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, claim(s) 1,3,7,11,17,22,30,33,40-41,46,51,53-54,56,60,111,132 in the reply filed on 03DEC2025 is acknowledged.
Claims 63,65 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Priority
Benefit of domestic priority of application 63/082,358 filed on 09/23/2020 under 35 U.S.C. 120, 121, or 119e is acknowledged.
Information Disclosure Statement
No Information Disclosure Statement has been filed.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The use of terms found in par. [135,137-143,145-147,182,189,205,213,218,225, 296,306] which are a trade name or a mark used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term (which the Applicant has done already).
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Interpretation
The claim term " chromatography resin" is defined in par. [0090] of the specification.
The claim term "residual nucleic acid molecule" is defined in par. [0097] of the specification.
Claim Objections
Claims 1,41,46,53 are objected to because of the following informalities: Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation, 37 CFR 1.75(i). See MPEP 6083.01(m). For example:
1. (Currently Amended) A method of purifying extracellular vesicles (EVs) from a sample suspected of comprising EVs and one or more nucleic acid molecules, the method comprising:
(i) contacting the sample with a chromatography resin and
(ii) washing the chromatography resin with a nuclease wash buffer;
wherein the nuclease wash buffer comprises a nuclease and a cation; and
wherein the (ii) washing follows the (i) contacting,
wherein the method reduces a concentration of residual nucleic acid molecules in the sample to purify the EVs.
Appropriate correction is required.
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 1,3,7,11,17,22,30,33,40-41,46,51,53-54,56,60,111,132 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 regards as the invention.
Claim 1 line(s) 2,6-7 sets forth the limitation “A method of purifying extracellular vesicles (EVs) from a sample suspected of comprising EVs […] wherein the method […] to purify the EVs”. The preamble of the claim appears to suggest the possibility of a sample without EVs, but purports to purify the EVs and thus the claim scope cannot be ascertained.
Claim 1 line(s) 2,6-7 sets forth the limitation “A method of purifying extracellular vesicles (EVs) from a sample suspected of comprising […] nucleic acid molecules, wherein the method reduces a concentration of residual nucleic acid molecules in the sample”. The preamble of the claim appears to suggest the possibility of a sample without nucleic acid molecules, but purports to reduce a concentration of residual nucleic acid molecules in the sample and thus the claim scope cannot be ascertained.
Claims 22,30,33,41,46,111 sets forth a range concluding with “at least”. A range concluding with “at least” does not make sense, because the endpoint is not a definitive end point and thus the claim scope cannot be ascertained.
Regarding claim 33, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, the claim recites a broad recitation of e.g. at least 2 times, and the claim also recites several additional ranges which are the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 40 line(s) 2 sets forth the limitation “the wash buffer”. There is insufficient antecedent basis for this limitation in the claim, because it is unclear whether “the wash buffer” of claim 40 refers to “a nuclease wash buffer” of claim 1 or is something else.
Claim 40 line(s) 4 sets forth the limitation “a nuclease wash buffer”. It is unclear whether “a nuclease wash buffer” of claim 40 is the same or different from “a nuclease wash buffer” of claim 1.
Claim 46 line(s) 4 sets forth the limitation “a nuclease wash buffer”. It is unclear whether “a nuclease wash buffer” of claim 46 is the same or different from “a nuclease wash buffer” of claim 1.
Claim 53 line(s) 3 sets forth the limitation “the eluent”. There is insufficient antecedent basis for this limitation in the claim. Perhaps the Applicant intended claim 53 to be dependent on claim 51.
Claim 56 line(s) 3 sets forth the limitation “the AEX resin”. There is insufficient antecedent basis for this limitation in the claim. Perhaps the Applicant intended claim 53 to be dependent on claim 54.
Claim 60 line(s) 2 sets forth the limitation “the AEX resin”. There is insufficient antecedent basis for this limitation in the claim. Perhaps the Applicant intended claim 53 to be dependent on claim 54.
Regarding claim 41, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, the claim recites a broad recitation of e.g. at least about 0.01 M, and the claim also recites several additional ranges which are the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Regarding claim 53, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, the claim recites the a broad recitation of e.g. less than about 10%, and the claim also recites several additional ranges which are the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Regarding claim 56, the limitation recited “HIC” is an acronym that is not clearly defined by the claim. It is suggested that claim 56 recite - - hydrophobic interaction chromatography ("HIC") - -.
Regarding claim 56, the limitation recited “CFT” is an acronym that is not clearly defined by the claim and thus the claim scope cannot be ascertained. The Applicant may spell out the acronym without adding new matter.
Regarding claim 60, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, the claim recites the a broad recitation of e.g. at least two times, and the claim also recites several additional ranges which are the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
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.
Claim(s) 1,3,7,11,17,22,40,41,46,51,53-54,60,132 are rejected under 35 U.S.C. 103 as being unpatentable over DHELLIN (US 6899863) in view of LIU (US 20080286850).
Regarding claims 1,11, DHELLIN teaches a method for preparing membrane vesicles (title) including a method of purifying extracellular vesicles (EVs) (via e.g. chromatography; abstract) comprising:
Treating the sample with a nuclease (e.g. a DNase (Sigma) and an RNase (Sigma); C17/L34), which enable the fine separation of membrane vesicles (e.g. exosomes) from cell proteins or certain macromolecular components (DNA, RNA) or macromolecular complexes (C2/L8-15);
(i) contacting the sample with a chromatography resin (e.g. SOURCE 15Q; C3/L49-58; C17/L37-38); and,
(ii) washing the chromatography resin with a wash buffer (e.g. BTP buffer including NaCl; C17/L41-44);
wherein the wash buffer comprises a cation (e.g. Na+ dissolved in BTP buffer); and
wherein the (ii) washing follows the (i) contacting,
wherein the method results in a reduction of a concentration of residual nucleic acid molecules (via the nuclease) in the sample to purify the EVs.
DHELLIN does not teach the nuclease wash buffer comprises a nuclease. However, LIU teaches mdck cell lines supporting viral growth to high titers and bioreactor process using the same (title), wherein the virus is treated with Benzonase or other a non-specific endonuclease either e.g. before the material is clarified, or at the same time as an affinity chromatography process, which may reduce processing steps (par. [0323]).
Therefore, before the effective filing date of the invention, it would have been obvious to one of ordinary skill in the art to modify the method of DHELLIN to wash the chromatography resin with a nuclease wash buffer comprising a nuclease in order to reduce step for enabling the fine separation of membrane vesicles from cell DNA and RNA as is known in the art. The references are combinable, because they are in the same technological environment of separations. See MPEP 2141 III (A) and (G).
Regarding claim 3, DHELLIN teaches the chromatography resin is e.g. an anion exchange (AEX) resin (C2/L40).
Regarding claim 7, DHELLIN teaches the nuclease is an endonuclease of e.g. benzonase (par. [0114]).
Regarding claim 17, DHELLIN teaches the nuclease wash buffer further comprises an anion of e.g. Cl- dissolved in BTP buffer.
Regarding claim 22, while DHELLIN teaches a RPMI buffer (C17/L30-31), LIU teaches a suitable loading buffer (e.g. a sucrose-phosphate buffer) comprising a salt concentration of 11mM (or 0.011M), which anticipates the claimed range of from about 0.01 M to about 2.0 M, wherein the salt of the loading buffer is KPO4 (potassium phosphate; par. [0329]). It is obvious to one having ordinary skill in the art to select a suitable loading buffer known in the art for the chromatography step.
Regarding claim 40, DHELLIN teaches the chromatography resin is contacted with a wash buffer that does not comprise a nuclease (BTP buffer; C17/L41-44).
Regarding claim 41, DHELLIN teaches the wash buffer comprises a salt at a concentration of 12mM (0.012 M), which anticipates the claimed range of e.g. at least about 0.01 M,
wherein the salt in the wash buffer is e.g. NaCl (BTP buffer; C17/L41-44).
Regarding claim 46, DHELLIN’s modified method teaches (iii) eluting the EVs from the chromatography resin by contacting the chromatography resin with an elution buffer (saline; C17/L44-46),
wherein (iii) occurs after (ii) contacting the chromatography resin with a nuclease wash buffer (nuclease wash buffer to wash the vesicles on the resin, LIU par. [0323], then elute the vesicles from the resin),
wherein the elution buffer comprises a salt concentration of 150mM-1M (DHELLIN C17/L44-46), which overlaps the claimed range of at least about 1.0 M to about 5.0 M and therefore establishes a case of prima facie obviousness. See MPEP 2144.05 I. It would have been obvious to one of ordinary skill in the art to select the instantly claimed range from the prior art range because prior art teaches the same utility over the selected range;
wherein the elution buffer has the result of releasing EVs from the chromatography resin (that’s the purpose of an elution buffer).
Regarding claim 51, DHELLIN teaches collecting an eluent after contacting the chromatography resin with the elution buffer (C14/L22-25).
Regarding claim 53, DHELLIN teaches the sample contacted with the chromatography resin comprises a starting concentration of the nucleic acid molecules (the sample has nucleic acid contaminants; see C10/L21-26; C12/L17-19), and
wherein the eluent comprises an eluted concentration of the nucleic acid molecules (as shown by peak analysis of the eluate),
wherein the eluted concentration of the nucleic acid molecules is less than that of the starting concentration of the nucleic acid molecules (materials are eluted with 25 column volumes and thus very dilute; C17/L44-46).
Differences in concentration […] will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration […] is critical (MPEP 2144.05.II.A. The concentration has not been established to provide any criticality or to provide any unexpected result/benefit over the prior art of record. It has been held that where the general conditions of a claim are disclosed in the prior art, discovering the optimum or workable ranges involves only routine skill in the art. In re Aller, 105 USPQ 233. Further, it has been held that discovering an optimum value of a result effective variable involves only routine skill in the art. In re Boesch, 617 F.2d 272, 205 USP 215 (CCPA 1980).+
Regarding claim 54, DHELLIN teaches subjecting the sample to an additional chromatography resin comprising e.g. an anion exchange chromatography (AEX) resin (“at least one anion exchange […] chromatography treatment of the sample”; abstract).
Regarding claim 60, DHELLIN teaches the sample is contacted with e.g. an AEX resin (C2/L40).
DHELLIN does not explicitly teach repeating the steps of contacting the sample with the chromatography resin; however, it has been held that it is common sense to one having ordinary skill in the art to repeat steps unless an unexpected result is established. Perfect Web Tech., Inc. v. InfoUSA, Inc., 587 F.3d 1324, 1328-29, 92 USPQ2d 1849, 1854 (Fed. Cir. 2009). See MPEP 2143.I.E.Example 9. In this case, repeating steps would be obvious to one having ordinary skill in the art in order to further improve purification of the liquid by subjecting the sample to the chromatography resin multiple times.
Regarding claim 132, DHELLIN is silent as to the concentration of EVs in the sample. However, differences in concentration […] will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration […] is critical (MPEP 2144.05.II.A. The concentration has not been established to provide any criticality or to provide any unexpected result/benefit over the prior art of record. It has been held that where the general conditions of a claim are disclosed in the prior art, discovering the optimum or workable ranges involves only routine skill in the art. In re Aller, 105 USPQ 233. Further, it has been held that discovering an optimum value of a result effective variable involves only routine skill in the art. In re Boesch, 617 F.2d 272, 205 USP 215 (CCPA 1980).
Claim(s) 30,33,111 are rejected under 35 U.S.C. 103 as being unpatentable over DHELLIN (US 6899863) in view of LIU (US 20080286850) and LANES (US 20140370514).
Regarding claim 30, LIU teaches the nuclease wash buffer comprises 50 units/mL (par. [0329]), which anticipates the claimed range of 1-100 units/mL. DHELLIN does not teach the nuclease wash buffer comprises SAN. However, LANES teaches endonucleases (title) and that the use of a salt active nuclease is convenient as salt can be added to limit DNA-protein interactions and remove DNA contaminations (par. [0141]).
Therefore, before the effective filing date of the invention, it would have been obvious to one of ordinary skill in the art to modify the method of DHELLIN to provide the nuclease wash buffer comprising SAN as taught by LANES in order to conveniently remove DNA contaminations. The references are combinable, because they are in the same technological environment of separations. See MPEP 2141 III (A) and (G).
Regarding claim 33, DHELLIN’s modified method teaches the nuclease wash buffer comprises 1-20mM (or 0.001-0.020 M; LANES par. [0035]), which overlaps the claimed range of about 0.01- 1.0 M of the cation and therefore establishes a case of prima facie obviousness. See MPEP 2144.05 I. It would have been obvious to one of ordinary skill in the art to select the instantly claimed range from the prior art range because prior art teaches the same utility over the selected range; and,
wherein the cation comprises Mg2+ (LANES par. [0035]); and,
DHELLIN’s modified method teaches the nuclease wash buffer is contacted with the chromatography resin 3 times (LIU par. [0329]).
Regarding claim 111, LANES teaches the eluent is contacted with the nuclease wash buffer by incubation for e.g. 15min., which anticipates the claimed range of at about 1 minute to about 14 days, and at or around 35-37°C (par. [0041]), which overlaps the claimed range of e.g. about 37ºC and therefore establishes a case of prima facie obviousness. See MPEP 2144.05 I. It would have been obvious to one of ordinary skill in the art to select the instantly claimed range from the prior art range because prior art teaches the same utility over the selected range.
Claim(s) 56 is rejected under 35 U.S.C. 103 as being unpatentable over DHELLIN (US 6899863) in view of LIU (US 20080286850), SMITH (US 20070078374), and JONES (US 12083448).
Regarding claim 56, DHELLIN does not teaches a CEX resin. However, SMITH teaches iontophoretic delivery of vesicle-encapsulated active agents (title) including an inner ion selective membrane, which may be an anion exchange membrane (par. [0048,0051]) and an outermost ion selective membrane, which may be a cation exchange membrane (par. [0048, 0053]). SMITH teaches that vesicles can be positively or negatively charged (par. [0022]) and that an anion exchange membrane and a cation exchange membrane may be used to capture the desired charged vesicles (par. [0073]).
Therefore, before the effective filing date of the invention, it would have been obvious to one of ordinary skill in the art to modify the method of DHELLIN to provide for a CEX resin after an AEX resin as taught by SMITH in order to capture the desired membrane vesicles. The references are combinable, because they are in the same technological environment of separations. See MPEP 2141 III (A) and (G).
DHELLIN does not teaches a MMC resin. However, JONES teaches purification and labeling of extracellular vesicles using a mixed mode resin composition (title) and that a mixed mode resin has several advantages including inter alia it is simple to use, fast, does not dilute the EV concentration and provides EVs with a high purity (C3/L24-32).
Therefore, before the effective filing date of the invention, it would have been obvious to one of ordinary skill in the art to modify the method of DHELLIN to provide for a MMC resin as taught by JONES in order to improve EV purity. The references are combinable, because they are in the same technological environment of separations. See MPEP 2141 III (A) and (G).
Regarding the arrangement of the resins (e.g. AEX, CEX, MMC order or AEX, MMC, CEX order), the arrangement is a simple rearrangement of parts. This design choice does not change the operation of the device and thus one having ordinary skill in the art would have found it obvious absent persuasive evidence that a new and unexpected result is produced (see MPEP 2144.04(VI)(C)).
Cited Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
ENDERLE (US 20150353920) discloses methods for isolating microvesicles (title) and for extracting nucleic acids from the microvesicles (abstract) via on-membrane lysis and release of the nucleic acids for further analysis (par. [0013]). Capture surfaces for vesicles may include a chromatography resin (par. [0191]), which are washed with a wash buffer comprising e.g. Na+ (par. [0522]) to remove any weakly bound plasma components. Furthermore, nucleic acid extraction enhancement agents including DNase may be added (par. [0232,0534]).
STOLL (US 20190284548) discloses automated and manual methods for isolation of extracellular vesicles and co-isolation of cell-free dna from biofluids (title) including contacting the biological sample with a solid capture surface (par. [0007]), which may be a chromatography bead or membrane (par. [0009]) that is washed with a buffer comprising e.g. Bis Tris Propane (par. [0137,0141]), eluting nucleic acids, adding a protein precipitation buffer including proteinase and a nuclease and extracting the nucleic acids. Furthermore, nucleic acid extraction enhancement agents including DNase may be added (par. [0169]).
CORSO et. al. 2017 “Reproducible and scalable purification of extracellular vesicles using combined bind-elute and size exclusion chromatography”.
Telephonic Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIAM A ROYCE whose telephone number is (571)270-0352. The examiner can normally be reached M-F ~08:00~15:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Benjamin Lebron can be reached at (571)272-0475. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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LIAM A. ROYCE
Primary Examiner
Art Unit 1777
/Liam Royce/ Primary Examiner, Art Unit 1777