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 .
Claims Status
Claims 140, 197, 240, & 242-255 filed on 11/06/2025 are pending. Claims 140, 197, 240, & 242-255 are currently under examination directed to the elected species MUC16 (see response dated 07/02/2025). The cancellation of claims 239 & 241 in the reply files 11/06/2025 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 112
Claims 140, 197, 240, & 242-255 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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.
Regarding claims 140, 197, & 254, claims 140, 197, & 254 have been amended to recite “a single-stranded oligonucleotide, wherein the single stranded oligonucleotides of the at least two probes are capable of hybridizing to each other when the probes are bound to the same EV” (see claim 140), “a single-stranded oligonucleotide, wherein the single-stranded oligonucleotides of the at least two probes are hybridized to each other” (see claim 197), and “wherein the single-stranded oligonucleotides of the at least three probes are capable of hybridizing to each other when the probes are bound to the same extracellular vesicle” (see claim 254). The specification of the instant application has been thoroughly reviewed but support for this newly added limitation was not found. While there is no in haec verba requirement, newly added claims or claim limitations must be supported in the specification through express, implicit, or inherent disclosure. In the instant situation, this limitation of “a single stranded oligonucleotide … capable of hybridizing to each other” is not expressly recited in the specification of the instant application. Additionally, there does not appear to be implicit or inherent support for this limitation of a single-stranded oligonucleotide because the specification of the instant application teaches “the oligonucleotide domain comprising a double-stranded portion and a single-stranded overhang extended from one end of the oligonucleotide domain” (paragraphs [62] & [68] of instant specification). Since it is not clear how the newly added limitations are implicitly or inherently disclosed, the claims are rejected under 35 USC 112(a). In response, applicant may cancel the new matter, or provide explanations as to where the limitations find express, implicit, or inherent support.
Claims 240 & 242-246 are rejected due to their dependence on claim 197 and claims 247-253 & 255 are rejected due to their dependence on claim 140.
Response to Arguments
The response traverses the rejection. The response asserts that the specification provides adequate written description for the claimed subject matter as the specification expressly describes single-stranded oligonucleotides in multiple locations. Specifically, the response asserts that paragraph [0447] describes detection probes comprising “a target binding moiety” and “an oligonucleotide domain”, that paragraphs [0456]-[0479] provide oligonucleotide sequence used in the examples including strands that are presented as individual single-stranded oligonucleotides and not as pre-formed duplexes and that each strand is synthesized with complementary regions that allow them to hybridize when brought in proximity by binding to the same target entity. Further, the response asserts that paragraph [0452] describes a mechanism where “each antibody is conjugated with one of the two double-stranded DNA templates” and when “the antibodies bind their target epitopes, the sticky ends are then ligated together by T7 ligase” indicating language that describes two separate antibody-DNA conjugates that come together when bound to proximate epitopes and the use of “sticky ends” that can be “ligated together” necessarily implies single-stranded complementary overhangs that hybridize before ligation. Further, the response asserts that paragraphs [0491]-[0494] describes a workflow that separate molecules bind to EVs and then undergo ligation, a process that requires the oligonucleotides to first hybridize via their single-stranded complementary regions. These arguments have been thoroughly reviewed but were not found persuasive. First, paragraph [0447] further describes that the “oligonucleotide domain” comprises a double-stranded portion and a single stranded overhang and not itself as a single-stranded oligonucleotide. Further, the use of “sticky ends” that can be ligated together further implies single-stranded complementary overhangs wherein the probe comprises a doubles-stranded portion and a single-stranded portion and not just a single-stranded portion. Finally, Figure 17 of the instant application further depicts probes that comprise both a double-stranded portion and a single-stranded portion (a single-stranded overhang) and not just a single-stranded oligonucleotide probe.
The response also asserts that, regarding paragraphs [0062] & [0068], stating “the oligonucleotide domain comprising a double-stranded portion and a single-stranded overhang portion…wherein the single-stranded overhang portions of the detection probes are hybridized to each other” and that when two single-stranded oligonucleotides with complementary regions hybridize, they form a double-stranded portion and a single-stranded overhang portion and this is precisely what occurs in proximity ligation assays where two separate single-stranded oligonucleotide-conjugated probes bind nearby targets, bringing their oligonucleotides in proximity, whereupon complementary regions hybridize to form the double-stranded portion with the single-stranded overhangs that can be ligated. Further, the response asserts that the specification describes both pre-hybridization (individual single-stranded oligonucleotides) and post-hybridization state (double-stranded complex) and this progression is exactly what the claims recite “single-stranded oligonucleotides…capable of hybridizing to each other when the probes are bound to the same EV”. These arguments have been thoroughly reviewed but were not found persuasive as the probe is recited to comprise a double-stranded portion and a single-stranded portion (a single-stranded overhang) and not just a single-stranded portion to form a single-stranded oligonucleotide probe.
The response also asserts that the limitation is also implicitly supported by proximity ligation methodology disclosed throughout the specification with references to “ligation” (paragraphs 62, 68, 493, 494, 540), “proximity” detection (paragraph 540), and the use of “sticky ends” (paragraph 540) and that one of ordinary skill would understand that the assays employ single-stranded oligonucleotide probes that hybridize upon proximity binding. Further the response asserts that the specification provides actual oligonucleotide sequences as separate single-stranded molecules, describes conjugating these oligonucleotides to binding moieties, details assay conditions where these probes bind to EVs and then undergo ligation, explains the mechanism where probes bind followed by oligonucleotide hybridization and ligation, and provides working examples of this methos and therefore reasonably conveys possession of probes comprising single-stranded oligonucleotides capable of hybridizing to each other when bound to the same EV. These arguments have been thoroughly reviewed but were not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Claim Rejections - 35 USC § 103
Claim(s) 140, 197, 240, 242-253 & 255 is/are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler (U.S. Patent Application Publication US 2016/0069889), as cited on the IDS dated 01/05/2024, in view of Zhang (Zhang et al.; Analyst, Vol. 145, pages 3557-3563, March 17th, 2020).
Regarding amended claim 140, Spetzler teaches a method of detecting a presence or level of one or more microvesicle in a biological sample by contacting the biological sample with one or more aptamers in order to provide a diagnosis, prognosis, or theranosis of disease, in which the disease can be cancer and comprises ovarian cancer, and the use of one or more reagents for the manufacture of a kit, a reagent, and/or a composition for carrying out the methods (a kit for the detection of ovarian cancer) (paragraph [0016] lines 1-10; paragraph [0021] lines 1-2& 45; paragraph [0026] lines 1-10; paragraph [0027] lines 1-12; paragraph [0083] lines 1-5 & 25-29). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamers target molecule present, including if a given microvesicles surface antigen is present on a cell-derived extracellular vesicle (a capture agent that binds a polypeptide on an extracellular vesicle) (paragraph [0075] lines 1-24). Spetzler also teaches that the aptamers are nucleic acid molecules (oligonucleotides) that comprise a binding agent (target binding moiety) that selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers (sets of probes) that are capable of selectively binding to distinguish one biological sample from another (at least two probes each comprising a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide) (paragraph [0033] lines 1-7; paragraph [0034] lines 1-16). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen is present on a cell-derived extracellular vesicle (polypeptide on the surface of the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker (at least one ovarian cancer biomarker) on the vesicle (at least one cancer biomarker (antibody) that is different from the polypeptide (antigen) on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Spetzler does not teach that the aptamers (oligonucleotides) comprises a single-stranded oligonucleotide that are capable of hybridizing to each other when the probes are bound to the same extracellular vesicle (EV).
Zhang teaches a method for biomolecular detection on EV using a proximity ligation assay strategy in which the set of aptamer probes comprise a single-stranded oligonucleotide that simultaneously recognizes (target binding moiety) the same target and when the set of aptamer probes binds to the target and come in close proximity they hybridize to each other to form duplex DNA (set of probes each comprising a target binding moiety and a single-stranded oligonucleotide that are capable of hybridizing to each other when the probes are bound to the same EV) (abstract lines 1-6; pg. 3557 paragraph bridging column 1 & 2 lines 1-23; pg. 3557 column 2 1st full paragraph lines 1-9; pg. 3558 column 1 1st full paragraph lines 1-10; pg. 3558 paragraph bridging column 1 & 2 lines 1-3 & 14-26; Scheme 1). In addition, Zhang teaches that the use of aptamers in a proximity ligation assay has advantages of easy production, low cost, chemical stability, high affinity, and high specificity and provides a powerful and convenient strategy for the detection of tumor-derived EVs and early cancer diagnosis (pg. 3558 column 1 1st full paragraph lines 1-5; pg. 3558 paragraph bridging column 1 & 2 lines 23-26).
Spetzler and Zhang are considered to be analogous to the claimed invention because they are all in the same field of detection of cancer biomarkers of EVs. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the kit with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate single-stranded aptamer probes that are capable of hybridizing to each other when bound to the same EV as taught in Zhang because Zhang teaches that doing so would provide a high affinity and specificity aptamer that can detect tumor-derived EVs and aid in early cancer diagnosis.
Regarding amended claim 197, Spetzler teaches a method of detecting a presence or level of one or more microvesicle in a biological sample by contacting the biological sample with one or more aptamers in order to provide a diagnosis, prognosis, or theranosis of disease, in which the disease can be cancer and comprises ovarian cancer, and the use of one or more reagents for the manufacture of a kit, a reagent, and/or a composition for carrying out the methods (a complex composition for the detection of ovarian cancer) (paragraph [0016] lines 1-10; paragraph [0021] lines 1-2& 45; paragraph [0026] lines 1-10; paragraph [0027] lines 1-12; paragraph [0083] lines 1-5 & 25-29). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamers target molecule present, including if a given microvesicles surface antigen is present on a cell-derived extracellular vesicle (a capture agent that binds a polypeptide on an extracellular vesicle) (paragraph [0075] lines 1-24). Spetzler also teaches that the aptamers are nucleic acid molecules (oligonucleotides) that comprise a binding agent (target binding moiety) that selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers (sets of probes) that are capable of selectively binding to distinguish one biological sample from another (at least two probes each comprising a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide) (paragraph [0033] lines 1-7; paragraph [0034] lines 1-16). In addition, Spetzler teaches the methods for generating an aptamer through the formation of nucleic acid-target complexes (complex comprising at least one polypeptide on the EV surface and at least two probes bound to the at least one ovarian cancer biomarker) (paragraph [0036] lines 1-3; paragraph [0041] lines 11-23). Finally, Spetzler teaches the molecules are immobilized to the substrate and the aptamers may be linked directly or indirectly linked to a solid surface or substrate to facilitate the detection of biomarkers (the EV is immobilized onto a solid substrate) (paragraph [0090] lines 1-6; paragraph [0091] lines 1-3). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen is present on a cell-derived extracellular vesicle (polypeptide on the surface of the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker (at least one ovarian cancer biomarker) on the vesicle (at least one cancer biomarker (antibody) that is different from the polypeptide (antigen) on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Spetzler does not teach that the aptamers (oligonucleotides) comprises a single-stranded oligonucleotide that are capable of hybridizing to each other.
Zhang teaches a method for biomolecular detection on EV using a proximity ligation assay strategy in which the set of aptamer probes comprise a single-stranded oligonucleotide that simultaneously recognizes (target binding moiety) the same target and when the set of aptamer probes binds to the target and come in close proximity they hybridize to each other to form duplex DNA (set of probes each comprising a target binding moiety and a single-stranded oligonucleotide that are capable of hybridizing to each other when the probes are bound to the same EV) (abstract lines 1-6; pg. 3557 paragraph bridging column 1 & 2 lines 1-23; pg. 3557 column 2 1st full paragraph lines 1-9; pg. 3558 column 1 1st full paragraph lines 1-10; pg. 3558 paragraph bridging column 1 & 2 lines 1-3 & 14-26; Scheme 1). In addition, Zhang teaches that the use of aptamers in a proximity ligation assay has advantages of easy production, low cost, chemical stability, high affinity, and high specificity and provides a powerful and convenient strategy for the detection of tumor-derived EVs and early cancer diagnosis (pg. 3558 column 1 1st full paragraph lines 1-5; pg. 3558 paragraph bridging column 1 & 2 lines 23-26).
Spetzler and Zhang are considered to be analogous to the claimed invention because they are all in the same field of detection of cancer biomarkers of EVs. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the complex composition with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate single-stranded aptamer probes that are capable of hybridizing to each other as taught in Zhang because Zhang teaches that doing so would provide a high affinity and specificity aptamer that can detect tumor-derived EVs and aid in early cancer diagnosis.
Regarding claim 240, Zhang teaches that set of aptamer probes comprise a single-stranded oligonucleotide that simultaneously recognizes (target binding moiety) the same target (the at least two probes is each directed to the same ovarian cancer biomarker (pg. 3557 column 2 1st full paragraph lines 1-9; pg. 3558 column 1 1st full paragraph lines 1-10; pg. 3558 paragraph bridging column 1 & 2 lines 1-3 & 14-26).
Regarding claim 242, Spetzler teaches that the aptamers may be linked directly or indirectly linked to a solid surface or substrate in which the solid surface can be a magnetic bead (paragraph [0091] lines 1-3 & 6-12).
Regarding claim 243, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen in present on a cell-derived extracellular vesicle and that the binding agent of the aptamer can include an antibody for a biomarker on the vesicle (the target-capture moiety is or comprises an antibody agent) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 10-23; paragraph [0077] lines 1-5).
Regarding claim 244, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 245, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 246, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles ad that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the target binding moiety are directed to MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 247, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen in present on a cell-derived extracellular vesicle (polypeptide on the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker on the vesicle (surface protein that is different from the polypeptide on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Regarding claim 248, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 249, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 250, Zhang teaches that set of aptamer probes comprise a single-stranded oligonucleotide that simultaneously recognizes (target binding moiety) the same target (the at least two probes is each directed to the same ovarian cancer biomarker (pg. 3557 column 2 1st full paragraph lines 1-9; pg. 3558 column 1 1st full paragraph lines 1-10; pg. 3558 paragraph bridging column 1 & 2 lines 1-3 & 14-26).
Regarding claim 251, Spetzler teaches the aptamers (oligonucleotides) selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers that are capable of selectively binding to distinguish one biological sample from another (the at least two probes is directed to a distinct ovarian cancer biomarker) (paragraph [0034] lines 1-16; paragraph [0075] lines 20-24; paragraph [0076] lines 1-3).
Regarding claim 252, Spetzler teaches that the biological sample that can be used for biomarker assessment includes the use of fresh frozen & formalin fixed paraffin embedded sample (further comprising a fixation agent) (paragraph [0149] lines 1-4 & 14-17; paragraph [0150] lines 1-8).
Regarding claim 253, Spetzler teaches that multiple sets of aptamers with binding agents may be used to distinguish biological sample from each other and that multiple different biomarkers can be analyzed in which the binding agent to the biomarker includes an aptamer that captures or isolates surface antigens in cell-derived extracellular vesicles (a second capture agent comprising a target-capture moiety to another biomarker and the biomarker is a surface protein (antigen) (paragraph [0034] lines 1-12; paragraph [0075] lines 1-24; paragraph [0076] lines 1-3).
Regarding claim 255, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles ad that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the target binding moiety are directed to MUC16) (paragraph [0166] lines 1-11; Table 3).
Claim(s) 254 is/are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler (U.S. Patent Application Publication US 2016/0069889), as cited on the IDS dated 01/05/2024, in view of Zhang (Zhang et al.; Analyst, Vol. 145, pages 3557-3563, March 17th, 2020) as applied to claims 140, 197, 239-253 & 255 above, and further in view of Schallmeiner (Schallmeiner et al.; Nature Methods, Vol. 4, pages 135-137, February 2007).
The teachings of Spetzler and Zhang with respect to claim 140 is discussed above.
Regarding claim 254, Spetzler teaches that multiple sets of aptamers with binding agents may be used to distinguish biological sample from each other and that multiple different biomarkers can be analyzed in which the binding agent to the biomarker includes an aptamer that captures or isolates surface antigens in cell-derived extracellular vesicles (a second capture agent and third capture agent comprising a target-capture moiety to another biomarker and the biomarker is a surface protein (antigen) (paragraph [0034] lines 1-12; paragraph [0075] lines 1-24; paragraph [0076] lines 1-3).
Zhang teaches set of aptamer probes comprise a single-stranded oligonucleotide that simultaneously recognizes (target binding moiety) the same target and when the set of aptamer probes binds to the target and come in close proximity they hybridize to each other to form duplex DNA ((abstract lines 1-6; pg. 3557 paragraph bridging column 1 & 2 lines 1-23; pg. 3557 column 2 1st full paragraph lines 1-9; pg. 3558 column 1 1st full paragraph lines 1-10; pg. 3558 paragraph bridging column 1 & 2 lines 1-3 & 14-26; Scheme 1).
Spetzler and Zhang does not teach wherein the at least two probes is at least three probes wherein the single-stranded oligonucleotides of the at least three probes are capable of hybridizing to each other.
Schallmeiner teaches a method for 3 proximity ligation assay in which sets of three single-stranded oligonucleotide probes are capable of hybridizing to each other when bound to a target molecules as these three probes are then brought in proximity to one another allowing for a complex to be formed between the three proximity probes and the target protein (abstract lines 1-9; pg. 135 paragraph bridging column 1 & 2 lines 1-9; Figure 1). In addition, Schallmeiner teaches that the use of three proximity oligonucleotide probes extends the sensitivity of detection and quantitative range as three target proteins can be evaluated (pg. 135 column 1 2nd full paragraph lines 1-7).
Spetzler, Zhang, and Schallmeiner are considered to be analogous to the claimed invention because they are all in the same field of detection of target polypeptides. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the kit with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate at least three single-stranded aptamer probes that are capable of hybridizing to each other as taught in Schallmeiner because Schallmeiner teaches that doing so would extend the sensitivity of detection and quantitative range of biomarkers than can be evaluated.
Claim(s) 140, 197, 240, 242-253 & 255 is/are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler (U.S. Patent Application Publication US 2016/0069889), as cited on the IDS dated 01/05/2024, in view of Tang (Tang et al.; Chemical Communications, Vol. 52, pages 1482-1485, November 2015).
Regarding amended claim 140, Spetzler teaches a method of detecting a presence or level of one or more microvesicle in a biological sample by contacting the biological sample with one or more aptamers in order to provide a diagnosis, prognosis, or theranosis of disease, in which the disease can be cancer and comprises ovarian cancer, and the use of one or more reagents for the manufacture of a kit, a reagent, and/or a composition for carrying out the methods (a kit for the detection of ovarian cancer) (paragraph [0016] lines 1-10; paragraph [0021] lines 1-2& 45; paragraph [0026] lines 1-10; paragraph [0027] lines 1-12; paragraph [0083] lines 1-5 & 25-29). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamers target molecule present, including if a given microvesicles surface antigen is present on a cell-derived extracellular vesicle (a capture agent that binds a polypeptide on an extracellular vesicle) (paragraph [0075] lines 1-24). Spetzler also teaches that the aptamers are nucleic acid molecules (oligonucleotides) that comprise a binding agent (target binding moiety) that selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers (sets of probes) that are capable of selectively binding to distinguish one biological sample from another (at least two probes each comprising a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide) (paragraph [0033] lines 1-7; paragraph [0034] lines 1-16). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen is present on a cell-derived extracellular vesicle (polypeptide on the surface of the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker (at least one ovarian cancer biomarker) on the vesicle (at least one cancer biomarker (antibody) that is different from the polypeptide (antigen) on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Spetzler does not teach that the aptamers (oligonucleotides) comprises a single-stranded oligonucleotide that are capable of hybridizing to each other when the probes are bound to the same extracellular vesicle (EV).
Tang teaches a method for the detection of a tumor specific biomarker through the use of split aptamers which are a set of two single stranded aptamers (oligonucleotides) which are non-functional until in the presence of the target cell in which the two independent and nonfunctional aptamers can be induced by the cell surface proteins to bind (hybridize) to one another (set of aptamer probes comprising a target binding moiety and a single-stranded oligonucleotide that are capable of hybridizing to each other) (pg. 1482 column 1 1st full paragraph lines 1-13; pg. 1482 column 2 1st full paragraph lines 1-14; pg. 1482-1483 paragraph bridging pg. 1482 & pg. 1483 lines 1-6; pg. 1483-1484 paragraph bridging pg. 1483 & pg. 1484 lines 1-8 & 20-24; Figure 3). In addition, Tang teaches the use of split aptamers in close proximity to each other once bound to the target provided similar target binding, less nonspecific adsorption, and additional thermosensitivity for detection of tumor cells (pg. 1485 column 1 1st full paragraph lines 1-9).
Spetzler and Tang are considered to be analogous to the claimed invention because they are all in the same field of detection of cancer biomarkers. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the kit with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate single-stranded aptamer probes that are capable of hybridizing to each other as taught in Tang because Tang teaches that doing so would provide less nonspecific adsorption and additional thermosensitivity for detecting cell surface proteins of tumor cells.
Regarding amended claim 197, Spetzler teaches a method of detecting a presence or level of one or more microvesicle in a biological sample by contacting the biological sample with one or more aptamers in order to provide a diagnosis, prognosis, or theranosis of disease, in which the disease can be cancer and comprises ovarian cancer, and the use of one or more reagents for the manufacture of a kit, a reagent, and/or a composition for carrying out the methods (a complex composition for the detection of ovarian cancer) (paragraph [0016] lines 1-10; paragraph [0021] lines 1-2& 45; paragraph [0026] lines 1-10; paragraph [0027] lines 1-12; paragraph [0083] lines 1-5 & 25-29). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamers target molecule present, including if a given microvesicles surface antigen is present on a cell-derived extracellular vesicle (a capture agent that binds a polypeptide on an extracellular vesicle) (paragraph [0075] lines 1-24). Spetzler also teaches that the aptamers are nucleic acid molecules (oligonucleotides) that comprise a binding agent (target binding moiety) that selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers (sets of probes) that are capable of selectively binding to distinguish one biological sample from another (at least two probes each comprising a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide) (paragraph [0033] lines 1-7; paragraph [0034] lines 1-16). In addition, Spetzler teaches the methods for generating an aptamer through the formation of nucleic acid-target complexes (complex comprising at least one polypeptide on the EV surface and at least two probes bound to the at least one ovarian cancer biomarker) (paragraph [0036] lines 1-3; paragraph [0041] lines 11-23). Finally, Spetzler teaches the molecules are immobilized to the substrate and the aptamers may be linked directly or indirectly linked to a solid surface or substrate to facilitate the detection of biomarkers (the EV is immobilized onto a solid substrate) (paragraph [0090] lines 1-6; paragraph [0091] lines 1-3). In addition, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen is present on a cell-derived extracellular vesicle (polypeptide on the surface of the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker (at least one ovarian cancer biomarker) on the vesicle (at least one cancer biomarker (antibody) that is different from the polypeptide (antigen) on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Spetzler does not teach that the aptamers (oligonucleotides) comprises a single-stranded oligonucleotide that are capable of hybridizing to each other.
Tang teaches a method for the detection of a tumor specific biomarker through the use of split aptamers which are a set of two single stranded aptamers (oligonucleotides) which are non-functional until in the presence of the target cell in which the two independent and nonfunctional aptamers can be induced by the cell surface proteins to bind (hybridize) to one another (set of aptamer probes comprising a target binding moiety and a single-stranded oligonucleotide that are capable of hybridizing to each other) (pg. 1482 column 1 1st full paragraph lines 1-13; pg. 1482 column 2 1st full paragraph lines 1-14; pg. 1482-1483 paragraph bridging pg. 1482 & pg. 1483 lines 1-6; pg. 1483-1484 paragraph bridging pg. 1483 & pg. 1484 lines 1-8 & 20-24; Figure 3). In addition, Tang teaches the use of split aptamers in close proximity to each other once bound to the target provided similar target binding, less nonspecific adsorption, and additional thermosensitivity for detection of tumor cells (pg. 1485 column 1 1st full paragraph lines 1-9).
Spetzler and Tang are considered to be analogous to the claimed invention because they are all in the same field of detection of cancer biomarkers. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the complex composition with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate single-stranded aptamer probes that are capable of hybridizing to each other as taught in Tang because Tang teaches that doing so would provide less nonspecific adsorption and additional thermosensitivity for detecting cell surface proteins of tumor cells.
Regarding claim 240, Tang teaches that set of aptamer probes comprise a single-stranded oligonucleotide that recognize (target binding moiety) and bind to the same target (the at least two probes is each directed to the same ovarian cancer biomarker (pg. 1482 column 1 1st full paragraph lines 1-13; pg. 1482 column 2 1st full paragraph lines 1-14; pg. 1482-1483 paragraph bridging pg. 1482 & pg. 1483 lines 1-6; pg. 1483-1484 paragraph bridging pg. 1483 & pg. 1484 lines 1-8 & 20-24; Figure 3).
Regarding claim 242, Spetzler teaches that the aptamers may be linked directly or indirectly linked to a solid surface or substrate in which the solid surface can be a magnetic bead (paragraph [0091] lines 1-3 & 6-12).
Regarding claim 243, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen in present on a cell-derived extracellular vesicle and that the binding agent of the aptamer can include an antibody for a biomarker on the vesicle (the target-capture moiety is or comprises an antibody agent) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 10-23; paragraph [0077] lines 1-5).
Regarding claim 244, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 245, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 246, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles ad that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the target binding moiety are directed to MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 247, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen in present on a cell-derived extracellular vesicle (polypeptide on the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker on the vesicle (surface protein that is different from the polypeptide on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
Regarding claim 248, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 249, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles and that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the polypeptide on the extracellular vesicle is or comprises MUC16) (paragraph [0166] lines 1-11; Table 3).
Regarding claim 250, Tang teaches that set of aptamer probes comprise a single-stranded oligonucleotide that recognize (target binding moiety) and bind to the same target (the at least two probes is each directed to the same ovarian cancer biomarker (pg. 1482 column 1 1st full paragraph lines 1-13; pg. 1482 column 2 1st full paragraph lines 1-14; pg. 1482-1483 paragraph bridging pg. 1482 & pg. 1483 lines 1-6; pg. 1483-1484 paragraph bridging pg. 1483 & pg. 1484 lines 1-8 & 20-24; Figure 3).
Regarding claim 251, Spetzler teaches the aptamers (oligonucleotides) selectively binds to or associates with biomarkers present in the biological sample and can comprise sets of aptamers that are capable of selectively binding to distinguish one biological sample from another (the at least two probes is directed to a distinct ovarian cancer biomarker) (paragraph [0034] lines 1-16; paragraph [0075] lines 20-24; paragraph [0076] lines 1-3).
Regarding claim 252, Spetzler teaches that the biological sample that can be used for biomarker assessment includes the use of fresh frozen & formalin fixed paraffin embedded sample (further comprising a fixation agent) (paragraph [0149] lines 1-4 & 14-17; paragraph [0150] lines 1-8).
Regarding claim 253, Spetzler teaches that multiple sets of aptamers with binding agents may be used to distinguish biological sample from each other and that multiple different biomarkers can be analyzed in which the binding agent to the biomarker includes an aptamer that captures or isolates surface antigens in cell-derived extracellular vesicles (a second capture agent comprising a target-capture moiety to another biomarker and the biomarker is a surface protein (antigen) (paragraph [0034] lines 1-12; paragraph [0075] lines 1-24; paragraph [0076] lines 1-3).
Regarding claim 255, Spetzler teaches that the biomarkers that can be assessed with the methods and compositions includes the biomarkers of Table 3 that are used for the capture and/or detection of vesicles ad that the biomarkers can be detected as vesicle surface antigens including the vesicle marker MUC16 (the target binding moiety are directed to MUC16) (paragraph [0166] lines 1-11; Table 3).
Claim(s) 254 is/are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler (U.S. Patent Application Publication US 2016/0069889), as cited on the IDS dated 01/05/2024, in view of Tang (Tang et al.; Chemical Communications, Vol. 52, pages 1482-1485, November 2015) as applied to claims 140, 197, 239-253 & 255 above, and further in view of Schallmeiner (Schallmeiner et al.; Nature Methods, Vol. 4, pages 135-137, February 2007).
The teachings of Spetzler and Tang with respect to claim 140 is discussed above.
Regarding claim 254, Spetzler teaches that multiple sets of aptamers with binding agents may be used to distinguish biological sample from each other and that multiple different biomarkers can be analyzed in which the binding agent to the biomarker includes an aptamer that captures or isolates surface antigens in cell-derived extracellular vesicles (a second capture agent and third capture agent comprising a target-capture moiety to another biomarker and the biomarker is a surface protein (antigen) (paragraph [0034] lines 1-12; paragraph [0075] lines 1-24; paragraph [0076] lines 1-3).
Tang teaches a method for the detection of a tumor specific biomarker through the use of split aptamers which are a set of two single stranded aptamers (oligonucleotides) which are non-functional until in the presence of the target cell in which the two independent and nonfunctional aptamers can be induced by the cell surface proteins to bind (hybridize) to one another (pg. 1482 column 1 1st full paragraph lines 1-13; pg. 1482 column 2 1st full paragraph lines 1-14; pg. 1482-1483 paragraph bridging pg. 1482 & pg. 1483 lines 1-6; pg. 1483-1484 paragraph bridging pg. 1483 & pg. 1484 lines 1-8 & 20-24; Figure 3).
Spetzler and Tang does not teach wherein the at least two probes is at least three probes wherein the single-stranded oligonucleotides of the at least three probes are capable of hybridizing to each other.
Schallmeiner teaches a method for 3 proximity ligation assay in which sets of three single-stranded oligonucleotide probes are capable of hybridizing to each other when bound to a target molecules as these three probes are then brought in proximity to one another allowing for a complex to be formed between the three proximity probes and the target protein (abstract lines 1-9; pg. 135 paragraph bridging column 1 & 2 lines 1-9; Figure 1). In addition, Schallmeiner teaches that the use of three proximity oligonucleotide probes extends the sensitivity of detection and quantitative range as three target proteins can be evaluated (pg. 135 column 1 2nd full paragraph lines 1-7).
Spetzler, Tang, and Schallmeiner are considered to be analogous to the claimed invention because they are all in the same field of detection of target polypeptides. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the kit with a capture agent that binds a polypeptide on an EV and a set of aptamers (probes) that comprise a target binding moiety for at least one ovarian cancer biomarker and an oligonucleotide in Spetzler to incorporate at least three single-stranded aptamer probes that are capable of hybridizing to each other as taught in Schallmeiner because Schallmeiner teaches that doing so would extend the sensitivity of detection and quantitative range of biomarkers than can be evaluated.
Response to Arguments
The response traverses the rejection. The response asserts that the claims are not obvious as the cited references report same-target binding systems where multiple probes or aptamer fragments bind to a single target molecule to achieve a high specificity and independent claims 140 and 197 require different-target detection to establish biomarker signatures on individual EVs. Further, the response asserts that independent claim 140 recites “at least two probes…each comprising…a target binding moiety for at least one ovarian cancer biomarker” where the probes detect different biomarkers on the same EV to establish a biomarker signature and that independent claim 197 similarly recites detection of multiple biomarkers on individual EVs and that this is a different approach from the same-target recognition systems reported by Zhang, Tang, and Schallmeiner. Further, the response asserts that the cited references would discourage a skilled artisan from modifying their systems for different-target detection because their specificity benefits come from requiring multiple binding events to the same target. Further, the response asserts that Spetzler reports separate biomarker analysis using aptamers to detect various biomarkers but reports analyzing them separately or as a panel and no detecting co-localized biomarkers on single EVs to establish a signature and that the Office Action has not articulated why a skilled artisan would take same-target binding systems and modify them against their teachings to detect different targets or to establish multi-biomarker signatures. These arguments have been thoroughly reviewed but were not found persuasive. First, the claims as currently amended do not exclude detection of the same ovarian cancer biomarker and independent claims 140 and 197, as currently amended, do not exclude detection of multiple biomarkers on individual EVs. For example, amended independent claims 140 and 197 recite “a target binding moiety for at least one cancer biomarker” and “at least one ovarian cancer biomarker”, respectively. Further, dependent claim 240 further limits amended claim 197 to specify that “the target binding moiety of the at least two probes is directed to the same ovarian cancer biomarker” and dependent claim 250 further limits amended claim 140 to specify that “the target binding moiety of the at least two probes is each directed to the same ovarian cancer biomarkers”, therefore comprising detection of the same ovarian cancer biomarker. Second, regarding the amendments to claims 140 & 197, Spetzler teaches that the aptamers are used to capture or isolate a component present in a biological sample that has the aptamer’s target molecule present, including if a given microvesicle surface antigen is present on a cell-derived extracellular vesicle (polypeptide on the surface of the extracellular vesicle) and that the binding agent of the aptamer can include an antibody for a biomarker (at least one ovarian cancer biomarker) on the vesicle (at least one cancer biomarker (antibody) that is different from the polypeptide (antigen) on the extracellular vesicle surface) (paragraph [0034] lines 1-7; paragraph [0075] lines 1-24; paragraph [0076] lines 18-21; paragraph [0077] lines 1-5).
The response also asserts that, regarding claim 254, that Schallmeiner reports using three oligonucleotides, including a padlock DNA probe, to ligate into a circle, followed by rolling circle amplification (RCA) for detection and that this is a different mechanism from the instant claims. Specifically, the response asserts that the instant claims recite single-stranded oligonucleotides that hybridize to each other and the specification reports linear ligation followed by PCR amplification, not RCA. Further, the response asserts that there is no requirement for three oligonucleotides, and no padlock probe or circular DNA in the claimed invention. These arguments have been thoroughly reviewed but were not found persuasive. First, in response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., linear ligation followed by PCR amplification and not RCA) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Second, claim 254 as currently amended, recites “wherein the at least two probes is at least three probes…and wherein the single-stranded oligonucleotides of the at least three probes are capable of hybridizing to each other when the probes are bound to the same extracellular vesicle” therefore reciting the requirement for three oligonucleotides in the claimed invention.
Finally, the response asserts that independent claims 140 and 197 are not obvious over the cited combinations and because the independent claims are not obvious, the dependent claims are likewise not obvious. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 140, 197, 240, & 242-255 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682