DETAILED ACTION
Applicant’s amendment submitted 8/12/2025 is acknowledged. Claims 1, 4-6, 9, 11, 15-17, 19-21, and 54-57 are currently amended. Claims 7, 16, and 18 have been canceled. Claims 1, 3-6, 9, 11-13, and 54-57 remain withdrawn pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention. Claims 1, 3-6, 9, 11-13, 15, 17, 19-22, and 54-57 remain pending in the instant application.
Claims 15, 17, and 19-22 are the subject of this Office Action.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
The instant application is a U.S. National Stage of PCT/US2020/036702, filed on 6/8/2020, and claims Domestic Benefit to U.S. Provisional Application No. 62/858,970, filed 6/7/2019.
Response to Amendment
Applicant’s amendment to the Specification overcomes each and every objection previously set forth in the Non-Final Rejection mailed on 2/13/2025.
Applicant’s amendment to claims 15, 17, and 19-22 to remove the recitation of “functional fragment or variant thereof” and cancelation of claim 16 renders moot the 35 U.S.C. § 112(a) rejection previously set forth in the Non-Final Rejection mailed on 2/13/2025. Accordingly, the rejection is withdrawn.
Applicant’s amendment to claims 17, 19, and 21 and cancelation of claim 16 has overcome the 35 U.S.C. § 112(b) rejections previously set forth in the Non-Final Rejection mailed on 2/13/2025.
Claim Objections
Claim 15 and 17 are objected to because of the following informalities:
Claim 15 recites “a biologically significant quantity of in a sample from the subject” in lines 7-8. Claim 15 appears to be missing the subject noun “TPP-1.”
Claim 17 recites “ and production of the fragment of the substrate of yields a fluorescent signal,” which is ungrammatical.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
New Rejection Necessitated by Amendment: Claims 15, 17 and 19-22 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for diagnosing a subject with a mucinous cyst of the pancreas by detecting a biologically significant quantity of gastricsin, cathepsin E, and/or tripeptidyl-peptidase 1 (TPP-1) in a cystic sample, does not reasonably provide enablement for diagnosing a subject with a mucinous cyst characterized by high-grade dysplasia or invasive cancer by detecting the presence or absence of TTP-1 in any other subject sample. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
In making a determination that a disclosure does not satisfy the enablement requirement, the factors that may be considered include: (A) the breadth of the claims, (B) the nature of the invention, (C) the state of the prior art, (D) the level of one of ordinary skill, (E) the level of predictability in the art, (F) the amount of direction provided by the inventor, (G) the existence of working examples, and (H) the quantity of experimentation needed to make or use the invention based on the content of the disclosure. While it is not essential that every factor be examined in detail, those factors deemed most relevant should be considered.
Nature of the invention. The invention concerns diagnosing a subject a with mucinous cyst of the pancreas characterized by high-grade dysplasia or invasive cancer by exposing a sample to an enzymatically effective amount of a substrate specific to TPP-1 for a time period sufficient to catalyze a reaction between the TPP-1 and the substrate to produce a fragment of the substrate; and detecting an amount of the fragment of the substrate and correlating the amount to TPP-1 presence, absence, or a biologically significant quantity in a sample from the subject.
Breadth of the claims. A sample is recited at a high level of generality. Claim 22 limits the sample to cystic fluid. A substrate specific to TPP-1 is recited at a high level of generality.
State of the prior art and predictability of the art. The state of the art with regards to diagnosing mucinous cysts of the pancreas characterized by high-grade dysplasia or invasive cancer by performing the claimed method was highly unpredictable at the time of the invention. The prior art teaches detection techniques in cystic samples with respect to diagnostic protocols for mucinous cysts of the pancreas characterized by high dysplasia or invasive cancer. The state of the art at the time of the invention did not adequately describe methods for detecting high grade dysplasia.
Hata et al. (Clin. Cancer Res., 2017, Vol. 23(14), p.3935-3944; of record in IDS filed 9/23/2022) teaches methods to predict the grade of dysplasia of pancreatic cysts. Hata teaches analyzing the methylation of select DNA genes to evaluate their accuracy at predicting the grade of dysplasia of pancreatic cysts (see Abstract). Hata teaches a number of different neoplasms with a wide spectrum of malignant potential can produce cysts in the pancreas (see p.2, 1st passage). Thus, accurately classifying cyst types is paramount for appropriate patient management. Hata teaches that intraductal papillary mucinous neoplasms (IPMNs) have a wide spectrum of malignant potential (see p.2, 1st passage). Hata teaches that mucinous cystic neoplasms (MCNs) arise in the pancreas body and tail of middle-aged women and are often resected because of their malignant potential. Hata teaches that serous cystic neoplasms (SCNs) have extremely low malignant potential and most asymptomatic SCNs can be safely clinically tracked. Hata teaches solid-pseudopapillary neoplasms (SPNs) have low malignant potential but require resection. Hata further teaches that pancreatic cysts are currently evaluated using pancreatic imaging and any associated clinical features (see p.2, 1st passage). The recent clinical guidelines, referred to as modified Sendai or Tanaka guidelines, used suggest that when an IMPN is diagnosed, only those suspected to have high-grade dysplasia or an associated invasive cancer need resection; while IMPNs having low- to intermediate-grade dysplasia are managed by surveillance (see p.2, 1st passage). These guidelines apply well to incidentally-detected pancreatic cysts and may not apply well to patients with predetermined susceptibility to pancreatic cancer due to family history or genetic predisposition (see p.2, 1st passage). Hata further teaches that pancreatic imaging techniques are not optimal for predicting malignant potential of pancreatic cysts, and that while cysts fluid cytology is highly specific, cytology has suboptimal sensitivity for identifying the presence of carcinoma (see p.2, last passage). Cyst fluid carcinoembryonic antigen (CEA) levels also exhibit suboptimal diagnostic accuracy. DNA mutations can be highly specific for the type of cyst but are not useful for assessing the grade of dysplasia (see passage bridging p.2-3). Hata observed that quantifying levels of cyst fluid methylated DNA could reliably predict whether cysts had high-grade dysplasia/invasive cancer or a lower grade of dysplasia (see p.10, last passage). That is to say, the methods taught in Hata were not always predictive of high-grade dysplasia in mucinous cysts of the pancreas. Additionally, Hata teaches cyst samples should be relied upon for such detections (see passage bridging p.10-11). Thus, the prior art with regards to detecting high-grade dysplasia of pancreatic cysts was not black and white; moreover, a person of ordinary skill in the art would not always be confident in determining whether a cyst should be resected or not based upon the determined prediction.
Ivry et al. (Clin. Cancer Res., 2017, Vol. 23(16), p.4865-4874, Author Manuscript; of record in IDS filed 9/23/2022) teaches that current diagnostics for pancreatic cysts do not accurately distinguish benign cysts from those that can progress into invasive cancer, and missregulated pericellular proteolysis is a hallmark of malignancy (see Abstract, p.2, 1st passage, and p.3, 1st passage). Ivry teaches that distinguishing nonmucinous from mucinous cysts remains a challenge in the prior art (see p.1, 1st-2nd passages). Ivry performed a global protease activity profiling approach to discover protease activities in cystic fluid samples from patients with a pathologically confirmed diagnosis of a pancreatic cyst (see Abstract and p.3, last passage). Fluorescent based peptide probes were utilized to detect proteolytic activity in the cystic fluid samples and to distinguish mucinous cysts from nonmucinous cysts (see passage bridging p.6-7, passage bridging p.8-9, and p.9, last passage). No major differences in protease activity were detected between mucinous cysts with low- or high-grade dysplasia (see p.7, 2nd passage). Ivry discovered protease activity was likely due to the presence of cathepsin E and gastricsin in mucinous cysts (see Abstract, p.7, 4th-5th passages, and passage bridging p.7-8). Gastricsin was observed to be primarily associated with regions of low-grade dysplasia, while cathepsin E did not exhibit a discernable dependence on the grade of dysplasia (see p.8, 2nd passage). Gastricsin and cathepsin E activity were discovered to be higher in mucinous rather than nonmucinous cysts (see p.9, last passage). Thus, not all proteases, even TPP-1, detected in cystic fluid can be determinative of high-grade dysplasia.
Ivry et al. (Global protease activity profiling for pancreatic cancer diagnosis and treatment, 2018, Dissertation retrieved from https://escholarship.org/uc/item/8w55d3jn; hereinafter Ivry II, of record) found through proteomic analysis that cathepsin E, gastricsin, and tripeptidyl peptidyl peptidase 1 (TPP1) had increased activity in mucinous pancreatic cysts (see paragraph bridging p.vii-viii, p.68, 1st passage, p.69, 2nd passage, p.71, last paragraph, paragraph bridging p.81-82, and passage bridging p.84-85). A combined analysis of gastricsin and cathepsin E with the most commonly applied biomarker, CEA, improved accuracy of differentiating a mucinous cyst from a nonmucinous cyst to 99% accuracy of distinguishment (see paragraph bridging p.vii-viii, p.86, 1st paragraph, Tables S3.5 and S5). TPP1 analysis alone demonstrated 89% accuracy for distinguishing a mucinous cyst from a nonmucinous cyst and only had 40% specificity for distinguishing mucinous cysts with high-grade dysplasia/invasive cancer from those with low-grade dysplasia (see paragraph bridging p.vii-viii, p.116, 1st passage, p.118, 1st paragraph, passage bridging p.124-125, p.126, 1st-2nd paragraphs, and paragraph bridging p.129-130). Thus, detection of these proteases can reliably distinguish a mucinous cyst from a nonmucinous cyst, but a less than 50% predictive rate for determining that the cyst has a high-grade of dysplasia or is an invasive cancer by detecting TPP1 is not alone reliable for one of ordinary skill in the art. Shotgun techniques were used to detect peptide substrates for each of the serine proteases identified above, and thus no teaching that can be correlated to a genus of peptide substrates has been set forth in the prior art (see passage bridging p.121-122).
Summary of species disclosed in the original specification. MPEP § 2163 states that a “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The examples provided in the specification mirror what is known in the state of the art, as taught in Hata, Ivry, and Ivry II above, and do not build on the deficiencies of the prior art. Only 9 peptide species of substrates of TPP1 are disclosed, and no method besides shotgun analysis of a plethora of peptide substrates has been disclosed to adequately support a genus of substrates as claimed. Given the potential variability encompassed by the genus of substrates, this disclosure cannot be considered representative of the full genus of substrates.
For all the reasons presented above, one of ordinary skill in the art would not know how to reliably diagnose high-grade dysplasia or invasive cancer of mucinous pancreatic cysts from the detection of TPP-1 or the substrates useful in the claimed invention besides the disclosed peptide substrates. Moreover, one of skill in the art would not know if the claimed method can be performed in samples other than cystic samples. Therefore, the skilled artisan would not reasonably conclude that the inventors, at the time the application was filed, was fully enabled for diagnosing high-grade or invasive cancer of mucinous cysts of the pancreas in any sample other than cystic fluid or had full possession of the genus of substrates as broadly claimed. Therefore, applicant was not in possession of the invention as claimed.
Applicant may obviate this rejection by amending claim 15 to remove diagnosing a high-grade or invasive cancer, narrowing the substrates of TPP-1 to the disclosed peptide substrates, and limiting the sample to cystic fluid.
Claim Rejections - 35 USC § 112(b) – Indefinite
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.
New Rejection Necessitated by Amendment: Claims 15, 17, and 19-22 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.
The term “high-grade” in claim 15 is a relative term which renders the claim indefinite. The term “high-grade” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The relative term “high-grade” is used in regards to dysplasia of a pancreatic mucinous cyst. The prior art does not provide a definition for “high-grade dysplasia.” Hata et al. (Clin. Cancer Res., 2017, Vol. 23(14), p.3935-3944; of record in IDS filed 9/23/2022) teaches methods to predict the grade of dysplasia of pancreatic cysts but does not elucidate a definition for this relative term. Further, the specification describes dysplasia in terms of degree by grading dysplasia in mucinous cysts (see paragraphs [00118], [00139], [00141], [00146], [00151], [00154], and Table 3). Thus, one of ordinary skill in the art would not be able to determine the metes and bounds of the claim limitation.
Claim 15 recites the limitation "the sample" in line 3. There is insufficient antecedent basis for this limitation in the claim. It is not clear to what sample “the sample” is intended to refer to and if it is the same sample recited in the last line of the claim. Accordingly, one of ordinary skill in the art would not be able to determine the metes and bounds of the claim.
Claim 15 recites “detecting an amount of the fragment of the substrate and correlating the amount to TPP-1 presence, absence, or a biologically significant quantity of in a sample from the subject” in lines 6-8. It is not exactly clear if the amount of the fragment of the substrate detected and correlated to the amount of TPP-1 is further associated with TPP-1 presence, absence, or biologically significant quantity because the recitation does not specify the subject noun after the recitation of the preposition “of,” resulting in confusion. Thus, the claim is indefinite because the scope is unclear. The subject noun is being interpreted as “TPP-1” for the sake of prosecution.
Claims 17 and 19-22 are also rejected for being dependent on a rejected base claim and failing to remedy the issue set forth above.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
New Rejection Necessitated by Amendment: Claims 15, 17 and 19-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more.
The claims recite diagnosing a subject a with mucinous cyst of the pancreas characterized by high-dysplasia or invasive cancer by detecting a presence, absence, or biologically significant quantity of TPP-1 in a sample from the subject indirectly by detecting an amount of fragment of substrates specific to TPP-1. This claimed method is directed to a judicial exception of a correlation of an indirectly detected amount or absence of TPP-1, from a subject sample to the subject having a mucinous cyst of the pancreas characterized by high-grade dysplasia or invasive cancer, which is a natural phenomenon. This judicial exception is not integrated into a practical application because claim 15 is considered to be directed to a naturally occurring process (natural phenomenon) and the additional elements recited amount to insignificant extra-solution data gathering activity. The additional elements recited in the dependent claims are either insignificant extra-solution activity or abstract mental processes. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they are directed to the naturally occurring process, an abstract idea involving mental process, and/or recite elements that are well-understood, routine, and conventional in the relevant field associated with data gathering.
The claimed invention seeks to correlate an indirect detection of TPP-1 from a subject sample to diagnose the subject with a mucinous cyst of the pancreas characterized by high-grade dysplasia or invasive cancer. Thus, the claimed invention correlates a biomarker occurrence in a subject sample with the disease of the pancreas, which is a naturally occurring process in the subject. Claim 15 further recites “exposing the sample to an enzymatically effective amount of a substrate specific to TPP-1 for a time period sufficient to catalyze a reaction between the TPP-1 and the substrate; and detecting an amount of the fragment of the substrate and correlating the amount to TPP-1 presence, absence, or a biologically significant quantity in a sample from the subject” which is insignificant extra-solution data gathering activity that seeks to indirectly determine an amount of TPP-1 in the sample. Thus, claim 15 does not recite significantly more than the natural phenomenon and remains directed to the natural phenomenon.
Claim 17 recites “wherein the step of detecting the biologically significant quantity of TPP-1 comprises calculating a score corresponding to a normalized amount of TPP-1, as compared to a control value, in the sample based upon the amount of the fragment compared to an amount of fragment of the substrate detected after exposure of a control sample to the enzymatically effective amount of the substrate, wherein the substrate is an internally quenched FRET substrate, and production of the fragment of the substrate yields a fluorescent signal” which concerns performing a mathematical calculation that can be practically performed in the human mind and insignificant extra-solution data gathering activity. Thus, this step is directed to abstract idea in the “mental process” grouping and insignificant extra-solution data gathering activity.
Claim 19 recites “correlating the amount of fragment of the substrate after the exposure for a time period sufficient to cause cleavage of the substrate into one or a plurality of fragments with a likelihood that the subject has a benign, pre-malignant, or malignant growth of the pancreas, wherein if the amount of fragment of the substrate is equal to or greater than three times the amount of fragment of the substrate found after exposure to the control sample, then the subject is diagnosed with a pre-malignant or malignant cyst of the pancreas; and wherein if the amount of fragment of the substrate is less than or equal to 1 times the amount of fragment of the substrate found after exposure to the control sample, then the subject is diagnosed with a benign, mucinous cyst of the pancreas.” This claim concerns performing a mathematical calculation that can be practically performed in the human mind. Thus, this step is an abstract idea in the “mental process” grouping.
Claim 20 recites “the TPP-1 comprises an amino acid sequence comprising SEQ ID NO: 10” which is directed to correlating indirectly detecting a TPP-1 biomarker to a disease state. Additionally, human TPP-1 has an amino acid sequence that is 100% identical to SEQ ID NO: 10 (see Appendix A for human TPP-1 and Appendix B for sequence alignments; of record). This is a natural process, and thus claim 20 is directed to the judicial exception of a natural phenomenon.
Claim 21 recites “detecting a biologically significant quantity of gastricsin and/or cathepsin E, individually or collectively, in the sample,” which is directed to the correlation of detecting gastricsin and/or cathepsin E biomarkers to a disease state. This is a natural process, and thus claim 21 is directed to the judicial exception of a natural phenomenon.
Claim 22 recites “wherein the sample is cystic fluid,” which is insignificant extra-solution activity required for data gathering.
Thus, the claimed method is directed to the natural phenomenon of correlating indirectly detecting TPP-1 in a subject sample to the subject having a mucinous cyst of the pancreas characterized by high-grade dysplasia or invasive cancer. The additional claim elements recited in claim 15 and the dependent claims do not amount to more than the judicial exception for the reasons discussed above. Therefore, the claims are directed to a natural phenomenon judicial exception without significantly more.
Response to Arguments
The rejection of claims 15-22 under 35 U.S.C. § 102(a)(1) over the Ivry Dissertation (hereinafter Dissertation) is withdrawn in view of Applicant establishing the Dissertation was published within the grace period of the effective filing date of the claimed invention. Accordingly, the rejection is withdrawn.
Applicant's arguments filed 8/12/2025 have been fully considered but they are not persuasive.
In Applicant’s Remarks, see p.18, 4th paragraph, Applicant argues that the amendment to claim 15 obviates the scope of enablement rejection. This is not found persuasive. Claim 15 remains directed to diagnosing a high-grade dysplasia or invasive cancer of a mucinous cyst of the pancreas, which is not enabled by the disclosure or state of the art as discussed in the rejection. Furthermore, claim 15 does not limit the subject sample to cystic fluid as set forth in the rejection. For these reasons and those further discussed in the rejection set forth above, the claims remain rejected as not being fully enabled.
In Applicant’s Remarks, see paragraph bridging p.18-19, Applicant argues that the state of the art demonstrates that the term “high-grade dysplasia” is a well-defined term of the art and provides https://www.rockymountaincancercenters.com/blog/high-grade-colon-dysplasia-is-it-cancer (hereinafter “Rocky Mountain” as evidence. This is not found persuasive. Rocky Mountain describes high-grade dysplasia as polyps that appear highly abnormal under a microscope and look like cancer. The term appears to be subjectively defined and relies on a skilled artisan’s own judgment to determine whether the polyp is characterized by high-grade dysplasia. There does not appear to be an objective manner for determining a high-grade dysplasia. Thus, the term “high-grade dysplasia” is considered to be relative and subjectively based on the skill and/or experience of the skilled artisan. Accordingly, the rejection is maintained.
In Applicant’s Remarks, see p.20, 1st paragraph-p.21, 2nd paragraph, Applicant argues that claim 15 is directed to detecting a fragment of substrate specific to TPP-1 and correlating the amount to TPP-1 presence, absence, or biologically significant quantity, a non-natural reaction that is not an abstract idea, a law of nature, or a natural phenomenon. Applicant further argues claim 15 as amended correlates the amount of a reaction product, a fragment of a substrate, to presence, absence, or a biologically significant amount of TPP-1. Applicant further argues exposing the sample to an enzymatically effective amount of a substrate specific to TPP-1 for a time period sufficient to catalyze a reaction between the TPP-1 and the substrate to produce a fragment of the substrate. Applicant further argues the step of transforming the amount of fragment to the presence, absence, or biologically significant amount of TPP-1 integrates the natural phenomenon into a practical application. Applicant argues that the FRET substrate yielding a fluorescent signal is wholly un-natural. This is not found persuasive.
The step of detecting a fragment of substrate specific to TPP-1 to correlate to an amount of TPP-1 is not considered to integrate the natural phenomenon of correlating an amount of TPP-1 in a subject sample to a disease state of the subject. Detecting a fragment of substrate is considered to be insignificant extra-solution data gathering activity that seeks to indirectly determine an amount of TPP-1 in a subject sample. This does not add significantly more to the natural phenomenon of correlating an amount of TPP-1 in a subject sample to a disease state in the subject. Furthermore, the recitation of a FRET substrate that yields a fluorescent signal in claim 17 does not add significantly more to the judicial exception as this limitation is also directed to insignificant extra-solution data gathering activity seeking to correlate a detected amount of fragment of substrate to an amount of TPP-1. For these reasons, the claims remain rejected under 35 U.S.C. § 101.
Conclusion
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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/J.P.S./ Examiner, Art Unit 1657
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1657