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 .
Status of Application/Amendments/Claims
Applicant’s response filed on 6/23/2026 has been considered. Claim 17 has been newly added. Claims 1, 8, 9, 13 and 14 have been amended. Claim 17 is withdrawn from further consideration pursuant to 37 CFR 1.142 (b) as being drawn to a nonelected invention, there being no allowable generic or linking claim given that applicant has elected negative regulation of the output molecule by the first and second actuator molecule in the reply filed on 12/22/2025. Claims 1-11 and 13-14 are pending and are the present Official action. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Priority
Applicant’s claim for the benefit of a prior-filed application EP 20206417.6 and EP21187316.1 and 371 of PCT/EP2021/081158 filed on 11/9/2020, 7/22/2021 and 11/9/2021, respectively, under 35 U.S.C 119(e) or under 35 U.S.C 120, 121 or 365(c) is acknowledged.
Accordingly, the effective priority date of the instant application is granted as 11/9/2020
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 6/23/2026 was received. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement was considered by the examiner.
Withdrawn Rejections
The 35 U.S.C. 101 rejection of claims 1-11 and 13-14 are withdrawn in light of applicants claim amendments which clarify “the at least one recombinant gene” and add further limitations to the end of claim 1 specifying that the method thereby controls the output of a molecule in a cell.
The 35 U.S.C. 112(b) rejection of claims 1-11 and 13-14 has been withdrawn in light of applicant’s amendments specifying that the recombinant gene encodes a first controller molecule.
The 35 U.S.C. 112(b) rejection of claims 1-11 and 13-14 has been withdrawn in light of applicant’s amendments specifying that the method thereby controls the output of a molecule in a cell.
Reply to Applicants Arguments
Applicant traverses the previous 101 rejection by arguing that the pending claims explicitly requires a sequence of concrete and affirmative steps including introducing recombinant genes encoding defined regulatory molecules into a cell, expressing those genes with in the cell, exposing the resulting engineered system to a perturbation, and adjusting the concentration OR biological activity of an output molecule to reach a maintained setpoint. Applicant argues that these steps involve manipulation of a cellular system and genetic material and thereby constitute a practical laboratory procedure.
The claims still recite a use (method for controlling an output molecule) but still fail to recite steps that would classify it as a process under 35 U.S.C 101, see MPEP 2173.05(q). The claims specify that the recombinant genes encode for a first controller and first anti-controller molecule which are used to reach a setpoint level of the output molecule concentration and/or biological activity through an actuator molecule. The claims conclude with amendments that specify that the method is an ex-vivo method and used to control the output molecule in a cell. However, the claims fail to provide a material use of the method for controlling a network in a cell.
With respect to the previous 112b rejections, applicant points to the newly amended claims and active steps.
It is noted that new 112b rejections are applied.
Claim Interpretation
The claims describe a method that is ex vivo and is still applied to controlling the output molecule in a living cell. Thus, ex vivo is interpreted as applying to a cell cultured outside of a living organism.
New 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.
Claims 1-11 and 13-14 are rejected under 35 U.S.C. 101 because the claimed invention directed to non-statutory subject matter as evidenced by Wolkenhauer et al. "A systems-and signal-oriented approach to intracellular dynamics." (2005): 507-515 (hereinafter Wolkenhauer, reference of record). The claims do not fall within at least one of the four categories of patent eligible subject matter because the claims do not purport to claim a process, machine, manufacture or composition. This rejection is newly applied to address applicants claim amendments filed on 6/23/2026.
The most recent update to the Office’s patent eligibility requirements are the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) published on January 7 and October 17, 2019 (84 Fed. Reg. 50), which provides the following analysis to determine patent eligibility, derived from the decisions rendered in Mayo Collaborative Svcs. V. Prometheus Labs., 566 U.S. _, 132 S. Ct. 1289, 101 U.S.P.Q.2d 1961 (2012) (hereinafter “Mayo”), and in Alice Corp. Pty. Ltd. v CLS Bank Int’l, 573 U.S._, 134 S. Ct. 2347, 110 U.S.P.Q.2d 1976 (2014) in subsequent court cases:
Step 1 is to determine whether the claim is directed to a process, machine, manufacture, or composition of matter. If the claim is directed to a statutory category, proceed to Step 2.
Step 2 is the two-part analysis from Alice Corp.
Step 2A has been divided into 2 prongs.
Step 2A, prong 1 requires determining whether the claim is directed to the judicial exceptions of an abstract idea, a product of nature, or a law of nature or natural phenomenon other than a product of nature. To determine if the claim recites a nature-based product limitation, the markedly different characteristics analysis is use to evaluate whether the claim is directed to a “product of nature” that falls under the law of nature and natural phenomenon exceptions. In this analysis, markedly different characteristics can be expressed in terms of the product’s structure, function, and/or other properties. If YES, the claim is directed to a judicial exception, proceed to step 2A, prong 2.
Step 2A, prong 2 requires evaluating whether a judicial exception is integrated into a particular application (e.g. improving technology, effecting a particular treatment or prophylaxis, implementing with a particular machine, ect.) identified by the Supreme Court and the Federal Circuit, to ensure that the claim as a whole “integrates [the] judicial exception into a particular application [that] will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial exception.”
If NO, the claim does not integrate the judicial exception into a practical application, then proceed to step 2B.
Step 2B requires analyzing whether the claim as a whole amounts to significantly more than the exception by determining whether any element, or combination of elements, in the claims is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception. To be patent-eligible, a claim that is directed to a judicial exception must include additional features to ensure that the claim describes a process or product that applies the exception in a meaningful way, such that it is more than a drafting effort designed to monopolize the exception. The Supreme Court has identified the following non-limiting considerations for determining whether a claim with additional elements amounts to significantly more than the judicial exception itself:
Improvements to another technology or technical field;
Improvements to the functioning of the computer itself;
Applying the judicial exception with, or by use of, a particular machine;
Effecting a transformation or reduction of a particular article to a different state or thing;
Adding a specific limitation other than what is well-understood, routine and conventional in the field, or adding unconventional steps that confine the claim to a particular useful application; or
Other meaningful limitation beyond generally linking the use of the judicial exception to a particular technological environment.
Claim 1 describes a method for controlling a network in a cell comprising expressing a recombinant gene encoding a first controller molecule and a recombinant gene encoding a first anti-controller molecule in a cell, wherein the network comprises an actuator molecule and an output molecule which is negatively regulated. Although claimed as a method, the claims fail to state a material use of the method for controlling a network in a cell. As stated in MPEP 2173.05(q), claim 1 merely recites a use but fails to recite steps which would classify it as a process under 35 U.S.C 101. The claims specify that the recombinant genes encode for a first controller and first anti-controller molecule which are used to reach a setpoint level of the output molecule concentration and/or biological activity through an actuator molecule. The claims conclude with amendments that specify that the method is an ex-vivo method and us used to control the output molecule in a cell. However, the claims fail to provide a material use of the method for controlling a network in a cell. This rejection is supported by the disclosure of Wolkenhauer, wherein negative synthetic feedback loops in molecular circuits are discussed (Wolkenhauer, abstract). For example, the Ras-MEK-ERK MAPK kinase pathway involves multiple negative feedback loops (RAF1 inhibition and MEK) which act to control the magnitude, duration and location of signaling (Wolkenhauer, p511 and Fig 2). Although this is a naturally occurring process, the molecular circuit is still used to generate an output of activated MAPKs like ERK which acts to regulate gene expression in the nucleus involving proliferation and differentiation (Wolkenhauer, p511 and Fig 2). In contrast, the instant claims merely recite a use but fails to recite steps which would classify it as a process under 35 U.S.C 101.
New Claim Rejections - 35 USC § 112b
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 1-11 and 13-14 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 pre-AIA the applicant regards as the invention. This rejection is newly applied to address applicants claim amendments filed on 6/23/2026.
Claim 1 describes a method for controlling an output molecule in a cell by reaching a “setpoint level” of an output molecule concentration and/or biological activity through an actuator molecule. It is unclear how one of ordinary skill in the art would determine such a setpoint level and further adjust the concentration and/or activity of the output molecule through negative regulation of an actuator molecule. The claims further describe exposing the system to a perturbation of the concentration OR the biological activity of the output molecule. It is unclear why the OR conjugation is used in this instance when previous recitations use the AND/OR when referencing the output molecule concentration and/or biological activity.
Furthermore, it is unclear if controlling an output molecule only applies to the concentration and/or biological activity of the output molecule or if the definition is more expansive including control over the subcellular localization, binding affinity and temporal dynamics.
As a result of this indefinite term, one of ordinary skill in the art would not understand how the output molecule is negatively controlled by the first and second actuator molecule. A claim is indefinite when it contains words or phrases whose meaning is unclear, see MPEP2173.05(e). Claims 2-11 and 13-14 are rejected for their dependency on indefinite claim 1.
Claims 1-11 and 13-14 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 pre-AIA the applicant regards as the invention. This rejection is newly applied to address applicants claim amendments filed on 6/23/2026.
Claim 1 describes a method for controlling a network in a cell comprising expressing a recombinant gene encoding a first controller molecule and a recombinant gene encoding a first anti-controller molecule in a cell, wherein the network comprises an actuator molecule and an output molecule which is negatively regulated.
Claim 1 merely recites a process without setting forth any active steps delimiting how the control of an output molecule is actually practiced which is considered indefinite, see MPEP 2173.05(q). Although the specification provides block diagram and abstract examples illustrating such control networks, it should be emphasized that it is improper to read limitations contained in the specification into the claims. Dependent claims 2-11 and 13-14 do not provide further active steps and merely describe further descriptive and abstract elements of the network. As a result, one of ordinary skill would not understand the practical steps needed in order to practice the claimed method for controlling a network in a cell.
Conclusion
No claims allowed.
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 extension fee 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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria Leavitt can be reached on (571)272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Alexander Nicol
Patent Examiner
Art Unit 1634
/ALEXANDER W NICOL/Examiner, Art Unit 1634
/FEREYDOUN G SAJJADI/Supervisory Patent Examiner, Art Unit 1699
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