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 .
Response to Amendment
Amendments to the specification and claims filed on 12 September 2025 are acknowledged. Claims 36 and 52 are amended. Claims 36-52 are pending and are presented for examination on the merits.
In response to the amendments filed on 12 September 2025, the objections to the specification are withdrawn; the objections to the claims are withdrawn; section (I) of the rejections under 35 U.S.C. 112(a) is maintained with modification; and section (II) of the rejections under 35 U.S.C. 112(a) is partially withdrawn and modified. Moreover, rejections under 35 U.S.C. 112(b) and 35 USC 103 have been added that were not necessitated by amendment. Accordingly, this action is non-final.
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.
Claims 36-52 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.
Independent claim 36 recites the limitation "detecting by-products in a portion of the purified target RNA sample by HPLC to determine the amount [singular] of said by-products [plural] relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides." It is unclear what is meant by the limitation "the amount of said by-products." Is "the amount" a singular value, as implied by the grammatical number of the term? In other words, does "the amount of said by-products" represent a plurality of respective amounts of each of said by-products? Or, contrary to the grammar of the limitation, is "the amount" a plurality of values, each value corresponding to a respective by-product? The specification provides the following guidance (page 35, line 24 to page 36, line 2; italics added):
The term “amount of each by-product”, as used herein, means the amount of a specific by-product present within a sample. It can be determined by calculating the area of the peak corresponding to said specific by-product and relating this area to the area of the peak of the target RNA.
The term “total amount of all by-products”, as used herein, means the total amount of all by-products present within a sample. It can be determined by calculating the area of all peaks representing by-products and relating this area to the area of the peak of the target RNA.
The above guidance in the specification does not match the claim language and does not explicitly consider the "amount" of a subset of byproducts. As discussed below in the rejections under 35 U.S.C. 112(a), the only support for the stand-alone limitation "the amount of said by-products …, said by-products having a length of 5 to 500 nucleotides" is found in original claim 31, which does not clarify the intended meaning of the limitation.
Dependent claims 37-53 are rejected for depending from independent claim 36.
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 36-52 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, had possession of the claimed invention.
The examiner respectfully reminds the Applicant that according to MPEP §2163:
"2163.02. Standard for Determining Compliance with Written Description Requirement:
The courts have described the essential question to be addressed in a description requirement issue in a variety of ways. An objective standard for determining compliance with the written description requirement is, “does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed.” In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). Under Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), to satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention, and that the invention, in that context, is whatever is now claimed. The test for sufficiency of support in a parent application is whether the disclosure of the application relied upon “reasonably conveys to the artisan that the inventor had possession at that time of the later claimed subject matter.” Ralston Purina Co. v. Far-Mar-Co., Inc., 772 F.2d 1570, 1575, 227 USPQ 177, 179 (Fed. Cir. 1985) (quoting In re Kaslow, 707 F.2d 1366, 1375, 217 USPQ 1089, 1096 (Fed. Cir. 1983)). Whenever the issue arises, the fundamental factual inquiry is whether the specification conveys with reasonable clarity to those skilled in the art that, as of the filing date sought, applicant was in possession of the invention as now claimed. See, e.g., Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991). An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing that the invention was “ready for patenting” such as by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention. See, e.g., Pfaff v. Wells Elecs., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641, 1647 (1998); Regents of the University of California v. Eli Lilly, 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997); Amgen, Inc. v. Chugai Pharmaceutical, 927 F.2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by “whatever characteristics sufficiently distinguish it”).
(I)
Independent claim 36 was first presented on 14 August 2024, which is after the filing date of this continuation application. Non-original claim 36 recites the following limitations:
A method for producing a pharmaceutical RNA product, the method comprising the steps of:
a) preparing a sample comprising a target RNA by in vitro transcription, wherein the target RNA is a mRNA of 500 to 10,000 nucleotides in length having a 5′ Cap and poly(A) sequence;
b) purifying the target RNA, thereby providing a purified target RNA sample;
c) detecting by-products in a portion of the purified target RNA sample by HPLC to determine the amount of said by-products relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides, …; and
d) further processing the remainder of the purified target RNA sample to produce a pharmaceutical RNA product.
The combination of the limitation "to determine the amount of said by-products relative to the total amount of RNA in the sample" with other limitations of the claim lacks sufficient written support in the original disclosure. Specifically, the combination of the limitations of a "method for producing a pharmaceutical RNA product" that comprises a step of "d) further processing the remainder of the purified target RNA sample to produce a pharmaceutical RNA product" with the limitation "to determine the amount of said by-products relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides" does not comply with the written description requirement.
As set forth above in the rejections under 35 USC 112(b), it is unclear what is meant by the limitation "the amount [singular] of said by-products [plural]." Is "the amount" a singular value, as implied by the grammatical number of the term? In other words, does "the amount of said by-products" represent a plurality of respective amounts of each of said by-products? Or, contrary to the grammar of the limitation, is "the amount" a plurality of values, each value corresponding to a respective by-product? The specification provides the following guidance (page 35, line 24 to page 36, line 2; italics added):
The term “amount of each by-product”, as used herein, means the amount of a specific by-product present within a sample. It can be determined by calculating the area of the peak corresponding to said specific by-product and relating this area to the area of the peak of the target RNA.
The term “total amount of all by-products”, as used herein, means the total amount of all by-products present within a sample. It can be determined by calculating the area of all peaks representing by-products and relating this area to the area of the peak of the target RNA.
The above guidance does not match the claim language and does not explicitly consider the "amount" of a subset of byproducts. Accordingly, the specification does not clarify the intended meaning of the limitation "the amount of said by-products …, said by-products having a length of 5 to 500 nucleotides."
For purposes of this rejection, the limitation "the amount of said by-products" is treated as a singular value, in accordance with the grammar of the limitation.
The closest support in the original disclosure for the stand-alone limitation "detecting by-products in a portion of the purified target RNA sample by HPLC to determine the amount of said by-products relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides" is found in original claim 31, which depends from original claim 5, which depends from original claim 1. Original claims 1, 5, and 31 are reproduced below:
1. Method for detecting by-products of in vitro transcription in a sample comprising an in vitro transcribed target RNA, the method comprising the steps of:
a) preparing a sample comprising a target RNA by in vitro transcription;
b) purifying the target RNA, thereby providing a purified target RNA sample;
c) detecting the by-products in the purified target RNA sample by HPLC.
5. Method according to any one of the preceding claims, wherein the by-products have a length of 5 to 500 nucleotides.
31. Method according to any one of the preceding claims, wherein the amount of the by-products relative to the total amount of RNA is determined.
Original claim 31 is not a "method for producing a pharmaceutical RNA product" comprising a step of "d) further processing the remainder of the purified target RNA sample to produce a pharmaceutical RNA product," as required by claim 36. Accordingly, original claim 31 does not support the combination of embodiments recited in claim 36.
Regarding the limitation "to determine the amount of said by-products relative to the total amount of RNA in the sample," there is one related teaching in the specification (page 5, lines 21 to 22; bolding added):
In one embodiment the amount of the by-products relative to the total amount of RNA is determined.
However, this teaching is broader than the disclosure of original claim 31 and like original claim 31 does not support the combination of embodiments recited in claim 36.
Elsewhere, the specification teaches the following embodiments, which differ from the claimed determination of "the amount of said by-products relative to the total amount of RNA in the sample" (page 35, line 20 to page 36, line 2; bolding added):
Within the method of the present invention the step of detecting by-products may also comprise determining the amount of each by-product or the total amount of all by-products present in the sample.
The term “amount of each by-product”, as used herein, means the amount of a specific by-product present within a sample. It can be determined by calculating the area of the peak corresponding to said specific by-product and relating this area to the area of the peak of the target RNA.
The term “total amount of all by-products”, as used herein, means the total amount of all by-products present within a sample. It can be determined by calculating the area of all peaks representing by-products and relating this area to the area of the peak of the target RNA.
In the above passage, the specification teaches determining either the amount or a specific by-product (singular) or the total amount of all by-products present within a sample, relative to the amount of target RNA (not "relative to the total amount of RNA in the sample" as claimed). Both options also differ from the claimed requirement of determining the amount of by-products (plural) having a length of 5 to 500 nucleotides relative to the total amount of RNA in the sample.
The original disclosure fails to explain what is meant by determining the amounts of plural by-products having a length of 5 to 500 nucleotides, relative to any standard. As noted above, the specification only defines determining the amount of a specific by-product or determining the total amount of all by-products present within a sample. It is noted that the original disclosure does not teach or suggest that all by-products present within a sample have a length of 5 to 500 nucleotides, instead teaching that "The by-products of the present invention do not have a predetermined size" (page 23, lines 1-2). The specification's teaching that "The by-products may comprise at least two nucleic acid molecules with different length and may have a length of 5 to 500 nucleotides" (page 3, lines 27-28) does not exclude other by-products, including the disclosed long RNAs and double-stranded RNA or DNA/RNA hybrids.
The original disclosure supports a method of producing a pharmaceutical RNA product from an analyzed batch of purified target RNA sample. The specification teaches that "The remainder of the purified target RNA sample can be further processed to the final RNA product, such as a RNA product for administration to a patient, if the HPLC analysis according to step c) of the method of the invention indicates that the amount of by-products is within a range which is acceptable for a final RNA product" (page 30, lines 22-25). This HPLC analysis of step c) is preferably performed at an analytical scale (page 30, lines 16-18).
The original disclosure supports a step of using analytical HPLC to determine a degree of purity of the target DNA based upon all peaks representing by-products (page 18, lines 16-23; bolding and italics added):
After the purification step, the target RNA has a higher purity than before the purification step, but may still contain by-products which may be detected by the method of the present invention. The degree of purity after the purification step may be more than 70% or 75%, in particular more than 80% or 85%, very particularly more than 90% or 95% and most favorably 99% or more. The degree of purity may for example be determined by an analytical HPLC as described herein, wherein the percentage provided above corresponds to the ratio between the area of the peak for the target RNA and the total area of all peaks representing the by-products.
However, the above teaching differs from the method of claim 36 in relating the total of all by-product peaks (as opposed to the amount of by-products having a length of 5 to 500 nucleotides) to the amount of target RNA (as opposed to the total amount of RNA in the sample). The "total amount of RNA in the sample," as recited in claim 36, includes RNA by-products, while the amount of target RNA does not include RNA by-products.
Regarding the nature of the by-products (and therefore the nature of all by-products in a sample), the specification teaches that "The by-products may be homooligomers of nucleotides, short single-stranded RNAs, double-stranded RNAs and/or DNA-RNA hybrids" (page 4, lines 1-2) and provides a definition of "By-product" as "a secondary product of a manufacturing process or a chemical reaction, which differs from the target product of said process or reaction in its size and/or chemical structure" (page 8, lines 11-14). The specification further teaches that "the by-product may comprise long RNAs which have a higher number of nucleotides than the target RNA" (page 8, lines 27-28). The specification does not identify double-stranded RNAs and/or DNA-RNA hybrids as having a length of 5 to 500 nucleotides. Moreover, by-products which have a higher number of nucleotides than the target RNA cannot have a length of 5 to 500 nucleotides for target RNA that is 500 to 10,000 nucleotides in length.
Accordingly, in the context of a method for producing a pharmaceutical RNA product, as required by claim 36, original disclosure supports a step of determining an amount of (all) by-products in the purified target RNA sample (relative to the amount of target RNA in the purified target RNA sample), where the by-products comprise by-products having a length of 5 to 500 nucleotides.
The claimed combination of the embodiment of original claim 31 with the disclosed embodiment of a method of producing a pharmaceutical RNA product does not comply with the written description requirement.
Dependent claims 37-52 are also rejected under this ground because they inherit the deficiencies of independent claim 36.
(II)
Dependent claim 52 has been amended to recite the limitation "wherein the HPLC of step c) is performed at a temperature of at least 60 °C."
Claim 52 requires that 60 °C is the lower endpoint of an open-ended range. The limitation "at least" as recited in claim 52 is new matter.
Regarding the temperature of the HPLC of step c), the original disclosure teaches the following (page 35, lines 1-5):
The method according to the invention is preferably performed at elevated temperature. For example, the sample comprising the purified target RNA or a fraction thereof may be applied to the column at a temperature of 4-12° C., and the subsequent steps may be performed at a higher temperature, preferably at 50° C or more, particularly preferably at 55° C or more and most preferably at about 60° C.
This passage does not teach that 60 °C is the lower endpoint of an open-ended range, as required by claim 52.
In the working example, mRNA was purified using HPLC using a porous reversed phase as stationary phase, as described in detail in WO2008/077592A1 (page 39, lines 22-24), and then analytical ion-pair, reversed-phase chromatography was performed with column temperature set to 60 °C (page 40, line 2). This passage does not teach that 60 °C is the lower endpoint of an open-ended range, as required by claim 52.
Therefore, the Applicants did not show possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention, by description of an actual reduction to practice, or by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention.
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.
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.
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 36-41 and 44-52 are rejected under 35 U.S.C. 103 as being unpatentable over Bancel (US 2016/0024547; IDS) in view of Spivak (US 2016/0017313; IDS) and Azarani ("RNA analysis by ion-pair reversed-phase high performance liquid chromatography," Nucleic Acids Research, 2001, Vol. 29, No. 2, e7; IDS).
Regarding claim 36, Bancel discloses a method for producing a pharmaceutical RNA product ([0005], [0007], producing clinical grade mRNA, [0023]), the method comprising the steps of:
a) preparing a sample comprising a target RNA by in vitro transcription (RNA transcript, abstract), wherein the target RNA is a mRNA of 500 to 10,000 nucleotides in length ([0066], [0082]) having a 5' Cap ([0076]) and poly(A) sequence (poly-A tail, [0076], [0084]);
b) purifying the target RNA, thereby providing a purified target RNA sample (Fig. 1; capping can be performed before further purification of the RNA transcript, [0070]; DNA template is separated chromatographically from the RNA transcript, [0089]; poly A capture-based affinity chromatography can be used to separate adenylated RNA from short aborts and other truncates, [0091]; [0095]);
c) detecting by-products in a portion of the purified target RNA sample by HPLC (analysis performed after additional purification steps, [0095]; analytical reverse phase HPLC, [0096]; purity can be measured by peak area of full-length RNA transcript relative to total peak, which includes by-products [0097]); and
d) further processing the remainder of the purified target RNA sample to produce a pharmaceutical RNA product ([0005], [0007], [0023]).
Bancel is silent regarding the conditions of the analytical reverse phase HPLC of step c) and therefore does not disclose that the HPLC of step c) is performed at a temperature of at least 55 °C and uses a mixture of an aqueous solvent and an organic solvent as mobile phase and wherein the proportion of organic solvent is increased during the HPLC to provide a gradient. However, these conditions are known for analytical HPLC.
The analogous prior art of Spivak (US 2016/0017313; IDS) discloses a method for producing a pharmaceutical RNA product (mRNA, "large scale manufacturing of therapeutics," abstract), comprising
a) preparing a sample comprising a target RNA by in vitro transcription ([0057], [0072]), wherein the target RNA is a mRNA of 500 to 10,000 nucleotides in length (abstract, [0008], [0076], [0099]) having a poly(A) sequence ([0057], [0118]);
b) purifying the target RNA (Fig. 1B steps 112 and 114; P1 purification process, [0036], [0115]; or P2 purification process, [0037], [0115], which is affinity chromatography, [0103]), thereby providing a purified target RNA sample;
c) detecting by-products in a portion of the purified target RNA sample by HPLC (Figs. 1B step 116, 10A, and 10B, [0036], [0037], [0074]; [0115]) to determine the amount of an individual by-product ("quantifying each peak to get the percentage of each impurity," [0085]), said by-products having a shorter length (short transcripts, [0051], "different lengths of mRNA, [0115], [0118]), wherein the HPLC of step c) uses a mixture of an aqueous solvent and an organic solvent as mobile phase (Mobile Phase A and B, Table 4, page 8) and wherein the proportion of organic solvent (acetonitrile in Mobile Phase B, Table 4, page 8) is increased during the HPLC to provide a gradient (%B from initial time to 44 minutes, Table 5, page 8); and
d) further processing the remainder of the purified target RNA sample to produce a pharmaceutical product comprising the final RNA product (abstract, [0005], [0074]).
Spivak teaches that step 116 of Fig. 1B (RP-HPLC of step c) "can be performed under denaturing conditions, non-denaturing conditions, or partially denaturing conditions" ([0087]) and that denaturing conditions can include thermally denaturing conditions of elevated temperature of 55 to 75 °C ([0078]). Spivak cites Azarani ([0142]).
The analogous prior art of Azarani discloses analysis of an RNA ladder having lengths ranging from 155 to 1770 nucleotides (Fig. 1) and transcription reaction products (Fig. 3) by IP RP HPLC under "fully denaturing conditions at 75 °C (page 2, right col., first para.). Azarani teaches that "we noticed a decrease in resolution for RNA at lower analysis temperatures (Fig. 2). Consequently, all RNA analyses were performed at 75°C" (page 3, first para.).
For the benefit of selecting known HPLC conditions that provide improved resolution of RNA, it would have been obvious to one of ordinary skill in the art before the time of filing that the analytical reverse phase HPLC of Bancel is applied using the conditions disclosed by Spivak and Azarani such that the HPLC of step c) is performed at a temperature of at least 55 °C and uses a mixture of an aqueous solvent and an organic solvent as mobile phase and wherein the proportion of organic solvent is increased during the HPLC to provide a gradient.
The use of a known technique to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. __,__, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, C.). “[W]here 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 In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). The discovery of an optimum value of a known result effective variable, without producing any new or unexpected results, is within the ambit of a person of ordinary skill in the art. See In re Boesch, 205 USPQ 215 (CCPA 1980) (see MPEP § 2144.05, II.).
Bancel teaches that purity can be determined via reverse phase HPLC and measuring peak area of full length RNA transcript relative to total peak ([0097]), from which a determination of the amount of the by-products relative to the total amount of RNA is easily available via arithmetic. Bancel discloses that purity can be measured by peak area of full-length RNA transcript relative to total peak ([0097]). Bancel's purity determination can be converted with simple arithmetic to a measure of purity based upon the amount of total byproducts relative to total RNA.
Bancel does not teach determining "the amount of said by-products relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides."
As set forth above in the rejections under 35 USC 112(b), it is unclear what is meant by the limitation "the amount [singular] of said by-products [plural]." Is "the amount" a singular value, as implied by the grammatical number of the term? In other words, does "the amount of said by-products" represent a plurality of respective amounts of each of said by-products? Or, contrary to the grammar of the limitation, is "the amount" a plurality of values, each value corresponding to a respective by-product?
For purposes of this rejection, the indefinite limitation "the amount of said by-products" is treated as encompassing plural amounts of each of said by-products.
The analogous prior art of Spivak discloses, in step c), determining the amount of an individual by-product ("quantifying each peak to get the percentage of each impurity," [0085]),
For the benefit of obtaining the percentage of each impurity, it would have been obvious to one of ordinary skill in the art before the time of filing to modify Bancel's determination of the amount of total byproducts relative to total RNA with Spivak's quantification of each peak to provide a step of quantifying each peak relative to total RNA.
For purposes of this rejection, the disclosure by Bancel in view of Spivak of determining the respective amount of each impurity relative to total RNA, where each impurity includes a plurality of by-products having a length of 5 to 500 nucleotides, is broadly interpreted as satisfying the indefinite limitation of determining "the amount of said by-products relative to the total amount of RNA in the sample, said by-products having a length of 5 to 500 nucleotides."
Regarding claim 37, Bancel discloses that in one embodiment the method excludes the use of DNase ([0010], [0042], [0091]) and therefore discloses that method does not comprise a step of treating the target RNA with a ribozyme. Moreover, Spivak's method of HPLC analysis does not comprise a step of treating the target RNA with a ribozyme, given that the presence of fragmentation is what is being studied in the stability tests ([0114]), and Azarani teaches away from exogenous RNAses because of the potential for RNA degradation (page 1, first para. of introduction).
Regarding claim 38, Bancel discloses that the by-products comprise at least two nucleic acid molecules with different length ("RNA transcripts that do not contain Poly A stretches (short aborts [plural] and other truncates [plural] formed during in vitro transcription)," [0091]). Likewise, Spivak teaches that the impurities are different length mRNA ([0115], [0118]). Moreover, Azarani's Fig. 3B illustrates that by-products in the crude transcript comprise at least two nucleic acid molecules with different lengths. The two left shoulder peaks of the target 5219 nucleotide peak are smaller size RNA transcripts and/or degraded RNA that would be expected to be difficult to resolve from the collected fraction of the target 5219 nucleotide peak.
Regarding claim 39, Bancel discloses that the RNA transcript includes a poly-A tail ([0076]), wherein a poly-A tail is at the 3' terminus ([0008], [0038]). Bancel further discloses that the short aborts and other truncates formed during in vitro transcription are RNA transcripts that do not contain Poly A stretches ([0091]). Accordingly, Bancel discloses that the by-products do not comprise the 3' terminus of the target RNA. Moreover, Spivak discloses that short abort sequences are generated during transcription ([0008], [0051]), and Azarani teaches that "early termination products of transcription also result in shorter RNA fragments" (page 3). One of ordinary skill in the art would understand that RNA polymerase builds an RNA strand in the 5' to 3' direction, and that short aborts and early termination products of transcription would result in a shorter RNA fragment that does not comprise the 3' terminus of the target RNA.
Regarding claim 40, both Spivak (Fig. 1B, [0087]) and Azarani (page 1, last two Introduction paragraphs) disclose performing RP-HPLC under denaturing conditions, which results in any short RNAs being single-stranded.
Regarding claim 41, Bancel is silent as to whether step b) is performed under denaturing conditions, including thermal denaturing conditions ([0078]). Spivak discloses that step b) is performed under denaturing conditions (Fig. 1B, steps 112 and 114, [0087]). Azarani discloses analysis of an RNA ladder having lengths ranging from 155 to 1770 nucleotides (Fig. 1) and transcription reaction products (Fig. 3) by IP RP HPLC under "fully denaturing conditions at 75 °C (page 2, right col., first para.). Azarani teaches that "we noticed a decrease in resolution for RNA at lower analysis temperatures (Fig. 2). Consequently, all RNA analyses were performed at 75°C" (page 3, first para.). For the benefit of selecting known HPLC conditions that provide improved resolution of RNA, it would have been obvious to one of ordinary skill in the art before the time of filing that the purification chromatography of Bancel is applied using the conditions disclosed by Spivak and Azarani such that step b) is performed under denaturing conditions.
The use of a known technique to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. __,__, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, C.). “[W]here 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 In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). The discovery of an optimum value of a known result effective variable, without producing any new or unexpected results, is within the ambit of a person of ordinary skill in the art. See In re Boesch, 205 USPQ 215 (CCPA 1980) (see MPEP § 2144.05, II.).
Regarding claim 44, Bancel discloses that the HPLC in step c) is reversed-phase HPLC (analytical reverse phase HPLC, [0096]) but does not disclose ion-pair, reversed-phase HPLC. Azarani teaches using ion-pair, reversed-phase HPLC to determine the quality and purity of RNA transcripts (page 3, second and third para.). Azarani teaches that components of an RNA ladder having lengths ranging from 155 to 1770 nucleotides were resolved by IP RP HPLC (abstract). For the benefit of resolution of small RNAs, it would have been obvious to one of ordinary skill in the art before the time of filing the replace the analytical RP HPLC of Spivak with the analytical IP RP HPLC of Azarani.
The simple substitution of one known element for another is likely to be obvious when predictable results are achieved. See KSR International Co. v. Teleflex Inc., 550 U.S. __,__, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, B.).
Regarding claims 45-47, Bancel discloses that the HPLC in step c) is reversed-phase HPLC (analytical reverse phase HPLC, [0096]) but does not explicitly disclose that the HPLC in step c) uses a carbon-chain bonded silica column or that the column has a particle size of 0.5 to 5 micrometers and/or a pore size of 50 to 300 angstrom. Spivak discloses that the HPLC in step c) uses a Waters XBridge C18 column, 2.1 x 50 mm (Table 4, page 8) without disclosing the particle size or the pore size of this column. The examiner takes official notice that a Waters XBridge C18 column is a carbon-chain bonded silica column. The examiner takes official notice that a Waters XBridge C18 column, 2.1 x 50 mm is available with a particle size of 0.5 to 5 micrometers and with a pore size of 50 to 300 angstrom. For the benefit of selecting from a known type of Waters XBridge C18 column, it would have been obvious to one of ordinary skill in the art at the time of filing that Bancel's analytical reverse phase HPLC uses a carbon-chain bonded silica column having a particle size of 0.5 to 5 micrometers and/or a pore size of 50 to 300 angstrom.
The simple substitution of one known element for another is likely to be obvious when predictable results are achieved. See KSR International Co. v. Teleflex Inc., 550 U.S. __,__, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, B.).
Regarding claim 48, Spivak discloses that at the beginning of the HPLC, the mobile phase contains a 5% proportion of organic solvent (20% Mobile Phase B, Table 5, where Mobile Phase B is 25% acetonitrile, Table 4, page 8), relative to the mobile phase, the rest being the aqueous solvent (TEAA buffer in Mobile Phases A and B, Tables 4 and 5, page 8).
Regarding claims 49-51, Spivak discloses that the organic solvent is acetonitrile (Table 4, page 8) and that the aqueous solvent comprises a buffer (triethylammonium acetate, TEAA, buffer Table 4, page 8).
Regarding claim 52, as applied to the rejection of claim 36 above, Azarani discloses that the HPLC of step c) is performed at a temperature of at least 60 °C. ("Consequently, all RNA analyses were performed at 75°C," page 3, first para.).
Claims 42 and 43 are rejected under 35 U.S.C. 103 as being obvious over Bancel in view of Spivak and Azarani as applied to claims 36-41 and 44-52 above, further in view of Ketterer (US 2010/0048883, IDS; previously relied upon).
Regarding claims 42 and 43, Bancel does not disclose that step b) comprises a step of purifying the target RNA by HPLC or reversed-phase HPLC.
Spivak discloses that purifying step b) is a "P1 purification process" ([0036], [0115]), which is not explained, or a "P2 purification process" ([0037], [0115]) which is affinity chromatography, [0103]), or uses a "reversed phase "(Fig. 1B, step 112, [0085]). Spivak does not explicitly teach that this reversed phase is reversed-phase HPLC.
In the analogous art of the preparative-scale preparation of mRNA for therapeutic purposes ([0001], [0019]), Ketterer teaches preparative purification of transcripted RNA ([0012]) via reversed-phase HPLC (abstract, [0007]) using completely denaturing conditions to achieve better separation ([0060]). Ketterer discloses that high-purity RNA-containing fractions may be separated from other RNA-containing fractions which still contain undesired impurities, albeit in very small quantities ([0059]). Ketterer discloses that larger RNA as well as smaller RNA fragments with a length of 20-200, 20-100, 20-50 or 20-30 nucleotides may be separated ([0018], [0027]).
For the benefit of providing purer RNA on a preparative scale via a known technique, it would have been obvious to one of ordinary skill in the art at the time of filing that Bancel's purifying step is reversed-phase HPLC, as taught by Ketterer.
The use of a known technique to improve similar methods in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. __,__, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, C.).
Response to Arguments
Applicant's arguments filed on 12 September 2025 have been considered and are not fully persuasive and/or are moot in view of the new grounds of rejection.
Regarding section (I) of the rejections under 35 U.S.C. 112(a) of the non-final office action, Applicant persuasively argues the following:
The Applicants also note that the original claims form part of the disclosure. As such, taking original claim 31, as it depends on original claim 5, as it depends on original claim 1, does in fact provide an embodiment where the amount of by-products having a length of 5 to 500 nucleotides is determined relative to the total amount of RNA by HPLC.
Accordingly, the rejections under 35 U.S.C. 112(a) have been updated to note the originally-disclosed subject matter of claim 31. However, claim 31 is not a method for producing a pharmaceutical product.
Applicant further traverses section (I) of the rejections under 35 U.S.C. 112(a).
Applicant draws a distinction between the phrase "all the by-products present" previously used in the rejection and the phrase "all peaks representing the by-products" used in the specification. In response, the language of the rejection has been corrected to more accurately reflect the language of the specification. It is not clear to the examiner how any potential distinction between these two phrases is relevant to the rejection.
Applicant highlights the following teaching of the specification (page 3, lines 10-13; bolding and italics added by Applicant):
Using this protocol, contamination of the RNA product with by-products can be determined and quantified. Additionally, fraction collection of selected peaks during HPLC purification allows the isolation and subsequent characterization of the RNA species comprised in the by-products …
Applicant does not specifically explain the relevance of the above passage to the rejection. The examiner notes that (i) the claims are a method for producing a pharmaceutical RNA product and do not recite isolation and characterization of by-products by either terminology or concept, (ii) the above passage does not describe by-products in a purified sample [c.f. step c) of claim 36], and (iii) in the specification's detailed description of the invention, the "characterization" of by-products is not performed on the same purified target RNA sample that is further processed to produce a pharmaceutical RNA product. Is Applicant arguing that the specification describes producing a pharmaceutical product [for administration to patients] from a purified batch when the same purified batch contains a mystery by-product that requires further characterization? This would not be good manufacturing practice. Instead, in the opinion of the examiner, the specification merely discloses quality control in the context of the preparation of RNA products for pharmaceutical use.
As highlighted in the rejection, the closest support in the original disclosure for the claimed invention is the specification's disclosure of using analytical HPLC to determine a degree of purity of the target DNA (page 18, lines 16-23). Step c) of claim 36 recites a particular manner of determining a degree of purity, and the claimed details of this particular manner of determining a degree of purity are not supported by the original disclosure.
Applicant further argues the following:
In addition, the specification, at page 35, lines 23-26, provides a definition relevant to this method: "The term 'amount of each by-product', as used herein, means the amount of a specific by-product present within a sample." In other words, the application as-filed specifically contemplates characterizing certain components from within the totality of all by-products.
In response, the claims do not recite the phrase "amount of each by-product." Because the intended meaning of the claim 36 limitation "the amount of said by-products" is unclear, rejections under 35 USC 112(b) have been added. The examiner notes that the definition of the term "amount of each by-product" provided by the specification at page 35, lines 23-26 contradicts claim 36 by stating that the amount of each by-product "can be determined by calculating the area of the peak corresponding to said specific by-product and relating this area to the area of the peak of the target RNA." In contrast, claim 36 requires that the amount of said by-products is determined relative to the total amount of RNA in the sample. The total RNA includes both target RNA and by-product RNA.
Applicant argues "the examples, and indeed FIG. 1A-B, discuss resolving by-product peaks to single nucleotide resolution." The relevance of this argument to the claims and to the rejection is unclear.
Applicant argues that "Example 2 demonstrates detection of such 'short' by-products by the claimed method" (bolding added). On the contrary, Example 2 is not a method for producing a pharmaceutical RNA product and does not involve a step of determining the amount of (any) by-products relative to the total amount of RNA in the sample.
Applicant argues that "The specification, at page 22, lines 10-18 specifically discloses lower peak by-products and their detection, wherein such by products are 5 to 500 nucleotides in length." However, the claims are not rejected for merely reciting a step of detecting by-products having a length of 5 to 500 nucleotides.
Section (II) of the rejections under 35 U.S.C. 112(a) have been partially overcome by amendment and modified. Applicant's arguments do not specifically address the modified ground of section (II) of the rejections under 35 U.S.C. 112(a).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHELLE ADAMS whose telephone number is (571)270-5043. The examiner can normally be reached on M, T, Th, and F, 12-4 P.M.
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/MICHELLE ADAMS/ Examiner, Art Unit 1797
/JENNIFER WECKER/Primary Examiner, Art Unit 1797