method of purifying rAAVs comprising an AEX step.
Fiedler et al does not disclose using polystyrene/divinyl benzene resin modified with quaternary ammonium groups in the AEX step.
Zatirakha et al discloses and anion exchanger resin comprising a polystyrene divinyl benzene (PS-DVB) with long hydrophilic alkyl substituent in the quaternary ammonium (reads on modified quaternary ammonium). The modification to the quaternary ammonium group improves column efficiency and separation selectivity(See Sec. 3.1 Synthesis).
Given that Fiedler et al discloses an rAAV purification method comprising an AEX step and Zatirakha et al discloses an anion exchange resin comprising PS-DVB with a modified quaternary ammonium group that results in improved column efficiency and separation, it would have been prima facie obvious, to one of ordinary skill in the art, to modify the AEX step of Fiedler et al to include the PS-DVB modified resin of Zatirakha et al. One would have been motivated to modify the method of Fiedler et al because Zatirakha et al discloses the modified resin improves column efficiency and separation selectivity. There is a reasonable expectation of success because PS-DVB resins are commercially available products for purification of AAVs.
Claims 1-5, 19-23, 25-28, and 33-35 are rejected under 35 U.S.C. 103 as being unpatentable over Fiedler et al (WO2018128688A1) in view of Su et al (CSH, Aug. 2020).
The teachings of Fiedler et al are set forth above.
Fiedler et al anticipates claims 1, 5, 21-23, 26-28, and 33-35 and renders claims 2-4 and 25 obvious.
Regarding claim 19: Following the discussion of claim 1 above, Fiedler et al discloses a method of purifying rAAVs comprising a ZUC step. The ZUC method of Fiedler et al uses a sucrose gradient.
Fiedler et al does not disclose using a cesium chloride (CsCl) gradient in the ZUC step.
Su et al teaches a protocol for purifying rAAVs using cesium chloride gradient ultracentrifugation (See abstract).
Given that both Fiedler et al and Su et al teach AAV purification methods comprising an ultracentrifugation step, it would have been prima facie obvious to substitute the sucrose gradient of Fiedler et al for the CsCl gradient of Su et al, in the ZUC step of Fiedler et al. One would have expected the CsCl gradient to work equivocally with the sucrose gradient in the ZUC method of Fiedler et al because Su discloses CsCl gradients can be used to purify AAV particles. Substitution of one element for another known in the field, wherein the result of the substitution would have been predictable is considered to be obvious. See KSR International Co. V Teleflex Inc 82 USPQ2d 1385 (US2007) at page 1395.
Regarding claim 20: Following the discussion of claims 1 and 19 above, Fiedler et al discloses a method of purifying rAAVs comprising a ZUC step.
Su et al teaches a protocol for purifying rAAVs using cesium chloride gradient ultracentrifugation. The method of Su et al comprises steps of adding ultrapure CsCl to the clarified lysate comprising AAV particles (reads on adding CsCl to the elute), adding a low concentration CsCl (L-CsCl) solution to a centrifuge tube (reads on overlaying a first CsCl solution) , adding a high concentration CsCl (H-CsCl) solution below the L-CsCl (reads on adding a second CsCl solution), and layering the lysate composition on top of the layered CsCl solutions (See steps 3-4). The protocol of Su et al further teaches collecting fractions containing rAAV after centrifugation from the CsCl gradient which reads on centrifuging to form a density gradient and collecting fractions from the density gradient (See steps 5-8 and Fig. 1).
It would have been prima facie obvious to substitute the sucrose gradient of Fiedler et al with the CsCl gradient of Su et al in the ZUC step of Fiedler et al (See rejection of claim 19 above).
Additionally, it would have been prima facie to optimize the concentration of the CsCl in the L-CsCl and H-CsCl solutions and arrive at a L-CsCl solution having a CsCl concentration less that the CsCl concentration in the lysate and an H-CsCl solution that has a greater CsCl concentration than the lysate in order to improve separation of the gradient and AAV particles during centrifugation. Additionally, it would have been prima facie obvious to optimize the order in which the CsCl solutions and lysate are layered in order to improve separation of the full and empty AAV particles. Where the general conditions of a claim are disclosed in the prior art it is not inventive to discover the optimum or workable ranges by routine experimentation. See MPEP2144.05(II).
Claims 1-5, 21-23, 25-28, and 32-25 are rejected under 35 U.S.C. 103 as being unpatentable over Fiedler et al (WO2018128688) in view of Giles et al (Mol. Ther., 2018).
The teachings of Fiedler et al are set forth above.
Fiedler et al anticipates claims 1, 5, 21-23, 26-28, and 33-35 and renders claims 2-4 and 25 obvious.
Regarding claim 32: Following the discussion of claim 21 above, Fiedler discloses a method of producing and purifying rAAV particles which comprises steps for separating empty capsids (reads on therapeutically ineffective particles) from full capsids. In exemplary embodiments, Fiedler et al uses AAV8 adenoviruses with VP1, VP2, or VP3 capsids. Thus, the empty capsids of Fiedler et al comprise VP1, VP2, or VP3 capsid proteins.
Fiedler et al does not teach the VP1, VP2, and VP3 capsid proteins have a deamidated amino acid.
Giles et al teaches deamidation of VP1, VP2, and VP3 capsid proteins is a spontaneous enzyme independent process that occurs during AAV production using AAV8 vectors (See pg. 2848, Sec. Introduction).
Given that Fiedler et al discloses a method of producing AAV8 adenoviruses comprising VP1, VP2, or VP3 capsid proteins and Giles et al discloses deamidation of VP1, VP2, and VP3 capsid proteins is a spontaneous process that occurs during AAV production, one would have expected empty capsids comprising deamidated VP1, VP2, or VP3 capsids in some embodiments of Fiedler et al.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARISOL A O'NEILL whose telephone number is (571)272-2490. The examiner can normally be reached Monday - Friday 7:30 - 5:00 EST.
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/MARISOL ANN O'NEILL/Examiner, Art Unit 1633
/ALLISON M FOX/Primary Examiner, Art Unit 1633