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 .
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-17 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.
Claim recites “c) lysing of permeabilizing the at least one vesicle to release the core biomarker away and separate from the solid support while retaining contact between the solid support and both the entire vesicle membrane and the at least one membrane associated protein”. Emphasis added.
It is not clear how the solid support can be in contact with the entire vesicle membrane, if section “c)” is interpreted to mean that all parts of the vesicle membrane is in contact with the support. There is also no support in Applicant’s specification for this interpretation, which would be considered new matter that is not disclosed in the originally filed application.
However, given the disclosures in Applicant’s specification, for examination purposes, Examiner interprets section “c)” of claim 1 to mean that the vesicle, as a whole and unlysed, is in contact with the solid support, during the step of lysing. Clarification however is required.
The remainder of the claims are rejected for lack of clarity since they depend from claim 1.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-15 and 17 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as anticipated by US 20170102397 (hereinafter “Zhang”),
Regarding Applicant’s claim 1, discloses the limitations of Applicant’s claims as follows.
With respect to claim 1, Zhang discloses a method comprising;
providing a biological sample comprising at least one vesicle (exosomes) wherein the at least one vesicle comprises a vesicle membrane and at least one membrane associated biomarker (see abstract and paras. 0035-0036);
contacting a solid support comprising capture agents associated therewith (antibody-coated
superparamagnetic microbeads, para. 0035) with the biological sample under conditions wherein the capture agents selectively bind to the at least one vesicle, thereby capturing said at least one vesicle on the solid support (superparamagnetic microbeads, para. 0035);
lysing of permeabilizing the at least one vesicle to release the core biomarker away and separate from the solid support while retaining contact between the solid support and both the entire vesicle membrane and the at least one membrane associated protein
(see para. 0028 disclosing that “[p]roteins markers can be measured in enriched exosomes while captured on a solid phase or after eluted from the solid phase”, and that for a protein marker that is exposed on the surface of exosomes, it can be measured without lysis, and for a protein biomarker that is contained within the exosomes, it can be measured after lysis of the exosomes)
(and see para. 0047 disclosing that Alix, a common exosome marker, and L1CAM were enriched with anti-L1Cam capture; Examiner notes that L1CAM is equivalent to Applicant’s “at least one membrane associated protein”)
(and see para. 0036 disclosing that exosomes were lysed by incubating the beads in Triton X-100 plus protease inhibitor cocktail for Luminex measurements and other analyses, as an alternative to eluting the exosomes for imaging [Examiner notes that this disclosure is equivalent to Applicant’s limitation of lysing the vesicle to release the core biomarker from the solid support while retaining contact between the solid support and both the vesicle membrane and the at least one membrane associated protein, as recited in claim 1 and as described in Applicant’s specification); and
isolating vesicle core from the captured vesicles (para. 0044 disclosing separation).
The following is a further elaboration of subsection (c) above, in claim 1.
Examiner notes that subsection (c) of Applicant’s claim 1 requires that during the lysing, which releases at least one biomarker, there is contact between the vesicle and the solid support. This is shown in Zhang in paragraph 0036 which discloses that exosomes were lysed by incubating the beads in Triton X-100 plus protease inhibitor cocktail for Luminex measurements and other analyses, as an alternative to eluting the exosomes for imaging. Thus it is understood that the beads (i.e., solid support) remain in contact with the vesicle during lysing.
Examiner notes that paragraphs 0028 and 0036 of Zhang recites the following.
“Protein biomarkers can be measured in enriched exosomes while captured on a solid phase, or after eluted from the solid phase. For a protein biomarker that is exposed on the surface of exosomes, it can be measured without lysis of the exosomes. For a protein biomarker that is contained within the exosomes, it can be measured after lysis of the exosomes. Protein biomarkers can be measured by any method known to a person skilled in the art. Immunoassays such as ELISA, Luminex, and more recently Quanterix are preferred methods for measuring protein biomarkers.” Para. 0028 (emphasis added).
“Exosomes were eluted from the beads with 60 μL of a 1:1 mixture of 0.1% BSA/PBS (pH 7.4) and a fixing buffer (4% paraformaldehyde/5% glutaraldehyde) for electron microscopy imaging. Or exosomes were lysed by incubating the beads in 110 μL of 1% Triton X-100 plus 10% of a protease inhibitor cocktail (P2714, Sigma-Aldrich, St Louis, Mo., USA; prepared in 10 ml of H.sub.2O) in 0.1% BSA/PBS (pH 7.4) for 1 hour at room temperature with gentle shaking for Luminex measurements and other analyses.” Para. 0036 (emphasis added).
Thus, Examiner notes that paragraph 0036 discloses two options: eluting the exosomes from beads, or lysing exosomes [that are on the beads] by incubating the beads in a Triton X-100 plus a protease inhibitor cocktail.
Since paragraph 0036 discloses an alternative in which “exosomes were lysed by incubating the beads in 110 μL of 1% Triton X-100 plus 10% of a protease inhibitor cocktail, the lysing step is clearly performed while the exosomes are on the beads, which means that the lysing step is performed while the exosomes are retained in contact between the solid support and the entire vesicle membrane, meeting Applicant’s claimed limitations, [interpreted to mean that the entire vesicle is retained on the solid support].
Subsection (c) also requires that, in addition to the above, there remains contact between the vesicle membrane and the at least one membrane associated protein, and the solid support. As indicated above, paragraph 0047 discloses that Alix, a common exosome marker, and L1CAM were enriched with anti-L1Cam capture. Examiner notes that L1CAM is equivalent to Applicant’s “at least one membrane associated biomarker”.
As mentioned earlier, it is understood that the exosome remains in contact with the solid phase during lysis. This is shown in paragraph 0036 which discloses that exosomes were lysed by incubating the beads in Triton X-100 plus protease inhibitor cocktail for Luminex measurements and other analyses, as an alternative to eluting the exosomes for imaging. Thus it is understood that the beads (i.e., solid support) remain in contact with the vesicle membrane and the at least one membrane associated protein, as recited in claim 1 and in the same manner as described in Applicant’s specification
Examiner notes that Triton-X 100, disclosed by Zhang, is also a lytic agent that Applicant discloses can be used in the present invention. See para. 00111.
Paragraph 00111 recites the following.
“In some embodiments, biomarkers inside exosomes are analyzed in addition to the inner membrane- bound biomarkers. In certain embodiments, the present invention relates to compositions for lysing or permeabilizing exosomes in biological samples obtained from a subject. Lytic agents useful in the methods of the present invention include: RIPA buffer; Tris-HCl (pH 6.8); glycerol; SDS; 2-mercaptoethanol; Triton-X 100; M-PER Reagent; T-PER solution; TRISOL, and CHAPS. Lytic agents may be incubated with biological samples to disrupt the membrane of the exosomes of the present invention and release exosome cargo (e.g., exosomal proteins) for subsequent analysis.” Para. 00111 (emphasis added).
Thus the same lytic agent disclosed by Applicant is also disclosed by Zhang for lysing the exosomes. Applicant’s invention is not distinguished from the teachings of Zhang.
As to claim 2, see Zhang in paragraph 0035 disclosing that exosomes were isolated from plasma.
As to claim 3, see Zhang in paragraph 0035 disclosing exosomes.
As to claims 4 and 20, see Zhang in paragraph 0035 disclosing that the exosomes were isolated from human plasma, which is equivalent to vascular-derived exosomes.
As to claim 5, see Zhang in paragraph 0035 which discloses use of superparamagnetic microbeads [which are magnetic beads].
As to claim 6, see Zhang in paragraph 0035 which discloses use of superparamagnetic microbeads [which inherently have metal.]
As to claim 7, see Zhang in paragraph 0035 disclosing use of antibodies to capture the exosomes.
As to claims 8-12, see Zhang in paragraph 0025 disclosing phosphorylated alpha-syn [i.e., phosphorylated alpha-synuclein, a phosphorylated protein and disease related protein] as biomarkers for PD [Parkinson’s Disease], and phosphorylated tau [a phosphorylated protein and disease related protein] in CNS-derived exosomes as a biomarker of AD. See also paragraph 0049 and 0053 disclosing detection of alpha-syn signal from exosomes to aid in PD diagnosis [alpha-syn referring to alpha-syncuclein, and PD referring to Parkinson’s Disease, see para. 0003].
Also, as to claim 9, the biomarkers in Zhang are cystolic biomarkers from the vesicle core [see para. 0025 disclosing detection of biomarkers in exosomes, and 0036 disclosing lysing exosomes for analyses].
As to claim 13, see Zhang in paragraphs 0037-0038.
As to claim 14, see Zhang in paragraphs 0044 and 0048 disclosing immunoassays and Western blot.
As to claim 15, see Zhang in paragraph 0049 and 0053 disclosing detection of alpha-syn signal from exosomes to aid in PD diagnosis [alphasyn referring to alpha-syncuclein, and PD referring to Parkinson’s Disease, see para. 0003]. See also general disclosures at paragraph 0025.
As to claim 17, see Zhang in abstract and paragraph 0017 regarding treatment.
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.
Claim(s) 16 is/are rejected under 35 U.S.C. 103 as obvious over US 20170102397 (hereinafter “Zhang”) in view of CA 2743211 (hereinafter “Kuslich”).
Zhang has been discussed above.
As to claim 16, Zhang does not disclose that the sample is obtained from a subject who has been
diagnosed or is suspected of having lung cancer, prostate cancer, etc.
However Kuslich teaches the motivation to detect analyte in a biological sample obtained from a subject who has been diagnosed or is suspected of having lung cancer, for example.
More specifically Kuslich teaches that the phenotype detected can be a disease or condition such as listed in Table 1, which can be for example lung cancer, colon cancer, [among many listed]. Para. 0095.
Kuslich further teaches that the subject can have a pre-existing disease or condition, such as cancer. Alternatively, the subject may not have any known pre-existing condition. The subject may also be non-responsive to an existing or past treatment, such as a treatment for cancer. Para. 00103.
Kuslich further teaches that the sample obtained from the subject may be any bodily fluid. For example, the biological sample can be peripheral blood, sera, plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breast milk, broncheoalveolar lavage fluid, semen (including prostatic fluid), etc. Para. 00105.
Furthermore, Examiner advises that Kuslich teaches a motivation to analyze both a membrane-bound biomarker that remains on the exosome and a biomarker that is released from inside the same exosome, as discussed below.
More specifically, Kuslich discloses the following.
“A bio-signature of an exosome from a subject can be used to characterize a phenotype. A bio- signature can reflect the particular antigens or biomarkers that are present on an exosome. In addition, a bio-signature can also reflect one or more biomarkers that are carried in an exosome. Alternatively, a bio- signature can comprise a combination of one or more antigens or biomarkers that are present on an exosome with one or more biomarkers that are detected in the exosome. Para. 0277 (emphasis added). Examiner notes that paragraph 0277 thus teaches detection of biomarkers on the exosome as well as biomarkers on the same exosome.
“The exosome can be purified or concentrated prior to determining the bio-signature of the exosome. Alternatively, the bio-signature of the exosome can be directly assayed from a sample, without prior purification or concentration. An exosome can also be isolated prior to assaying. For example, a cell-of-origin specific exosome can be isolated and its bio-signature determined. The bio-signature is used to determine a diagnosis, prognosis, or theranosis of a disease or condition. Therefore, a bio- signature can also be used to determine treatment efficacy, stage of a disease or condition, or progression of a disease or condition. Furthermore, a bio-signature may be used to determine a physiological state, such as pregnancy.” Para. 0278 (emphasis added).
“Also disclosed herein are methods of conducting retrospective analysis on samples (e.g., serum and tissue biobanks) for the purpose of correlating qualitative and quantitative properties, such as exosome bio-signatures, with clinical outcomes in terms of disease state, disease stage, progression, prognosis; therapeutic efficacy or selection; or physiological conditions. Furthermore, methods and compositions disclosed herein are utilized for conducting prospective analysis on a sample (e.g., serum and/or tissue collected from individuals in a clinical trial) for the purpose of correlating qualitative and quantitative exosome bio-signatures with clinical outcomes in terms of disease state, disease stage, progression, prognosis; therapeutic efficacy or selection; or physiological conditions can also be performed. As used herein, exosome bio-signatures can be to cell-of-origin specific exosomes. Furthermore, bio-signatures can be determined based on an exosome surface marker profile and/or exosome contents (e.g., biomarkers)…” Para. 0313 (emphasis added).
“A binding agent can also be linked directly or indirectly to a solid surface or substrate. A solid surface or substrate can be any physically separable solid to which a binding agent can be directly or indirectly attached including, but not limited to, surfaces provided by microarrays and wells, particles such as beads, columns, optical fibers, wipes, glass and modified or functionalized glass, quartz, mica, diazotized membranes (paper or nylon), polyformaldehyde, cellulose, cellulose acetate, paper, ceramics,..” Para. 00130.
“Modifications or binding of molecules in solution or immobilized on an array may be detected using detection techniques known in the art. Examples of such techniques include immunological techniques such as competitive binding assays and sandwich assays; fluorescence detection using instruments such as confocal scanners, confocal microscopes, or CCD-based systems and techniques such as fluorescence, fluorescence polarization (FP), fluorescence resonant energy transfer (FRET), total internal reflection fluorescence (TIRF), fluorescence correlation spectroscopy (FCS); colorimetric/spectrometric techniques; surface plasmon resonance, by which changes in mass of materials adsorbed at surfaces may be measured; techniques using radioisotopes, including conventional radioisotope binding and scintillation proximity assays (SPA); mass spectroscopy…”
Para. 0694 (emphasis added).
“The amount of captured biomarkers on each individual bead can be measured by the second color fluorescence specific for the bound target. This allows multiplexed quantitation of multiple targets from a single sample within the same experiment. Sensitivity, reliability and accuracy are compared, or can be improved to standard microtiter ELISA procedures. An advantage of bead-based systems is the individual coupling of the capture biomolecule, or binding agent for an exosome, to distinct microspheres, which provides multiplexing. For example, as depicted in FIG. 64B, a combination of 5 different biomarkers to be detected (detected by antibodies to antigens such as CD63, CD9, CD81, B7H3, and EpCam) and 20 biomarkers for which to capture the exosome (using capture antibodies, such as antibodies to CD9, PSCA, TNFR, CD63, B7H3, MFG-E8, EpCam, Rab, CD81, STEAP, PCSA, PSMA, and 5T4) can result in 100 combinations to be detected. Thus, captured exosomes can be detected using detection agents, such as antibodies. The detection agents can be labeled directly or indirectly, such as described above.” Para. 00703 (emphasis added).
“The particles may be externally labeled, such as with a tag, or they may be intrinsically labeled. Each differentially labeled particle can be coupled to a capture agent, such as a binding agent, for an exosome, resulting in capture of an exosome. Biomarkers of the captured exosomes can then be detected by a plurality of binding agents. The binding agent can be directly labeled and thus, detected. Alternatively, the binding agent is labeled by a secondary agent. For example…For example, as depicted in FIG. 70, multiple detectors, i.e. detection of multiple biomarkers of a captured exosome, can increase the signal obtained, permitted increased sensitivity, specificity or both, and the use of smaller amounts of samples.” Para. 0704 (emphasis added).
“ELISA based methods, so sandwich assay can also be used to detect biomarkers on an exosome. A binding agent or capture agent can be bound to a well, for example an antibody to an exosomal antigen. Biomarkers on the captured exosome can be detected based on the methods described herein.” Para. 00705 (emphasis added).
“ Binding agents can used to isolate exosomes by binding to exosomal components, as described above. The binding agents can be used to detect the exosomes, such as for detecting cell-of-origin specific exosomes. A binding agent or multiple binding agents can themselves form a binding agent profile that provides a bio-signature for an exosome. One or more binding agents can be selected from FIG. 2. For example, if an exosome population is detected or isolated using two, three or four binding agents in a differential detection or isolation of an exosome from a heterogeneous population of exosomes, the particular binding agent profile for the exosome population provides a bio-signature for the particular exosome population.” Para. 00732 (emphasis added).
“Also provided herein is an isolated exosome with a particular bio- signature. The isolated exosome can comprise one or more biomarkers or bio-signatures specific for specific cell type, or for characterizing a phenotype, such as described above. For example, the isolated exosome can comprise one or more biomarkers, such as CD63, EpCam, CD81, CD9, PCSA, PSMA, B7H3, TNFR, MFG-E8, Rab, STEAP, 5T4, or CD59. The isolated exosome can have the one or more biomarkers on its surface [or] within the exosome. The isolated exosome can also comprise one or more miRNAs, such as miR-9, miR- 629, miR-141, miR-671-3p, miR-491, miR-182, miR-125a-3p, miR-324-5p, miR-148B, or miR-222. An isolated exosome can comprise a biomarker such as CD66, and further comprise one or more biomarkers…” Para. 00812 (emphasis and correction of an obvious typographical error added). Examiner notes that paragraph 00812 discloses that an isolated exosome has multiple biomarkers on the surface of the exosome as well as biomarkers inside the exosome (miRNAs).
“…Exosomes may then be isolated using antigens or cellular binding partners that are specific to such cell-of-origin specific exosomes using methods as previously described. Biomarkers and bio-signatures can then be isolated and characterized by methods known to those skilled in the art.
Para. 00851 (emphasis added).
Thus, Kuslich teaches an isolated exosome can multiple biomarkers on its surface and within the exosome (paras. 0277 and 0704 and 00812). Thus Kuslich teaches a motivation to analyze both a membrane-bound biomarker that remains on the exosome and a biomarker that is released from inside the same exosome, from a sample that is obtained from a subject who has been diagnosed or is suspected of having, for example, lung cancer. It would have been obvious to one skilled in the art to combine the teachings of Zhang and Kuslich to detect biomarkers in exosomes of patients suspected of cancer, such as lung cancer, for diagnosis of the disease, as suggested by Kuslich, or to detected biomarkers in exosomes of patients known to have cancer and are undergoing treatment for cancer, as suggested by Kuslich, to monitor the disease during treatment.
Response to Arguments
Applicant's arguments have been fully considered but they are not persuasive.
Applicant has amended claim 1 to recite “c) lysing or permeabilizing the at least one vesicle to release the core biomarker away and separate from the solid support while retaining contact between the solid support and both the entire vesicle membrane and the at least one membrane associated protein”.
Applicant argues that provision “c” allows for the analysis of the membrane-associated biomarkers bound to the solid matrix surface separately from the core biomarker, and provision “d” allows for the assessment of the vesicle “core” biomarker material with minimal to no membrane-associated marker contamination. Applicant asserts that this claimed method allows for both vesicle membrane and core biomarker analysis to happen independently of one another, and that this feature is not found or appreciated in the Zhang reference.
Applicant further asserts that the Zhang publication is limited to L1-cam (CD171) expressing exosomes. Applicant also asserts that Zhang either captures L1-cam exosomes for analysis and releases them for electron microscopy or may lyse the exosomes on the magnetic beads with Triton X 100 (paras. 0035 and 0036) for analysis of the lysate and Triton X solubilized membrane associated markers.
Applicant states that Examiner cites paragraph 0036 to support that Zhang reads on [provision “c”].
Applicant argues that in paragraph 0036, there are two options: 1) that exosomes are removed (eluted” from the beads as a whole, wherein the exosome is separated from the bead but kept in tact, and 2) the exosome is lysed or broken apparat and given the description, the lysed exosome and its components are then separated from the beads and everything becomes a part of the solution. Applicant argues that there is not a situation where Zhang lyses the exosomes, separates the core biomarkers from the exosome, and leaves the exosome attached to the bead.
Examiner notes that paragraphs 0028 and 0036 of Zhang recites the following.
“Protein biomarkers can be measured in enriched exosomes while captured on a solid phase, or after eluted from the solid phase. For a protein biomarker that is exposed on the surface of exosomes, it can be measured without lysis of the exosomes. For a protein biomarker that is contained within the exosomes, it can be measured after lysis of the exosomes. Protein biomarkers can be measured by any method known to a person skilled in the art. Immunoassays such as ELISA, Luminex, and more recently Quanterix are preferred methods for measuring protein biomarkers.” Para. 0028 (emphasis added).
“Exosomes were eluted from the beads with 60 μL of a 1:1 mixture of 0.1% BSA/PBS (pH 7.4) and a fixing buffer (4% paraformaldehyde/5% glutaraldehyde) for electron microscopy imaging. Or exosomes were lysed by incubating the beads in 110 μL of 1% Triton X-100 plus 10% of a protease inhibitor cocktail (P2714, Sigma-Aldrich, St Louis, Mo., USA; prepared in 10 ml of H.sub.2O) in 0.1% BSA/PBS (pH 7.4) for 1 hour at room temperature with gentle shaking for Luminex measurements and other analyses.” Para. 0036 (emphasis added).
Thus, Examiner notes that paragraph 0036 discloses two options: eluting the exosomes from beads, or lysing exosomes [that are on the beads] by incubating the beads in a Triton X-100 plus a protease inhibitor cocktail.
Since paragraph 0036 discloses an alternative in which “exosomes were lysed by incubating the beads in 110 μL of 1% Triton X-100 plus 10% of a protease inhibitor cocktail, the lysing step is clearly performed while the exosomes are on the beads, which means that the lysing step is performed while the exosomes are retained in contact between the solid support and the entire vesicle membrane, meeting Applicant’s claimed limitations, [interpreted to mean that the entire vesicle is retained on the solid support].
Examiner does not find any support for Applicant’s assertion that the lysed exosome and its components are then separate from the beads and everything becomes part of the solution.
Examiner notes that Triton-X 100, disclosed by Zhang, is also a lytic agent that Applicant discloses can be used in the present invention. See para. 00111.
Paragraph 00111 recites the following.
“In some embodiments, biomarkers inside exosomes are analyzed in addition to the inner membrane- bound biomarkers. In certain embodiments, the present invention relates to compositions for lysing or permeabilizing exosomes in biological samples obtained from a subject. Lytic agents useful in the methods of the present invention include: RIPA buffer; Tris-HCl (pH 6.8); glycerol; SDS; 2-mercaptoethanol; Triton-X 100; M-PER Reagent; T-PER solution; TRISOL, and CHAPS. Lytic agents may be incubated with biological samples to disrupt the membrane of the exosomes of the present invention and release exosome cargo (e.g., exosomal proteins) for subsequent analysis.” Para. 00111 (emphasis added).
Thus the same lytic agent disclosed by Applicant is also disclosed by Zhang for lysing the exosomes. Applicant’s invention is not distinguished from the teachings of Zhang for the reasons set forth above.
Conclusion
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/Ann Montgomery/ Primary Examiner, Art Unit 1678