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 .
Applicant’s election of the species of: a fluorescent detection moiety from claim 6, a degradable P space that is a polysaccharide of claim 7, and an antigen recognizing moiety Y that is an antibody from claim 8 in the reply filed on 12/03/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-15 are pending and under examination on the merits.
Priority
This application is a 371 of PCT/EP2020/074898, filed 09/07/2020.
Specification
The disclosure is objected to because of the following informalities: paragraph 0011 at page 2 of the specification should begin “An object of the invention” and paragraph 0012 should state “the spacer unit P is enzymatically degradable.” Also all mentions of “a covalent bound” should be corrected to “covalent bond”. Additionally, paraformaldehyde is missing an e in paragraph 0082 at line 17 of page 14.
Appropriate correction is required.
Claim Objections
Claim 1 is objected to because of the following informalities: “Conjugate having the general formula…” should read “A conjugate having the general formula…”. Additionally, the recitation of “Y an antigen recognizing moiety” in line 5 should read “Y is an antigen recognizing moiety”. Further, the recitation of “B an antigen recognizing moiety” in line 6 should read “B is an antigen recognizing moiety”.
Claims 2-8 are objected to because of the following informalities: “Conjugate according to claim…” should read “The conjugate of claim…”.
Claims 2-8 and 11-15 are objected to because of the following informalities: all recitations of “characterized in that…” should read “…,wherein...” to conform to conventional claim drafting language.
Claim 4 is objected to because of the following informalities: “antigen recognizing Y” should read “antigen recognizing moiety Y”.
Claim 8 is objected to because of the following informalities: “…an fragmented antibody, an fragmented antibody derivative…” should read “…a fragmented antibody, a fragmented antibody derivative…”.
Claim 9 is objected to because of the following informalities: “Library of conjugates according to claim…” should read “A library of conjugates of claim 1…”.
Claim 10 is objected to because of the following informalities: “Method for detecting a target moiety” should read “A method for detecting a target moiety”. Further, step d recites “erasing detection moiety X”, but should read “erasing the detection moiety X”. Additionally, the recitation of “Y an antigen recognizing moiety” in line 5 should read “Y is an antigen recognizing moiety”. Further, the recitation of “B an antigen recognizing moiety” in line 6 should read “B is an antigen recognizing moiety”.
Claims 11-15 are objected to because of the following informalities: “Method according to claim 10…” should read “The method of claim 10…”.
Claims 11 and 12 are objected to because of the following informalities: “…provisio…” should read “…proviso…”.
Claim 15 is objected to because of the following informalities: “…in that a the detection moiety X…” should read “…in that the detection moiety X…”. Additionally, “…a covalent bound to the cell…the covalent bound of the crosslinker…” should read “…a covalent bond to the cell…the covalent bond of the crosslinker…”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC § 112(a)
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.
Claims 4-5 and 15 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 a conjugate comprising a crosslinker unit that is a primary amino group with crosslinking initiated/induced chemically (i.e.: by PFA) and a method of using said conjugate for detection of a target moiety on a cell, does not reasonably provide enablement for a conjugate comprising other, non-primary amino group, crosslinker units and/or for crosslinking induced by radiation or enzymatic activity to form a covalent bond between the antigen and the Y and/or B moieties of the claimed conjugate and a method of using a conjugate comprising other, non-primary amino group, crosslinker units and/or for crosslinking induced by radiation or enzymatic activity to form a covalent bond between the antigen and the Y and/or B moieties of the claimed conjugate for detecting a target moiety on a cell. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
MPEP 2164.01(a) states that in order to determine compliance with the enablement requirement, the Federal Circuit developed a framework of factors in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988), referred to as the Wands factors to assess whether any necessary experimentation required by the specification is “reasonable” or is “undue.”
These factors include but are not limited to: (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.
The breadth of the claims
Claims 4-5 and 15 are broadly directed to a product or a method using a conjugate having a crosslinker unit which provides a covalent bond between the Y and/or B moiety and the antigen, where the crosslinking is induced by chemical, enzymatic, or radiological activity. This encompasses a broad genus of crosslinker units and means for inducing crosslinking.
The nature of the invention
The claims are directed to biological subject matter which is understood to be complex and often unpredictable.
The state of the prior art
The state of the prior art supports that cross-linking using an amino group induced by a chemical such as formaldehyde (see for example: Kamps et al (Commun Chem 2, 126 (2019). https://doi.org/10.1038/s42004-019-0224-2; see additionally for example: Hoffman et al ( J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679). The prior art does not appear to teach other predictable crosslinker units and/or predictable induction of crosslinking using radiation or enzymatic activity. The prior art only seems to clearly support/describe/enable chemically-induced crosslinking (see for example: Boster: antibody and ELISA experts, Boster Bio Life Science Blog, posted 01/28/2026 and accessed 02/02/2026; obtained from: https://www.bosterbio.com/blog/antibody-crosslinking?srsltid=AfmBOorXY_Zi5zE_Y40aNJV2bJOGO_eIhotaS61yeNOJy6krxZiMdRx0).
The level of one of ordinary skill
As the claims are directed to a conjugate comprising an X moiety, P moiety, Y moiety, B moiety, and a crosslinker unit and a method of using said conjugate, the artisan is presumed to be highly skilled, tending to have an advanced degree (such as a Ph.D. or an M.D.).
The level of predictability in the art
A search of the prior art fails to demonstrate predictable use of crosslinker units other than primary amino groups and further fails to demonstrate predictable induction of covalent bond crosslinking using radiation or enzymatic activity. These features are further not discussed in connection with crosslinking between a barcode and/or antigen-binding moiety of a conjugate and antigen. Therefore, the state of the art fails to provide the enablement lacking from the instant disclosure such that the entirety of the claim scope is only partially enabled.
(F) The amount of direction provided by the inventor
Applicant does not disclose a single instance/example and/or definition/description of a non-amino group crosslinker unit and/or enzymatic or radiation-induced crosslinking. The instant disclosure only contemplates (by description or example) the use of a primary amino group crosslinker unit where crosslinking is induced by PFA (see for example, paragraph 0082 at page 14 of the instant specification). No description or exemplification is made to enable other crosslinker units and/or induction of covalent bond crosslinking by radiation or enzymatic activity.
The existence of working examples
The only working examples (see Examples 1-2 at pages 14-15 of the instant specification) pertain to an animo group crosslinker with crosslinking induced by PFA. There are no working examples provided using other (non-amino group) crosslinker units or induction of crosslinking by radiation or enzymatic activity.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure
The case is directed to biological subject matter, which is by nature complex. There are no working example provided using other (non-amino group) crosslinker units or induction of crosslinking by radiation or enzymatic activity and the state of the art fails to provide enablement where the instant disclosure is lacking. The artisan would be forced into burdensome experimentation so as to effectively invent what applicant only generically suggests may be possible.
Thus, disclosure of a crosslinker unit that is a primary amino group where covalent crosslinking is induced by PFA alone is not enabling for the genus of crosslinker units other than non-amino groups and/or induction of covalent crosslinking by radiation or enzymatic activity.
35 USC § 112(b)
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 1-15 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.
Regarding claims 1-15, the term "erasable" renders the claim(s) vague and indefinite because it is unclear as to what the term will encompass. The specification defines the term as “the elimination of a fluorescence emission by X,” (see for example, paragraphs 0024-0026 of page 4 of the instant specification). However the broadest reasonable interpretation of the claim is not limited to the definition in the disclosure. As such the metes and bound of the claim are ambiguous. It is suggested that the term “erasable” is defined in the claims in order to obviate the rejection. The artisan is otherwise left to dispute the broadest reasonable interpretation of the claim scope. Furthermore, the “(I)” after the “…Bo…” should be removed as it is redundant an unnecessarily invites confusion as to whether the (I) is merely intended to note that the formula is formula I or to denote a separate, unidentified element of the formula. All claims depending from claim 1 incorporate and fail to remedy these noted ambiguities.
Claims 4, 5, and 15 are unclear regarding the “crosslinker unit capable of” because the configuration of the crosslinker is not known. In particular, it is vague as to how the crosslinker relates to formula (I) in claim 1. For example, if the crosslinker is (C), will the formula be defined as Xn-P-YmCBo or is the crosslinker a part of Y and/or B wherein an additional component is not intended? The claimed conjugate is indefinite because artisans are left to dispute the intended conjugate configuration. Definition of the intended conjugate configuration is required in order to obviate the rejection.
Claim 5 recites the limitation "the covalent bound" in line 1. Claim 5 additionally recites the limitation "the crosslinker" in line 2. There is insufficient antecedent basis for these limitation in the claim (note that the Examiner believes the Applicant intends for the recited crosslinker to refer back to the crosslinker unit of claim 4. However, the terms should be made to be consistent across the claims for clarity).
Claim 9 is vague and indefinite because it is not clear what is meant by the recitation of “oligonucleotides B having different sequences”. Artisans are left to dispute the degree of difference required to meet the claim limitations and whether only the oligonucleotide B must have a different sequence versus the entire conjugate differing in sequence.
Claim 10 recites the limitation "the sample" in step b. There is insufficient antecedent basis for this limitation in the claim.
Appropriate correction is required.
Claim 11 is vague and indefinite because it is not clear whether the claim requires that steps a-d of the method of instant claim 10 be carried out once with a first conjugate and then repeated with a second conjugate having a different barcode (B moiety) or whether the repetition (second series) of steps a-d require the use of 2 conjugates having different barcode (B moieties). The metes and bounds of the claim are indefinite as drafted.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 1-4, 6-8, and 10-14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dose et al (EP 3037820 A1) in view of Gordon et al (WO 2016145416 A2).
Regarding claim 1, Dose et al teach a method for detecting a target moiety in a sample of biological specimens by providing at least one conjugate with the general formula (I) Xn - P - Ym, where X is an detection moiety, P an enzymatically degradable spacer and Y an antigen recognizing moiety and n, m are integers between 1 and 100 and wherein X and Y are covalently bound to P (see for example, the abstract on the cover page and claim 1).
Dose et al do not teach an oligonucleotide (B) covalently bound to the antigen-recognizing moiety (Y).
However, Gordon et al teach compositions comprising formula (I) in at least figure 6 (see for example, page 7/36). In figure 6, target proteins P1 to P10 represent "detection moieties X", because they can be specifically detected via their corresponding specific antibodies; the part that connects P1 to P10 with the FLAG- or His-tag represents an enzymatically degradable "spacer unit P” (compare left rectangle with middle rectangles); the FLAG- or His-tag represent "antigen recognizing moieties Y" considering that a FLAG-tag-specific antibody or a nickel chelate, respectively, represent the antigens; the oligo barcode represents the "oligonucleotide B" (see for example, paragraph 0081 at page 22 regarding its length (4-100 nucleotides)). Note further that Gordon et al teach that some embodiments of the method include labeling the target molecule by attaching origin-specific nucleic acid barcode to the target molecule, via a target molecule specific binding agent and/or an specific binding agent that binds to an affinity tag linked to the target molecule, such as an antibody that includes or is otherwise coupled to an origin-specific nucleic acid barcode (see for example, paragraph 0005 at page 3). Gordon et al teach that one or more nucleic acid barcodes and/or UMIs can be attached, or "tagged," to a target molecule and/or target nucleic acid. This attachment can be direct (for example, covalent or noncovalent binding of the barcode to the target molecule) (see for example, paragraph 0081 at page 22).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of Dose et al and Gordon et al. The artisan would have been motivated to make and use the invention as claimed because both Dose et al and Gordon et al pertain to conjugates and methods for detecting cells, where Gordon teaches that the identity, quantity, and/or activity of target molecules originating from particular discrete volumes, such as droplets, for example water-in-oil emulsions, can be determined by determining the sequence of the origin-specific nucleic acid barcodes (optionally in combination with additional barcodes, such as one or more additional nucleic acid and/or peptide barcode) (see for example, the abstract at the cover page). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 2, as discussed above, Dose et al teach that P is an enzymatically degradable spacer (see for example, claim 1 of Dose et al).
Regarding claim 3, as discussed above, Dose et al teach that the spacer P may be enzymatically degraded amounting to cleavage of the detection X moiety from the conjugate (see for example, claim 1 of Dose et al) which is consistent with the instant Application’s description of erasure (see for example, paragraphs 0024-0026 at page 4 of the instant specification). Dose et al further teach that, for already detected antigens the antibody-fluorochrome-conjugates can be enzymatically released or are quenched by oxidative or radiation-induced destruction of the fluorescent moiety (held to teach radiologic erasure of the detection X moiety; see for example, paragraph 0051 at column 10 of page 6 of Dose et al).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have been motivated to make and use the invention as claimed because Does et al teach that the detection moiety X may be functionally erased/released/removed through degradation, by radiation or enzymatic action, from the antibody (Y) (which the artisan would have found it obvious to covalently attach one or more oligonucleotide barcodes to for reasons iterated above). The artisan would have been motivated to use the degradable spacer P of Dose et al in order to provide a method for specific labeling and detection of one or multiple targets in a sample of a biological specimen and subsequent removing the detection moiety in order to provide reversible labeling and/or enable further different labeling and detection cycles as an improvement in the art in a fast and reliable manner (see for example, paragraphs 0010-0012 at column 3 of page 3 of Dose et al). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 4, Dose et al teach that the antigen recognizing moieties Y, especially antibodies, can be coupled to the spacer P through side chain amino or sufhydryl groups and heterofunctional cross-linking reagents. In some cases the glycosidic side chain of the antibody can be oxidized by periodate and coupled with free amino groups of the spacer P (see for example, paragraph 0036 at column 7 of page 5 of Dose et al).
Throughout the instant Application, the only described cross-linking unit is a primary amino group (see for example, paragraphs 0082 and 0092 at pages 14 and 15 of the instant specification, respectively).
The teaching of Dose et al that the antigen recognizing moieties Y can be coupled to the spacer P through heterofunctional cross-linking reagents, where in some cases the glycosidic side chain of the antibody can be oxidized by periodate and coupled with free amino groups of the spacer P, is deemed to teach read upon the limitation of instant claim 4 that the antigen recognizing moiety Y is provided with a crosslinker unit (noting that the instant Application and claims do not narrow or provide a specific configuration for providing either the Y or B moieties with a crosslinker unit an no specific configuration is required).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have been motivated to make and use the invention as claimed because Does et al teach that this conjugate formulation/configuration is successfully used for detecting a target moiety in a sample of biological specimens (see for example, the abstract at the cover page of Dose et al). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 6, Dose et al teach that the detection moiety may be a fluorescent moiety (see for example, claim 3 of Dose et al).
Regarding claim 7, Dose et al teach that the enzymatically degradable spacer P may be a polysaccharide (see for example, claim 4 of Dose et al).
Regarding claim 8, Dose et al teach that the Y moiety may be an antibody (see for example, claim 5 of Dose et al).
Regarding claim 10, Dose et al and Gordon et al make obvious the conjugate of claim 1 where Dose et al teach the conjugate (lacking the barcode of Gordon et al) for use in detecting a target moiety in a sample of a biological specimen (understood to encompass detecting the moiety on a cell; see for example, claim 1 and paragraph 0001 at column 1of page 1 of Dose et al) comprising steps of contacting the sample with at least 1 conjugate thereby labeling the target moiety recognized by the antigen recognizing moiety Y, detecting the target moiety labeled with the conjugate with the detecting moiety X, and enzymatically cleaving the covalent bonded detection moiety X from spacer P (understood to be a means of erasing the detection moiety as claimed; see for example, paragraphs 0051 and 0059 at column 10 of page 6 and column 11 of page 7, respectively of Dose et al).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of Dose et al and Gordon et al. The artisan would have been motivated to make and use the invention as claimed because both Dose et al and Gordon et al pertain to conjugates and methods for detecting cells, where Gordon teaches that the identity, quantity, and/or activity of target molecules originating from particular discrete volumes, such as droplets, for example water-in-oil emulsions, can be determined by determining the sequence of the origin-specific nucleic acid barcodes (optionally in combination with additional barcodes, such as one or more additional nucleic acid and/or peptide barcode) (see for example, the abstract at the cover page and paragraphs 0002-0003 at pages 1-3). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 11, Dose et al teach a method for detection using one or more conjugates which may have different antigen-binding (Y moieties) (see for example, claims 1 and 12). The teachings of Dose et al and Gordon et al pertain to conjugates and methods for detecting cells, where Gordon et al teach that the identity, quantity, and/or activity of target molecules originating from particular discrete volumes, such as droplets, for example water-in-oil emulsions, can be determined by determining the sequence of the origin-specific nucleic acid barcodes (optionally in combination with additional barcodes, such as one or more additional nucleic acid and/or peptide barcode) (see for example, the abstract at the cover page and paragraphs 0002-0003 at page 1).
The limitations of instant claim 11 would have been prima facie obvious to the artisan because, where different conjugates of Dose et al (such as those binding different antigens) are used in tandem (such as for cell analysis) and are analyzed by a barcode moiety (such as the barcodes of Gordon et al), the artisan would have found it obvious to use different barcodes (B moieties) to allow for distinction of the conjugates during analysis using the barcodes. The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 12, Dose et al in view of Gordon et al teach a method making obvious instant claim 10, where Dose et al further teach that the method may be characterized by contacting the sample of biological specimens with at least a first and a second conjugate having different detection moieties X and/or different enzymatically degradable spacers P and/or different antigen recognizing moieties Y in subsequent sequences comprising steps a) to d) (optionally washing step e) to remove cleaved detection moieties X) (see for example, claim 12 and paragraphs 0063-0064 at column 12 of page 7 of Dose et al).
The recitation of contacting the conjugates in subsequent sequences comprising steps a) to d) is deemed to read upon the scope of repeating steps a-d with at least 2 conjugates having different Y moieties as recited in instant claim 12.
Regarding claim 13, Dose et al teach that the method is especially useful for detection and/or isolation of specific cell types from complex mixtures and teach one or more variations that provide a fast and specific multiple parameter labeling for detecting and/or isolating cell subpopulations or different cell populations simultaneously (see for example, paragraphs 0037 and 0062 at column 7 of page 5 and column 12 of page 7, respectively of Dose et al).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined references. The artisan would have been motivated to make and use the invention as claimed because Dose et al teach that the method is especially useful for detection and isolation of specific cell types from complex mixtures. This implied that detection occurs prior to isolation and that the method should be practiced as claimed where isolation is the final step, such that the method as claimed by Dose et al would have the steps of providing the conjugate, contacting the conjugate and the sample, detecting, erasing the detection moiety (cleaving/removing the X moiety), an optional washing step, and then isolation of the cells, which would read upon and make obvious the instantly claimed sequence of steps (see for example, claims 1-12 and paragraphs 0037 and 0062 at column 7 of page 5 and column 12 of page 7, respectively of Dose et al). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Regarding claim 14, Dose et al teach that for already detected antigens the antibody-fluorochrome-conjugates can be enzymatically released or are quenched by oxidative or radiation-induced destruction of the fluorescent moiety (see for example, paragraph 0051at column 10of page 6). This is deemed to read upon the recitation that the detection moiety (X moiety-the elected species being a fluorescent moiety) is erased by radiation or enzymatic degradation of the spacer unit P. Dose et al additionally teach that the space P is enzymatically degradable (see for example, claim 10 of Dose et al, which would lead to removal (understood to be encompassed by and read upon the recitation of erasure) of the detection (X) moiety.
Claim(s) 5 and 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dose et al in view of Gordon et al, as applied to claims 1-4, 6-8, and 10-14 above, in further view of Namiki et al (Anal Biochem. 2008 December 15; 383(2): 265–269. doi:10.1016/j.ab.2008.08.024) and Hoffman et al (J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679).
Regarding claims 5 and 15, as discussed above, Dose et al and Gordon et al teach the conjugate of instant claim 4 and the method of instant claim 10.
Dose et al and Gordon et al do not teach that the covalent bond of the crosslinker unit (understood to be a primary amino group) is initiated by chemical reaction.
However, Namiki et al teach a method for crosslinking antigens and their respective primary antibodies using cupric ions at high pH as an optimized a new approach that stabilizes antibody-antigen complexes and improves the affinity and lowers cross-reactivity with non-specific bands of ∼20% of antibodies tested. Namiki et al further teach that this method can enhance antigen-antibody specificity and can improve the utility of some poorly reactive primary antibodies (see for example, the abstract at page 1).
Dose et al, Gordon et al, and Namiki et al do not teach explicitly that the crosslinking is accomplished via covalent bond.
However, Hoffman et al teach that formaldehyde reacts with macromolecules in several steps. In the first step, a nucleophilic group on an amino acid or DNA base (for example) forms a covalent bond with formaldehyde, resulting in a methylol adduct, which is then converted to a Schiff base. Methylols and Schiff bases can decompose rapidly or may be stabilized in a second chemical step involving another functional group, often on another molecule, leading to formation of a methylene bridge. A methylene bridge might form between a solvent-exposed group on a macromolecule and a small molecule in solution such as glycine, which is frequently used as a formaldehyde quencher. Alternatively, and of most interest to biologists, is the formation of a covalent bond linking functional groups in two different macromolecules. The small size of formaldehyde dictates its linkage of groups that are ∼2 Å apart, making it well suited for capture of interactions between macromolecules that are in close proximity (see for example, column 2 of page 26404 of Hoffman et al).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined disclosures of the prior art references. The artisan would have been motivated to make and use the invention as claimed because Namiki et al teach that crosslinking between the antigen and antibody can enhance sensitivity, specificity, and improve antibody-utility (as discussed above). The artisan would have understood crosslinking using formaldehyde to be a functional equivalent of the cupric ion crosslinking of Namiki et al because both means accomplish the shared goal of crosslinking. Hoffman et al teach that formaldehyde crosslinking of antibody to antigen is known in the art and conditions are easily worked out/optimized so that the cross-linking does not adversely affect antibody-recognition (see for example, pages 26405-26406). The artisan, looking to realize the advantages of antibody-antigen crosslinking of Namiki et al, would look to the art to further optimize methods for said achievement, and would have found crosslinking using formaldehyde (or an equivalent thereof such as paraformaldehyde) to be an obvious functional equivalent with better known parameters to be adjusted to optimize the method while avoiding adverse impacts to antibody-recognition (and for use with components in close proximity) as taught by Hoffman et al (as discussed above; see also MPEP sections 2143(I)(B) and 2144.06 (II)). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Claim(s) 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dose et al in view of Gordon et al, as applied to claims 1-4, 68-, and 10-14 above, in further view of Hindson et al (US 9388465) and Kebschull et al (Nat Methods 15, 871–879 (2018). https://doi.org/10.1038/s41592-018-0185-x).
Regarding claim 9, Dose et al and Gordon et al teach the conjugate of instant claim 1, as discussed above. Dose et al teach that conjugates composed of an antigen binding moiety covalently linked via an enzymatically degradable spacer to a detection moiety may provide a fast and reliable method to specifically detect one or more different targets by specific detection signals and release the detection moiety after analysis and/or sorting via these signals by enzymatic degradation of the spacer (see for example, paragraph 0012 at column 3 of page 3). Gordon et al teach that in some embodiments, each of the origin-specific barcodes comprises one or more indexes, one or more sequences that enable gene specific capture and/or amplification, and/or one or more sequences that enable sequencing library construction. Additionally, in specific examples, the target molecules represent a library of randomly mutated polypeptides. In specific embodiments, the target molecule is expressed on the surface of a cell (see for example, paragraphs 0014, 0149, 0156, 0171, 0201, 0219 at respective pages 5, 51, 54, 64, 79, and 88-89 of Gordon et al).
The combined references do not clearly teach means for generating a library of conjugates having different barcode (B moiety) sequences.
However, the instant specification cites to and incorporates by reference Hindson et al (see for example, paragraph 0036 at page 6 of the instant specification) as providing enablement and description for such a library and its generation.
Kebschull et al teach that in vitro barcode production is very efficient, such that vector libraries containing billions of barcodes can be relatively easily constructed and used to label millions of cells. Moreover, in vitro construction allows for very compact barcode design (e.g., 30 random bases), thus facilitating readout by short-read sequencing technologies (see for example, column 1 of page 872). Kebschull et al further explain that cellular barcoding is a technique in which individual cells are labeled with unique nucleic acid sequences, termed barcodes, so that they can be tracked through space and time. Cellular barcoding can be used to track millions of cells in parallel, and thus is an efficient approach for investigating heterogeneous populations of cells. Over the past 25 years, cellular barcoding has been used for fate mapping, lineage tracing and high-throughput screening, and has led to important insights into developmental biology and gene function. Driven by plummeting sequencing costs and the power of synthetic biology, barcoding is now expanding (see for example, the abstract at page 871).
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosures of the combined disclosures of the prior art references. The artisan would have been motivated to make and use the invention as claimed because Kebschull et al teach that library generation of barcodes for use in cell screening is cost-efficient, well-established in the art, and predictably used in fate mapping, lineage tracing and high-throughput screening, where both Kebschull et al and Hindson et al teach means for generation of a library of barcodes having different sequences meeting the claim limitation (noting that if Hindson et al does not enable generation of such a library, the instant application may suffer deficiencies under 35 USC 112(a)). The artisan looking to adapt the conjugates and methods of Dose et al and Gordon et al for further applications such as high-throughput screening or cell sorting/mapping, would have understood the need to have a library of barcode (B moieties) for use with the conjugates (which may be further adapted, such as by altering the antigen bound) in order to enable investigation of a number of different cells/cell types, particularly where Dose et al teach that an object of the invention to provide a method for specific labeling and detection of one or multiple targets in a sample of a biological specimen and subsequent removing the detection moiety in order to provide reversible labeling and/or enable further different labeling and detection cycles (see for example, paragraph 0011). The artisan would have had a reasonable expectation of success based on the cumulative disclosures of these prior art references.
Non-Statutory Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-15 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of prior U.S. Patent No. 12436151 B2 (reference A). Although the claims at issue are not identical, they are not patentably distinct from each other because the substance of the claims, including the conjugates and methods in which they are employed, are substantially similar.
Regarding claim 1, reference A claims a conjugate having the general formula (I)Xn-P-YmBo (I)
with X is an detection moiety,
P is a spacer unit,
Y an antigen recognizing moiety,
B an oligonucleotide comprising 2 to 100 nucleotide residues
and n, m, o are independent integers between 1 and 100
wherein P and B are covalently bound to Y and X is covalently bound to P and wherein X is erasable by eliminating the fluorescence emission of the detection moiety through radiation or enzymatic degradation of the spacer unit P, and wherein the antigen recognizing moiety Y and/or the oligonucleotide B comprises a crosslinker unit as a functional group that forms a covalent bond with the antigen recognized by the antigen recognizing moiety Y (see claim 1 of reference A).
Thus, claim 1 of the reference A anticipates claim 1 of this application.
Regarding claim 2, reference A claims the conjugate according to claim 1 of reference A, characterized in that the spacer unit P is enzymatically degradable (see claims 1-2 of reference A).
Regarding claim 3, as discussed above, claim 1 of reference A claims the construct of instant claim 1 wherein the detection moiety X is erasable by eliminating the fluorescence emission of the detection moiety through radiation or enzymatic degradation of the spacer unit P (see claim 1 of reference A).
Regarding claim 4, reference A claims the conjugate of instant claim 1, wherein the antigen recognizing moiety Y and/or the oligonucleotide B comprises a crosslinker unit as a functional group that forms a covalent bond with the antigen recognized by the antigen recognizing moiety Y (see claim 1 of reference A).
Regarding claim 5, reference A claims the conjugate according to claim 1 of reference A, characterized in that that the covalent bond of the crosslinker to an antigen is initiated by radiation or enzymatic reaction (see claims 1- 3 of reference A).
Regarding claim 6, reference A claim a conjugate meeting the limitations of instant claim 1, characterized in that the detection moiety is selected from the group consisting of chromophore moiety, fluorescent moiety, phosphorescent moiety, luminescent moiety, light absorbing moiety, radioactive moiety, transition metal and isotope mass tag moiety (see for example, claims 1 and 4 of reference A).
Regarding claim 7, reference A claims a conjugate meeting the limitations of instant claim 1, characterized in that the enzymatically degradable spacer P is selected from the group consisting of polysaccharides, proteins, peptides, depsipeptides, polyesters, nucleic acids, and derivatives thereof (see for example, claims 1 and 5 of reference A).
Regarding claim 8, reference A claims a conjugate meeting the limitations of instant claim 1, characterized in that the antigen recognizing moiety Y is an antibody, an fragmented antibody, an fragmented antibody derivative, peptide/MHC-complexes targeting TCR molecules, cell adhesion receptor molecules, receptors for costimulatory molecules or artificial engineered binding molecules (see for example, claims 1 and 6 of reference A).
Regarding claim 9, reference A claims a library of conjugates (said conjugates meeting the limitations of instant claim 1) comprising at least 10,000 conjugates provided with oligonucleotide B having nucleotide sequences that differ by at least one nucleotide (see for example, claims 1 and 7 of reference A).
Regarding claim 10, reference A claims a method for detecting a target moiety on a cell by:
a) providing at least one conjugate having the general formula (I)Xn-P-YmBo (I)
with X is an detection moiety,
P is a spacer unit,
Y an antigen recognizing moiety,
B an oligonucleotide comprising 2 to 100 nucleotide residues
and n, m, o are independent integers between 1 and 100
wherein P and B are covalently bound to Y and X is covalently bound to P and wherein X is erasable; and
b) contacting the sample of biological specimens with the at least one conjugate, thereby labelling the target moiety recognized by the antigen recognizing moiety Y
c) detecting the target moiety labelled with the conjugate with the detecting moiety X
d) isolating the cell labelled with the conjugate with the detecting moiety X
e) erasing detection moiety X, by eliminating the fluorescence emission of the detection moiety through radiation or enzymatic degradation of the spacer unit P, and wherein the antigen recognizing moiety Y and/or the oligonucleotide B comprises a crosslinker unit as a functional group that forms a covalent bond with the antigen recognized by the antigen recognizing moiety Y,
(see for example, claim 8 of reference A).
Thus, claim 10 of reference A anticipates claim 10 of this application.
Regarding claim 11, reference A claims a method reading on the limitations of instant claim 10 and further claims that said method is characterized in that steps a) to e) are repeated subsequently at least with two conjugates having different antigen recognizing moieties Y and different oligonucleotides B (see for example claims 1, 8, and 12 of reference A).
Reference A does not explicitly claim that the at least 2 conjugates having different oligonucleotides B are characterized in that the oligonucleotides B have different sequences of nucleotide residues.
However, this would have been prima facie obvious to the artisan. The recitation that the subsequently at least with two conjugates have different oligonucleotides B (see for example, claim 12 of reference A) would have suggested to one of ordinary skill in the art that the sequences must be different. At the very least, the recitation of claim 12 of reference A would suggest that different oligonucleotides, differing in nucleic acid sequence, could be predictably and desirably used in the method(s) of reference A, with a reasonable expectation of success.
Regarding claim 12, reference A claims a method meeting the limitations of instant claim 10, characterized in that steps a) to e) are repeated subsequently at least with two conjugates having different antigen recognizing moieties Y (see for example, claims 1, 8, and 11 of reference A).
Regarding claim 13, reference A claims a method reading on the limitations of instant claim 10 and further claims that after step c) detecting the target moiety labelled with the conjugate with the detecting moiety X step d) isolating the cell labelled with the conjugate with the detecting moiety X is performed (see for example, claims 1, 8, and 13 of reference A).
Reference A claims a method of detecting the cell by the X moiety, isolating the cell labeled with the X moiety, then erasing the X moiety. The instant method slightly alters the steps to recite detecting the cell by the X moiety, isolating the cell labeled with the X moiety, then erasing the X moiety.
It would have been obvious to one of ordinary skill in the art to isolate the cells before erasing the X moiety with predictable results and a reasonable expectation of success, absent evidence to the contrary. Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959) (Prior art reference disclosing a process of making a laminated sheet wherein a base sheet is first coated with a metallic film and thereafter impregnated with a thermosetting material was held to render prima facie obvious claims directed to a process of making a laminated sheet by reversing the order of the prior art process steps.). See also In reBurhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946) (selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results) (MPEP 2144.04 IV). The artisan would have had a reasonable expectation of success in view of the disclosure of reference A.
Regarding claim 14, reference A claims a method meeting the limitations of instant claim 10, characterized in that the detection moiety X is erased by eliminating the fluorescence emission of the detection moiety through radiation or enzymatic degradation of the spacer unit P (see for example, claims 1 and 8 of reference A).
Regarding claim 15, reference A claims a method meeting the limitations of instant claim 10, characterized in that that the antigen recognizing moiety Y and/or the oligonucleotide B is provided with a crosslinker unit capable of providing a covalent bound to the antigen recognized by antigen recognizing moiety Y and that the covalent bound of the crosslinker to the antigen is initiated by radiation or enzymatic reaction (see for example, claims 1, 8, and 10 of reference A).
Reference A states that the covalent bond is to the antigen recognized by the antigen moiety (not the cell).
However, the artisan would have understood that the antigen recognized by the Y moiety is on the cell and that the cell recognized by the Y moiety would be recognized by the Y moiety recognizing an antigen on the cell. Therefore, the recitation of reference A is merely a more specific/narrow recitation of the recitation of instant claim 15.
It would have been prima facie obvious to the person of ordinary skill in the art to arrive at the claimed invention from the disclosure of reference A. The artisan would have been motivated to make and use the invention as claimed because reference A teaches a successful method for detection where the difference of the recitations is an obvious semantic variation and where it could appear that the covalent bond could be obviously altered/tried at any point on the cell with a reasonably expectation of successfully obtaining predictable results (see MPEP §2141(I)). The artisan would have had a reasonable expectation of success based on the cumulative disclosure of reference A.
Conclusion
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/Ashley Gao/
Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678