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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission filed on 1/30/26 has been entered.
Election/Restrictions and Claim Status
Applicant’s amendments and arguments filed 1/12/26 are acknowledged. Any objection or rejection from the 9/11/25 office action that is not addressed below is withdrawn based on the amendments.
Previously, Group 1 and the species of SEQ ID NO:10 were elected. Claims to the elected species are rejected as set forth below. Any relevant art that was uncovered during the search for the elected species is cited herein in order to advance prosecution.
Claims 1, 4 and 11-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3/10/25.
Claims 2-3, 5-10, 15-16 and 18-22 have been canceled.
Claims 14, 17 and 23 are being examined.
Priority
The priority information is found in the filing receipt dated 5/28/24
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 14, 17 and 23 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 14 recites that ‘the preservative is selected from’ and then recites options including ‘polyglycol-polyamine condensation resins’. The use of the term ‘resins’ makes it unclear if multiple different resins are required. It is unclear if a single polyglycol-polyamine condensation resin would meet the limitation of ‘preservative’ based on the current claim language. None of the dependent claims clarify the claim scope.
Claim Rejections - 35 USC § 101
Claims were previously rejected under 101. Since the claims have been amended, the rejection is updated to correspond to the instant claims.
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.
Claims 14, 17 and 23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon (product of nature) without significantly more. The claim(s) recite(s) peptides/compositions which correspond to products of nature (protein fragments in a composition). This judicial exception is not integrated into a practical application because the claims are product claims and there is no additional elements that apply or use the judicial exception. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception as discussed below.
This 101 rejection is consistent with the most recent training provided by the office (set forth in MPEP 2106 including the flowchart in section MPEP 2106 III) which will be referred to as 'guidance'.
In comparison to the subject matter eligibility test as set forth in the guidance, the claims are drawn to peptides/compositions. Thus the answer to step 1 of the flowchart is yes.
Instant section 0024 of the specification (dated 2/28/24) states that numerous peptides are based on natural proteins including Nek2a, TTK, PLK1 and MELK. BLAST of SEQ ID NO:10 (retrieved from https://blast.ncbi.nlm.nih.gov/Blast.cgi on 4/1/25, 32 pages; first cited 4/25/25) shows that the elected species is present in numerous natural proteins. Schultz et al. (‘Cell cycle-dependent expression of Nek2, a novel human protein kinase related to the NIMA mitotic regulator of Aspergillus nidulans’ Cell Growth & Differentiation v5 June 1994 pages 625-635; cited with IDS 2/28/24) teach the Nek2 sequence (figure 2) and residues 194-214 correspond to instant SEQ ID NO:15. The answer to step 2a is yes because the peptides correspond to protein fragments (i.e. products of nature which are a natural phenomenon).
In relation to prong two of step 2a, the instant claims are product claims and do not require any additional elements that apply the judicial exception in a manner that imposes a meaningful limit on the judicial exception. Thus the answer to prong two of step 2a is no.
The instant claims recite SEQ ID NO:10 which is a fragment of a known protein. The Myriad Supreme Court decision (Association for Molecular Pathology v. Myriad Genetics, 569 U.S. 12-398 (2013)) stated: “Myriad’s claims are not saved by the fact that isolating DNA from the human genome severs the chemical bonds that bind gene molecules together” (page 2 and 14). In the instant case, applicants’ claims are not saved by the fact that certain peptides of the instant claims correspond to fragments (the protein with severed bonds).
In relation to step 2b, the claims refer to compositions which can correspond to the peptide in water (which itself is naturally occurring) with a preservative. The instantly claimed compositions are like the novel bacterial mixture of Funk Brothers which contained multiple naturally occurring components, which was held ineligible because each species of bacteria in the mixture (like each component in the peptide composition) continued to have “the same effect it always had”, i.e., it lacked markedly different characteristics. Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 131 (1948), discussed in Myriad Genetics, 133 S. Ct. at 2117 (explaining that the bacterial mixture of Funk Brothers “was not patent eligible because the patent holder did not alter the bacteria in any way”).
Claim 14 recites a preservative that can be ‘sorbic acid’. Hall et al. (US 2015/0342195) teach that sorbic acid is a natural product isolated from berries (section 0068).The instantly claimed compositions are like the novel bacterial mixture of Funk Brothers which contained multiple naturally occurring components, which was held ineligible because each species of bacteria in the mixture (like each component in the peptide composition) continued to have “the same effect it always had”, i.e., it lacked markedly different characteristics. Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 131 (1948), discussed in Myriad Genetics, 133 S. Ct. at 2117 (explaining that the bacterial mixture of Funk Brothers “was not patent eligible because the patent holder did not alter the bacteria in any way”).
With respect to a markedly different characteristic, MPEP 2106.04(c) II states
“The markedly different characteristics analysis compares the nature-based product limitation to its naturally occurring counterpart in its natural state” and further states “The final step in the markedly different characteristics analysis is to compare the characteristics of the claimed nature-based product to its naturally occurring counterpart in its natural state, in order to determine whether the characteristics of the claimed product are markedly different. The courts have emphasized that to show a marked difference, a characteristic must be changed as compared to nature, and cannot be an inherent or innate characteristic of the naturally occurring counterpart or an incidental change in a characteristic of the naturally occurring counterpart. Myriad, 133 S. Ct. at 2111, 106 USPQ2d at 1974-75. Thus, in order to be markedly different, applicant must have caused the claimed product to possess at least one characteristic that is different from that of the counterpart”.
Applicants’ own specification recognizes that the peptides were identified from a list of proteins associated with cancer (section 0022 page 6 of the specification). Further, Cravatt BF (WO 2017/210600; ‘Cravatt’; cited with IDS 2/28/24) teach compositions for modulating an immune response (abstract) by administering a molecule of formula I (pages 1-2 connecting paragraph and claim 1). Cravatt teach that in some embodiments that the molecule of formula I comprises a polypeptide that induces an immune response (section 0006 page 2). Cravatt teach that in some cases the molecule becomes antigenically active due to the protein and recognizes the protein is expressed in cancerous cells (sections 0019-0020 page 10). Cravatt teach that a vaccine is formulated with the protein (section 0140 page 46) where the vaccine is administered for treatment of a cancer where it can be administered before, during or after the onset of cancer (section 0269 page 76). Cravatt teach specific proteins including SEQ ID NO:3854 (Table 2 caption page 137 and entry on page 153). WO 2017/210600 SEQ ID NO: 3854 (retrieved from https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2017210600&_cid=P10-KZR8YP-18331-1 on 2/17/22; document dated 7 December 2017, 3 pages; cited with IDS 2/28/24) reveals that SEQ ID NO: 3854 (page 153) comprises a sequence of instant SEQ ID NOs: 2 and 5 (and portions of instant SEQ ID NO:10). Thus peptides comprising portions as claimed were already suggested to be cancer peptide agents.
Response to Arguments - 101
Applicant's arguments filed 1/12/26 have been fully considered but they are not persuasive with respect to the rejection set forth above.
Although applicants refer to previous arguments, all previous arguments have been addressed and the response to arguments remains of record.
Although applicants argue that peptides do not fall within and are not analogous to any of the 11 judicially recognized natural phenomenon and laws of nature, MPEP 2106.04(b) II states:
“It is important to keep in mind that product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. See, e.g., Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244 ("Contrary to Myriad's argument, it makes no difference that the identified gene sequences are synthetically replicated. As the Supreme Court made clear, neither naturally occurring compositions of matter, nor synthetically created compositions that are structurally identical to the naturally occurring compositions, are patent eligible."). “
Although applicants argue about previous training examples, in the instant case, as set forth in the 101 rejection the subject matter eligibility test for products and processes as set forth in MPEP 2106 (specifically the flowchart in MPEP 2106 III) was followed. Importantly, as set forth in MPEP 2106.04(b) II product of nature exceptions include non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart.
With respect to the Myriad case, MPEP 2106.04(c) states:
“In sum, the claimed genes were different, but not markedly different, from their naturally occurring counterparts (the BRCA genes), and thus were product of nature exceptions.” Thus, any difference from a naturally occurring counterpart does not automatically exclude from being a product of nature. It appears that appellants are requiring a different test or standard as to what is expressly set forth in the MPEP (and is different from what the courts have used).
Although applicants argue that a lengthy printout is cited but most of the proteins are unnamed, a close inspection of the printout [BLAST of SEQ ID NO:10 (retrieved from https://blast.ncbi.nlm.nih.gov/Blast.cgi on 4/1/25, 32 pages; first cited 4/25/25)] shows many named proteins (see first column on pages 3-5) with further details provided in further pages (pages 6-20).
Although applicants argue that the claimed peptides represent a portion of a naturally occurring protein and that there are structural differences, as set forth in MPEP 2106.04(b)II, product of nature exceptions include non-naturally occurring products that lack markedly different characteristic. In the instant case, the claimed peptides have an identical amino acid sequence as to what occurs in naturally occurring proteins.
Although applicants argue about differences based on Das et al., the only IDS of record is dated 2/28/24 and it does not reference Das et al. Further, the argument recites ‘compartment partners, ANKS6 and NPH3 are believed to be necessary for left-right determination’ (page 9 last paragraph). It is unclear what such ‘belief’ is based on. It is unclear how such belief would lead one to conclude a structural difference.
Although applicants argue that the instant claims are different from the claims in Myriad, MPEP 2106.04(c) states:
“The Supreme Court concluded that these isolated but otherwise unchanged genes were not eligible, because they were not different enough from what exists in nature to avoid improperly tying up the future use and study of the naturally occurring BRCA genes. See, e.g., Myriad, 569 U.S. at 585, 106 USPQ2d at 1977 ("Myriad's patents would, if valid, give it the exclusive right to isolate an individual’s BRCA1 and BRCA2 genes … But isolation is necessary to conduct genetic testing") and 569 U.S. at 593, 106 USPQ2d at 1980 (describing how would-be infringers could not avoid the scope of Myriad’s claims). In sum, the claimed genes were different, but not markedly different, from their naturally occurring counterparts (the BRCA genes), and thus were product of nature exceptions.”
In the instant case, the peptides and their naturally occurring counterparts share identical amino acid sequences so there is no basis to conclude that anything has been created or altered.
Although applicants argue about examples involving denveric acid or a pacemaker cell, the current Patent Office guidance related to subject matter eligibility is set forth in MPEP 2106.
MPEP 2106.04(c) II C 2 recites:
“In Ambry Genetics, the court identified claimed DNA fragments known as "primers" as products of nature, because they lacked markedly different characteristics. University of Utah Research Foundation v. Ambry Genetics Corp., 774 F.3d 755, 113 USPQ2d 1241 (Fed. Cir. 2014). The claimed primers were single-stranded pieces of DNA, each of which corresponded to a naturally occurring double-stranded DNA sequence in or near the BRCA genes. The patentee argued that these primers had markedly different structural characteristics from the natural DNA, because the primers were synthetically created and because "single-stranded DNA cannot be found in the human body". The court disagreed, concluding that the primers’ structural characteristics were not markedly different than the corresponding strands of DNA in nature, because the primers and their counterparts had the same genetic structure and nucleotide sequence. 774 F.3d at 760, 113 USPQ2d at 1243-44. The patentee also argued that the primers had a different function than when they are part of the DNA strand because when isolated as a primer, a primer can be used as a starting material for a DNA polymerization process. The court disagreed, because this ability to serve as a starting material is innate to DNA itself, and was not created or altered by the patentee:
In fact, the naturally occurring genetic sequences at issue here do not perform a significantly new function. Rather, the naturally occurring material is used to form the first step in a chain reaction--a function that is performed because the primer maintains the exact same nucleotide sequence as the relevant portion of the naturally occurring sequence. One of the primary functions of DNA’s structure in nature is that complementary nucleotide sequences bind to each other. It is this same function that is exploited here--the primer binds to its complementary nucleotide sequence. Thus, just as in nature, primers utilize the innate ability of DNA to bind to itself.
Ambry Genetics, 774 F.3d at 760-61, 113 USPQ2d at 1244. In sum, because the characteristics of the claimed primers were innate to naturally occurring DNA, they lacked markedly different characteristics from nature and were thus product of nature exceptions. A similar result was reached in Marden, where the court held a claim to ductile vanadium ineligible, because the "ductility or malleability of vanadium is . . . one of its inherent characteristics and not a characteristic given to it by virtue of a new combination with other materials or which characteristic is brought about by some chemical reaction or agency which changes its inherent characteristics". In re Marden, 47 F.2d 958, 959, 18 CCPA 1057, 1060, 8 USPQ 347, 349.
There is no requirement that there must be an example or case law specifically relating to the instant claims prior to rejecting a claim. In Ambry, it was acknowledged that the claimed primers were single-stranded pieces of DNA which themselves are not found in the human body. Even though the claimed product was not necessarily naturally found in the body, the Court still analyzed the products and determined that they were a product of nature exception. Here, the analysis is consistent with that set forth in Ambry. The single stranded DNA in Ambry is analogous to the instantly claimed peptide fragments. In Ambry, the court concluded that that the primers’ structural characteristics were not markedly different than the corresponding strands of DNA in nature, because the primers and their counterparts had the same genetic structure and nucleotide sequence. In the instant case, the structural characteristics of the peptide are not markedly different than the corresponding sequence of the polypeptide in nature, because the peptides and their counterparts had the same amino acid sequence.
Although applicants argue that the claims refer to a preservative, amended claim 14 is addressed above. The instantly claimed compositions are like the novel bacterial mixture of Funk Brothers which contained multiple naturally occurring components, which was held ineligible because each species of bacteria in the mixture (like each component in the peptide composition) continued to have “the same effect it always had”, i.e., it lacked markedly different characteristics. Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 131 (1948), discussed in Myriad Genetics, 133 S. Ct. at 2117 (explaining that the bacterial mixture of Funk Brothers “was not patent eligible because the patent holder did not alter the bacteria in any way”). MPEP 2106.04(c) does recite:
‘In Ambry Genetics, the court identified claimed DNA fragments known as "primers" as products of nature, because they lacked markedly different characteristics. University of Utah Research Foundation v. Ambry Genetics Corp., 774 F.3d 755, 113 USPQ2d 1241 (Fed. Cir. 2014). The claimed primers were single-stranded pieces of DNA, each of which corresponded to a naturally occurring double-stranded DNA sequence in or near the BRCA genes. The patentee argued that these primers had markedly different structural characteristics from the natural DNA, because the primers were synthetically created and because "single-stranded DNA cannot be found in the human body". The court disagreed, concluding that the primers’ structural characteristics were not markedly different than the corresponding strands of DNA in nature, because the primers and their counterparts had the same genetic structure and nucleotide sequence. 774 F.3d at 760, 113 USPQ2d at 1243-44. The patentee also argued that the primers had a different function than when they are part of the DNA strand because when isolated as a primer, a primer can be used as a starting material for a DNA polymerization process. The court disagreed, because this ability to serve as a starting material is innate to DNA itself, and was not created or altered by the patentee:
In fact, the naturally occurring genetic sequences at issue here do not perform a significantly new function. Rather, the naturally occurring material is used to form the first step in a chain reaction--a function that is performed because the primer maintains the exact same nucleotide sequence as the relevant portion of the naturally occurring sequence. One of the primary functions of DNA’s structure in nature is that complementary nucleotide sequences bind to each other. It is this same function that is exploited here--the primer binds to its complementary nucleotide sequence. Thus, just as in nature, primers utilize the innate ability of DNA to bind to itself.
Ambry Genetics, 774 F.3d at 760-61, 113 USPQ2d at 1244. In sum, because the characteristics of the claimed primers were innate to naturally occurring DNA, they lacked markedly different characteristics from nature and were thus product of nature exceptions. A similar result was reached in Marden, where the court held a claim to ductile vanadium ineligible, because the "ductility or malleability of vanadium is . . . one of its inherent characteristics and not a characteristic given to it by virtue of a new combination with other materials or which characteristic is brought about by some chemical reaction or agency which changes its inherent characteristics". In re Marden, 47 F.2d 958, 959, 18 CCPA 1057, 1060, 8 USPQ 347, 349 (CCPA 1931).
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In the instant case, any claimed property is not brought about by some chemical reaction which changes its inherent characteristics. One would not recognize a preservative acting as a preservative as a marked difference (see MPEP 2106.04(c)). The Funk Brothers decision refers to components that have ‘the same effect it always had’ lacked markedly different characteristics.
Although applicants argue that Cravatt does not disclose the claimed peptides, Cravatt is not used currently in a 35 USC 102 rejection. Cravatt is cited to develop the record related to known properties of peptides that comprise a sequence of the elected species. MPEP 2106.04(c) does refer to making comparisons and the Patent Office does not have the facilities for testing.
Although applicants argue about various teachings in Cravatt and argue that Cravatt does not suggest activity against cancer, Cravatt BF (WO 2017/210600; ‘Cravatt’) teach compositions for modulating an immune response (abstract) by administering a molecule of formula I (pages 1-2 connecting paragraph and claim 1). Cravatt teach that in some embodiments that the molecule of formula I comprises a polypeptide that induces an immune response (section 0006 page 2). Cravatt teach that in some cases the molecule becomes antigenically active due to the protein and recognizes the protein is expressed in cancerous cells (sections 0019-0020 page 10). Cravatt teach that a vaccine is formulated with the protein (section 0140 page 46) where the vaccine is administered for treatment of a cancer before, during or after the onset of cancer (section 0269 page 76). Cravatt teach specific proteins including SEQ ID NO:3854 (Table 2 caption page 137 and entry on page 153). WO 2017/210600 SEQ ID NO: 3854 (retrieved from https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2017210600&_cid=P10-KZR8YP-18331-1 on 2/17/22; document dated 7 December 2017, 3 pages) reveals that SEQ ID NO: 3854 (page 153) comprises a sequence of the elected species. Thus peptides similar to those claimed were already suggested to be cancer peptide agents.
MPEP 2106.04(c)II C expressly states that the “final step in the markedly different characteristics analysis is to compare the characteristics of the claimed nature-based product to its naturally occurring counterpart in its natural state”. Without a meaningful comparison, no analysis can be done.
In summary, the guidance refers to comparing the nature-based product and the naturally occurring counterpart and recite that a claim is patent eligible when there is a resultant change in characteristics sufficient to show a marked difference. For the reasons set forth above the comparisons made are not sufficient to show a marked difference. Further, claim 14 encompasses at least 4 different peptides. There is no sufficient evidence to conclude a marked difference for the full scope of the claims.
Conclusion
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RONALD T. NIEBAUER
Primary Examiner
Art Unit 1658
/RONALD T NIEBAUER/Examiner, Art Unit 1658
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