DETAILED ACTION
Status of Claims
Claims 1-7 and 14-24 are pending. Claims 1-2, 14-16, 18-20 have been amended. Claims 21-24 have been newly added.
Claims 1-7 and 14-24 are under examination.
Withdrawn Claim Objections and/or Rejections
The arguments filed on 09/05/2025 have been considered by the examiner.
The rejection of claims 10 and 12-13 under 112(a) for being indefinite as set forth on pp. 7-8 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the cancelled claims (filed on 09/05/2025).
The rejection of claims 1-8, 14-15, and 17-20 under 35 USC 102(a)(1) as being anticipated over Ebrahimi et al., as set forth on pp. 15-23 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the amended claims (filed on 09/05/2025).
The rejection of claims 9-10, 12-13, and 16 under 35 USC 103 as being unpatentable over Ebrahimi and Hirose et al., as set forth on pp. 24-30 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the cancelled and amended claims (filed on 09/05/2025).
The rejection of claim 11 under 35 USC 103 as being unpatentable over Ebrahimi, Hirose, and Garcia et al., as set forth on pp. 30-31 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the cancelled claims (filed on 09/05/2025).
The rejection of claim 15 for provisional double patenting over copending Application No. 17802500 as set forth on pp. 32-34 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the amended claim (filed on 09/05/2025).
The rejection of claims 10 and 20 for nonstatutory double patenting over copending Application No. 17802500 as set forth on pp. 35-37 of the previous office action (mailed on 06/06/2025) has been withdrawn in view of the amended and cancelled claim (filed on 09/05/2025).
Claim Rejections - 35 USC § 112
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 1-7 and 14-24 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-7 and 14-24 recite the use of any “anti-histone H3.1 antibody”. Specifically, claim 20 reads on a subgenus of an antibody that has a specific function i.e., either specifically binds to histone H3.1 at an epitope higher than amino acid position 21 of the histone H3.1 protein, or an anti-nucleosome antibody that specifically binds to an epitope present in intact nucleosomes. The claims recite the anti-histone H3 binds to the histone H3.1 epitope located higher than amino acid position 21 of the histone H3.1 protein (claim 21), an anti-histone H3.1 antibody that specifically binds to an epitope at amino acids 29-25 of the histone H3.1 protein (claim 22), an anti-histone H3.1 antibody that specifically binds to an epitope at amino acids 30-33 of the histone H3.1 protein (claim 23), and an anti-nucleosome antibody that is directed to bind to a conformational nucleosome epitope (claim 24).
However, claims 1-7 and 14-24 recite broadly the use of any specific antibodies. Further, the claims fail to recite a specific sequence for the antibodies. The claims are inclusive to a genus or antibodies which possess the unique capabilities of specifically binding to histone H3.1 at an epitope higher than amino acid position 21 of the histone H3.1, binding specifically to an epitope at amino acids 29-25 of the histone H3.1 protein, specifically binding to an epitope at amino acids 30-33 of the histone H3.1 protein.
In summary, claims 1-7 and 14-24 require a genus of antibody products having (1) specifically binding to histone H3.1 at an epitope higher than amino acid position 21 of the histone H3.1, (2) binding specifically to an epitope at amino acids 29-25 of the histone H3.1 protein, and (3) binding to an epitope at amino acids 30-33 of the histone H3.1 protein.
Furthermore, claims 15-16 and 20 recite the use of an “anti-nucleosome antibody” that binds specifically to an epitope present in intact nucleosomes”. The claims do not recite any specific antibodies. Further, the claims fail to recite a specific sequence for the antibodies. The claims are inclusive to a genus or antibodies which possess the unique capabilities of specifically binding to an epitope present in intact nucleosomes. The specification does not teach any examples of an “anti-nucleosome antibody”. In summary, the claim 15-16 and 20 further require a genus of antibody products having (1) of specifically binding to an epitope present in intact nucleosomes.
MPEP § 2163 states that the written description requirement for a claimed genus may be
satisfied through establishment of a structure-function correlation (by disclosure of relevant,
identifying characteristics, i.e., structure or other physical and/or chemical properties, by
functional characteristics coupled with a known or disclosed correlation between function and
structure, or by a combination of such identifying characteristics) or through a sufficient
description of a representative number of species. Either is considered sufficient to show the
applicant was in possession of the claimed genus.
Regarding structure-function correlation, it is noted that one of skill in the art was aware
that there is a lack of structure-function correlation in antibody molecules. Evidence of such in
the form of publications in the art include the following.
First, the prior art recognizes that the full six CDR sequences are required to form the
part of an antibody, i.e., the paratope, that specifically binds the target antigen. See Al Qaraghuli
et al. (2020, Nature Scientific Reports 10:13969), who state that the six CDRs form a continuous
surface to form the paratope that binds the epitope of the cognate antigen.
However, the prior art also recognizes that a single protein can be bound by a very large
and structurally diverse genus of antibodies (i.e., there is no common structural relationship
even for antibodies that bind to the same protein, epitope, or overlapping epitopes). For
example, Edwards et al. (2003, JMB 334:103-118) teach that over 1,000 different antibodies to
a single protein can be generated, all with different sequences, and representative of almost the
entire extensive heavy and light chain germline repertoire (42/49 functional heavy chain
germlines and 33 of 70 V-lambda and V-kappa light chain germlines), and with extensive
diversity in the HCDR3 region sequences (that are generated by VDJ germline segment
recombination) as well.
Lloyd et al. (2009, Protein Engineering, Eng. Design & Selection 22(3): 159-168) teach
that a large majority of VH/VL germline gene segments are used in the antibody response to an
antigen, even when the antibodies were selected by antigen binding. Said reference further
teaches that in their studies, of the 841 unselected and 5,044 selected antibodies sequenced,
all but one of the 49 functional VH gene segments was observed, and that there are on average
about 120 different antibodies generated per antigen. Said reference also teaches that a wide
variety of VH and VL pairings further increase diversity. (See entire reference.)
Goel et al. (2004, J. Immunol. 173: 7358-7367) teach that three mAbs that bind to the
same short (12-mer) peptide, exhibit diverse V gene usage, indicating their independent
germline origin. Said reference further teaches that two of these mAbs recognize the same set
of amino acid residues defining the epitope (alternate amino acid residues spread over the
entire sequence), however, the relative contribution of each set of residues in the peptide
showed significant variation. The reference notes that all of the mAbs do not show any kind of V gene restriction among themselves, implying variable paratope structure, despite that two of
these mAbs bind to the peptide through a common set of residues. (See entire reference).
Khan et al. (2014, J. Immunol. 192: 5398-5405) teach that two structurally diverse
germline mAbs recognizing overlapping epitopes of the same short peptide do so in different
topologies, the antibodies possessing entirely different CDR sequences. Said reference teaches
that unrelated mAbs structurally adjust to recognize an antigen, indicating that the primary B cell
response is composed of BCRs having a high degree of structural adaptability. Said reference
also teaches that the common epitope(s) also adopt distinct conformations when bound to
different mAbs, with the higher degree of structural plasticity inherent to the mAbs. Said
reference further teaches “It has been shown that both the framework region and the CDRs
have a considerable amount of inherent conformational plasticity...Therefore, it is not surprising
that distinct germline Abs recognize the same epitope by rearranging the CDR conformations.
This may well have implications of Ag specificity beyond the naïve BCR repertoire, because Kaji
et al... have shown in a recent report that the B cell memory can contain both germline-encoded
and somatically mutated BCRs.” (See entire reference).
Poosarla et al. (2017, Biotechn. Bioeng. 114(6): 1331 -1342) teach substantial diversity
in designed mAbs (sharing less than 75% sequence similarity to all existing natural antibody
sequences) that bind to the same 12-mer peptide, binding to different epitopes on the same
peptide. Said reference further teaches “most B-cell epitopes... in nature consist of residues
from different regions of the sequence and are discontinuous...de novo antibody designs
against discontinuous epitopes present additional challenges...". (See entire reference.)
Rabia, et al. (2018, Biochemical Engineering Journal 137:365-374) teach what effects
mutations can have on an antibody's stability, solubility, binding affinity and binding specificity.
Rabia et al. report that an increase in antibody affinity can be associated with a decrease in
stability (p. 366, col. 2 last paragraph; Fig. 2). Rabia et al. thus teach that affinity and specificity
are not necessarily correlated and that and increase in affinity does not indicate an increase in specificity (Fig. 3; p. 368, col. 1, section 3,1st full paragraph to col. 2, 2nd full paragraph).
Conversely, evidence also shows that some functionally diverse antibodies can share
some structural similarities, including an entire CDR region. See Igawa et al. (US 9,334,331 B2),
who disclose antibody Q153 that binds human Factor IXa. Q153 comprises a VH-CDR1
identical to the VH-CDR1 of antibody 11E12 disclosed by Gonzales et al. (US 10,421,807 B2).
However, 11E12 specifically binds canine IL-31, a protein having no structural or functional
similarity to human Factor IXa. This illustrates that even when some CDR regions share 100%
structural identity, the antibodies in which they are comprised can have completely different
functions (i.e., binding specificities).
The combination of evidentiary publications thus underscores a lack of structure-function
correlation in antibody molecules.
Regarding a representative number of species, the instant specification fails to describe
a representative number of species to provide adequate written description of the claimed
genus as per MPEP § 2163. The specification does not provide a specific examples of the anti-H3.1 antibodies and anti-nucleosome antibodies, nor does the specification provide a description of the structural make-up of the anti-H3.1 antibodies and anti-nucleosome antibodies and the structural-feature correlation with the anti-H3.1 antibodies and anti-nucleosome antibodies. The specification also does not disclose the genus as broadly encompassed in the claims.
Applicant’s attention is directed to the recent decision in Amgen Inc. v. Sanofi, 872 F.3d
1367 (Fed. Cir. 2017). The court discussed whether an antibody is adequately described by
describing a newly characterized antigen. Specifically, the court referred to the decision in
Centocor Ortho Biotech, Inc. v. Abbott Labs., 636 F.3d 1341 (Fed. Cir. 2011). In that case, the
patentee claimed a genus of antibodies containing a human variable region that has particularly
desirable therapeutic properties: high affinity, neutralizing activity, and A2 specificity. Despite
the fact that the specification disclosed human TNF-α protein, and despite the disclosure of the
structures of more than one species of antibody related to the genus, the court ruled that that
the generic antibody claims at issue were invalid for lack of written description. The fact patterns similar in the instant case. As in the court case, the instant claims recite a genus of
antibodies that have affinity for a specific antigen and have a desirable special property, i.e.,
ability to detect and assess liver cancer.
Following the finding in Centocor, the instant claims are found to lack adequate written
description. Similarly, in Juno Therapeutics, Inc., Sloan Kettering Institute for Cancer Research
v. Kite Pharma, Inc. (Case 2020-1758, CAFC August 2021), the court found that the disclosure
of two antibody products (scFv molecules) was insufficient to support written description for the
claimed genera, specifying that the specification at issue failed to disclose “structural features
common to the members of the genus to support that the inventors possessed the claimed
invention;” i.e., the specification and evidence of record failed to provide a structure-function
correlation. In the instant case, there is also no evidence of a structure-function correlation for
binding agents, and thus the claims are properly rejected for lack of adequate written
description.
Claim Rejections - 35 USC § 112-Response to Arguments
The arguments filed on 09/05/2025 has been considered by the examiner.
On p. 6 applicant argues that the amendments to the claims overcome the 112(a) written description rejection. However, the amendments do not overcome the 112(a) written description rejection because the amendment to include the anti- histone H3.1 antibody does not teach a specific sequence, while specifically binding to an epitope at amino acids at specific positions on the h3.1 protein.
Further, claims 15-16 and 20 recite the use of an anti-nucleosome antibody, but does not provide any specific examples of anti-nucleosome antibodies. The specification does not provide a specific example of the anti-nucleosome antibodies, nor does the specification provide a description of the structural makeup of the anti-nucleosome antibodies and the structural-feature correlation with the anti-nucleosome antibodies.
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 1-7 and 14-24 are rejected under 35 U.S.C. 101 because the claimed method is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The judicial exception is not integrated into a practical application and the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Step 1
Claims 1-7 and 14-24 are to a statutory method of determining the presence of cell free
nucleosomes and correlating it to an infection.
Step 2A prong 1: Does the claim recite a judicial exception?
The correlation between biomarkers and the presence of medical conditions is a
naturally occurring phenomenon.
Regarding claim 1, the method of using the judicial exception, the extra solution activity
of (i) contacting a body fluid sample obtained from the subject with a binding agent to detect or
measure the level of cell free nucleosomes comprising histone H3.1, wherein the binding agent comprises an anti-histone H3.1 antibody; (ii) repeating step (i) on one or more occasions; and (iii) using any changes in the level of cell free nucleosomes or component thereof to monitor the progression of the infection in the subject is directed toward a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The steps do not add a meaningful limitation to the method as they are insignificant extra- solution activity or mere data gathering steps.
Regarding claim 2, the method of using the judicial exception, the extra solution activity
of (i) contacting a body fluid sample obtained from the subject with a binding agent to detect or measure the level of cell free nucleosomes comprising histone H3.1, wherein the binding agent comprises an anti-histone H3.1 antibody; and (ii) using the level of cell free nucleosomes comprising histone H3.1 detected to assign the likelihood of an adverse outcome to said subject, wherein a subject identified with a high likelihood of an adverse outcome is assigned for medical intervention is directed toward a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The steps do not add a meaningful limitation to the method as they are insignificant extra- solution activity or mere data gathering steps.
Regarding claim 20, the method of using the judicial exception, the extra solution activity of (i) contacting a body fluid sample obtained from the subject with a binding agent to detect or measure the level of cell free nucleosomes comprising histone H3.1; and (ii) using the level of cell free nucleosomes comprising histone H3.1 as an indicator that the subject is in need of medical treatment for sepsis or septic shock, wherein the method is a two-site immunoassay method that employs an immobilized antibody and a labelled antibody, wherein either the immobilized antibody or labelled antibody is an anti-histone H3.1 antibody which specifically binds to histone H3.1 at an epitope located higher than amino acid position 21 of the histone H3.1 protein, and the other antibody is an anti- nucleosome antibody which specifically binds to an epitope present in intact nucleosomes is directed toward a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The steps do not add a meaningful limitation to the method as they are insignificant extra- solution activity or mere data gathering steps.
Step 2A prong 2: Does the claim recite additional elements that integrate the exception into a practical application?
Regarding the method of using the judicial exception, the data gathering steps of relating
the presence and expression levels of a biomarker are required to use the law of nature and do not add a meaningful limitation to the method as they are insignificant extra-solution activity or
mere data gathering steps.
Step 2B: Does the claim recite significantly more?
The claim does not include additional elements that are sufficient to amount to
significantly more than the judicial exception because the claimed elements are considered
separately and in combination, do not add significantly more to the exceptions. The natural
law/phenomenon is analogous to the correlation of biomarkers found ineligible by the courts, for
example, in Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 71, 101
USPQ2d 1961, 1965 (2012), Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859
F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017) (Using well -known standard
laboratory techniques to detect enzyme levels in a bodily sample such as blood or plasma), and
Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157
(Fed. Cir. 2015) (ineligible claims were directed to a method of detecting paternally inherited
cell-free fetal DNA, which is naturally occurring in maternal blood).
Regarding claim 3, the infection being a viral, bacterial, fungal or microbial infection does not add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al., teaches that the infection being a viral, bacterial, fungal or microbial infection is routine and
conventional in the art.
Regarding claim 4, the infection being a respiratory tract infection does not add a
meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al., teaches that
the infection being a respiratory tract infection is routine and conventional in the art.
Regarding claim 5, the respiratory tract infection being selected from: influenza, pneumonia and severe acute respiratory syndrome (SARS) does not add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al., teaches that the infection being selected from influenza, pneumonia and severe acute respiratory syndrome (SARS) is routine and conventional in the art.
Regarding claim 6, where the subject is suffering from sepsis or septic shock does not
add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al.,
teaches where the subject is suffering from sepsis or septic shock is routine and conventional in the art.
Regarding claim 7, the body fluid sample is a blood, serum or plasma sample does not
add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al.,
teaches the body fluid sample being a blood, serum, or plasma sample is routine and
conventional in the art.
Regarding claim 14, where the level of cell free nucleosomes or component thereof is
detected or measured using an immunoassay does not add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al., teaches that the level of cell free nucleosomes or component thereof is detected or measured using an immunoassay is routine and conventional in the art.
Regarding claim 15, where the method of detection or measurement comprises
contacting the body fluid sample with a solid phase comprising a binding agent that detects cell
free nucleosomes or a component thereof, and detecting binding to said binding agent does not
add a meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al.,
teaches the method of detection or measurement comprises contacting the body fluid sample
with a solid phase comprising a binding agent that detects cell free nucleosomes or a
component thereof, and detecting binding to said binding agent is routine and conventional in
the art.
Regarding claim 16, where the method of detection or measurement comprises: (i)
contacting the sample with a first binding agent which binds to an epigenetic feature of a cell free nucleosome; (ii) contacting the sample bound by the first binding agent in step (i) with a
second binding agent which binds to cell free nucleosomes; and (iii) detecting or quantifying the
binding of the second binding agent in the sample does not add a meaningful limitation, as it is
an insignificant extra-solution activity. Hirose et al., teaches that where the method of detection
or measurement comprises: (i) contacting the sample with a first binding agent which binds to
an epigenetic feature of a cell free nucleosome; (ii) contacting the sample bound by the first
binding agent in step (i) with a second binding agent which binds to cell free nucleosomes; and
(iii) detecting or quantifying the binding of the second binding agent in the sample is routine and
conventional in the art.
Regarding claim 17, where the subject is a human or an animal subject does not add a
meaningful limitation, as it is an insignificant extra-solution activity. Ebrahimi et al., teaches that
the use of a human or animal subject is routine and conventional in the art.
Regarding claim 18, where additionally comprising comparing the level of cell free
nucleosomes or component thereof in the body fluid sample of the subject with one or more
controls does not add a meaningful limitation, as it is an insignificant extra-solution activity.
Ebrahimi et al., teaches that comparing the level of cell free nucleosomes or component
thereof in the body fluid sample of the subject with one or more controls is routine and
conventional in the art.
Regarding claim 19, where the level of cell free nucleosomes is detected or measured
as one of a panel of measurements does not add a meaningful limitation, as it is an insignificant
extra-solution activity. Ebrahimi et al., teaches where the level of cell free nucleosomes is
detected or measured as one of a panel of measurements is routine and conventional in the art.
Regarding claim 21, wherein the anti-histone H3.1 antibody specifically binds to histone H3.1 at an epitope located higher than amino acid position 21 of the histone H3.1 protein does not add a meaningful limitation, as it is an insignificant extra-solution activity.
Regarding claim 22, wherein the anti-histone H3.1 antibody specifically binds to an epitope at amino acids 29-35 of the histone H3.1 protein does not add a meaningful limitation, as it is an insignificant extra-solution activity.
Regarding claim 23, wherein the anti-histone H3.1 antibody specifically binds to an epitope at amino acids 30-33 of the histone H3.1 protein does not add a meaningful limitation, as it is an insignificant extra-solution activity.
Regarding claim 24, wherein the labelled anti-nucleosome antibody is directed to bind to a conformational nucleosome epitope does not add a meaningful limitation, as it is an insignificant extra-solution activity.
Thus, the claims are rejected as ineligible under 35 USC 101.
Claim Rejections - 35 USC § 101-Response to Arguments
The arguments filed on 09/05/2025 have been considered by the examiner.
On pp. 9-10 applicant argues that the claims are significantly more than a mere judicial exception. Applicant argues that the limitations are not taught in the art and thus are significantly more.
However, the limitations are routine and convention as taught by Ebrahimi, Hirose, and Albright.
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.
Claims 1-7, 14, and 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Ebrahimi et al., “Markers of neutrophil extracellular traps predict adverse outcome in community-acquired pneumonia: secondary analysis of a randomized controlled trial” (2018) (IDS filed on 02/17/2023), in view of Albright et al., “Canonical and Variant Forms of Histone H3 Are Deposited onto the Human Cytomegalovirus Genome during Lytic and Latent Infections.” Journal of virology vol. 90,22 10309-10320. 28 Oct. 2016, doi:10.1128/JVI.01220-16.
Regarding claim 1, Ebrahimi teaches a method of monitoring the progress of a disease
in a subject suffering from an infection, comprising: (i) contacting a body fluid sample obtained
from the subject with a binding agent to detect or measure the level of cell free nucleosomes or
a component thereof.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “Blood samples (plasma and serum) from each patient were collected
upon emergency department admission and on days 3, 5 and 7, and processed as
previously described [9]. Cell-free nucleosomes as surrogate of NETosis were measured
in serum samples of the total study population using Human Cell Death Detection
ELISAPLUS (Roche Diagnostics, Basel, Switzerland). The concentrations of neutrophil
elastase and MPO were measured in sera and plasma by sandwich ELISA, utilising the Elastase/α1- PI complex ELISA kit (Calbiochem/EMD, Gibbstown, NJ, USA) and the
human MPO ELISA kit (Hycult Biotech, Plymouth Meeting, PA, USA), respectively. To
specifically characterize the source of cell-free nucleosomes as NET-associated MPO–
DNA complexes, MPO-specific capture and subsequent DNA-specific detection
antibodies were used as previously described [12]. For detailed methodology, see
supplementary material [13–20].”.
Ebrahimi teaches (ii) repeating step (i) on one or more occasions.
Ebrahimi teaches these claimed limitations in the following disclosures.
• See pages 4-5: “At baseline, serum cell-free nucleosomes as surrogates of NET
formation were highly increased (2.67±1.32 absorbance units (AU)) compared with
values in healthy controls reported as ∼0.2 AU [13, 15, 17, 18]. They subsided gradually
until day 7 (day 3: 1.48±1.03 AU; p<0.0005; day 5: 1.19±0.87 AU; p<0.0005; day 7:
0.98±0.79 AU; p=0.042; figure 1), when they were still markedly elevated compared with
values of randomly selected healthy controls (characteristics of healthy controls are
shown in supplementary table S1). In the plasma, cell-free nucleosomes were much
lower and maximum values were reached at day 3 (data not shown). Quantification of
MPO–DNA complexes showed a high correlation with values of cell-free nucleosomes,
indicating that they represent NETs (r=0.55, R2=0.3 p=0.012) (supplementary figure
S3).”.
• See figure 1.
Ebrahimi teaches (iii) using any changes in the level of cell free nucleosomes or component thereof to monitor the progression of the infection in the subject.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 5: “Relevant disease outcome measures were analysed for NET surrogates
at baseline as well as for the AUCs, integrating values of NET surrogates over 7 days.
The primary end-point, i.e. TTCS, was significantly longer in patients from the highest AUC NET quartile (median (IQR) 5.0 (2.6–9.0) days) compared with the lower three
quartiles (4.0 (2.0–7.4) days) with an adjusted hazard ratio (HR) of 0.97 (95% CI 0.94–
0.99; p=0.041; figure 2 and table 3); a HR<1.0 corresponding to prolonged TTCS. For
high baseline NET levels, a trend towards prolonged TTCS was noted (adjusted HR
0.91, 95% CI 0.82–1.01; p=0.088).”.
• See page 9: “Further studies are required to characterise NETosis in lower respiratory
tract infections and to determine the relative importance to the progression and
remission of the condition, and whether targeting this pathway would be of therapeutic
benefit to patients’ outcomes.”.
Ebrahimi does not teach the histone being H3.1 and the antibody being anti-histone H3.1.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314). Albright teaches the use of H3.1 antibodies (see 10313 “During the course of our work, ChIP-grade antibodies that recognize H3.1/2 or H3.3 became commercially available. The H3.1/2 antibody recognizes a linear epitope found in both H3.1 and H3.2 while the H3.3 antibody recognizes an epitope unique to H3.3.”).
Regarding claim 2, Ebrahimi teaches a method of assigning a risk of an adverse
outcome to a subject suffering from an infection, comprising: (i) contacting a body fluid
sample obtained from the subject with a binding agent to detect or measure the level of cell
free nucleosomes or a component thereof.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “Blood samples (plasma and serum) from each patient were collected upon emergency department admission and on days 3, 5 and 7, and processed as previously
described [9]. Cell-free nucleosomes as surrogate of NETosis were measured in serum
samples of the total study population using Human Cell Death Detection ELISAPLUS
(Roche Diagnostics, Basel, Switzerland). The concentrations of neutrophil elastase and
MPO were measured in sera and plasma by sandwich ELISA, utilising the Elastase/α1-
PI complex ELISA kit (Calbiochem/EMD, Gibbstown, NJ, USA) and the human MPO
ELISA kit (Hycult Biotech, Plymouth Meeting, PA, USA), respectively. To specifically
characterize the source of cell-free nucleosomes as NET-associated MPO–DNA
complexes, MPO-specific capture and subsequent DNA-specific detection antibodies
were used as previously described [12]. For detailed methodology, see supplementary
material [13–20].”.
Ebrahimi teaches (ii) using the level of cell free nucleosomes detected to assign the
likelihood of an adverse outcome to said subject, wherein a subject identified with a high
likelihood of an adverse outcome is assigned for medical intervention.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “The primary end-point was TTCS, defined as time to clinical stabilisation
of vital signs at two consecutive measurements ⩾12 h apart [9]. Secondary end-points
included time to effective hospital discharge, all-cause mortality, duration of intravenous
and overall antibiotic treatment, and CAP complications (including recurrence, acute
respiratory distress syndrome, empyema, nosocomial infections until day 30, severe
adverse events possibly related to CAP, intensive care unit (ICU) admission and
readmission to hospital).”.
• See page 6: “The second important finding is that high levels of NETs at admission as
well as a high integral of NETs during the course of CAP over 7 days (AUC) were strong
independent risk factors for adverse outcome.”.
Ebrahimi does not teach the histone being H3.1 and the antibody being anti-histone H3.1.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314). Albright teaches the use of H3.1 antibodies (see 10313 “During the course of our work, ChIP-grade antibodies that recognize H3.1/2 or H3.3 became commercially available. The H3.1/2 antibody recognizes a linear epitope found in both H3.1 and H3.2 while the H3.3 antibody recognizes an epitope unique to H3.3.”).
Regarding claim 3, Ebrahimi teaches wherein the infection is a viral, bacterial, fungal or
microbial infection.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 8: “These observations are in line with experimental data showing that intense pulmonary NET generation determines the disease severity in both viral and bacterial
pneumonia [22, 41].”.
• It is known in the art that community-acquired pneumonia can be caused by bacteria,
viruses, or fungi.
Regarding claims 4-5, Ebrahimi teaches wherein the infection is a respiratory tract infection and the respiratory tract infection is selected from influenza, pneumonia and severe
acute respiratory syndrome (SARS).
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 1: “This study aims to characterise the impact of NETs on clinical outcomes in pneumonia…CAP is accompanied by pronounced NET formation. Patients with elevated
serum NET markers were at higher risk for clinical instability, prolonged length of
hospital stay and 30-day all-cause mortality. NETs represent a novel marker for outcome
and a possible target for adjunct treatments of pneumonia.”).
Regarding claim 6, Ebrahimi teaches the subject is suffering from sepsis or septic shock.
Ebrahimi teaches the claimed limitations in the following disclosures:
• See page 8: “Likewise, a retrospective observational study on 80 severe sepsis patients revealed high prognostic utility of cfDNA levels to predict ICU and hospital mortality [37]. Further observational studies support evidence of NETosis as a hallmark in the
pathogenesis of systemic inflammation, hypercoagulability and sepsis [38–40].”.
Regarding claim 7, Ebrahimi teaches the body fluid sample is a blood, serum or plasma
sample.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “Blood samples (plasma and serum) from each patient were collected upon emergency department admission…”.
Regarding claim 14, Ebrahimi teaches the level of cell free nucleosomes or component
thereof is detected or measured using an immunoassay.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “Cell-free nucleosomes as surrogate of NETosis were measured in serum
samples of the total study population using Human Cell Death Detection ELISAPLUS
(Roche Diagnostics, Basel, Switzerland). The concentrations of neutrophil elastase and
MPO were measured in sera and plasma by sandwich ELISA, utilising the Elastase/α1-
PI complex ELISA kit (Calbiochem/EMD, Gibbstown, NJ, USA) and the human MPO
ELISA kit (Hycult Biotech, Plymouth Meeting, PA, USA), respectively.”
Ebrahimi does not teach the histone being H3.1.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314).
Regarding claim 17, Ebrahimi teaches the subject is a human or an animal subject.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 3: “Cell-free nucleosomes as surrogate of NETosis were measured in serum
samples of the total study population using Human Cell Death Detection ELISAPLUS
(Roche Diagnostics, Basel, Switzerland).”.
Regarding claim 18, Ebrahimi teaches additionally comprising comparing the level of cell free nucleosomes or component thereof in the body fluid sample of the subject with one or
more controls.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See pages 4-5: “At baseline, serum cell-free nucleosomes as surrogates of NET
formation were highly increased (2.67±1.32 absorbance units (AU)) compared with
values in healthy controls reported as ∼0.2 AU [13, 15, 17, 18]. They subsided gradually
until day 7 (day 3: 1.48±1.03 AU; p<0.0005; day 5: 1.19±0.87 AU; p<0.0005; day 7:
0.98±0.79 AU; p=0.042; figure 1), when they were still markedly elevated compared with
values of randomly selected healthy controls (characteristics of healthy controls are
shown in supplementary table S1). In the plasma, cell-free nucleosomes were much
lower and maximum values were reached at day 3 (data not shown). Quantification of MPO–DNA complexes showed a high correlation with values of cell-free nucleosomes,
indicating that they represent NETs (r=0.55, R2=0.3 p=0.012) (supplementary figure
S3).”.
• The instant applications specification teaches that the control may be a healthy subject
([0108]).
Ebrahimi does not teach the histone being H3.1.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314).
Regarding claim 19, Ebrahimi teaches the level of cell free nucleosomes is detected or
measured as one of a panel of measurements.
Ebrahimi teaches these claimed limitations in the following disclosures:
• See page 1: “In total, 310 patients were included in the analysis. Levels of cell-free
nucleosomes as surrogate markers of NETosis were significantly increased at admission
and declined over 7 days.”.
• See table 1. Table 1 lists various laboratory values, including various markers
(procalcitonin, C-reactive protein, white blood cell count, neutrophil granulocytes, fasting
glucose).
• See table 2. Table 2 lists clinical variables, including neutrophil granulocyte and
leukocyte values.
Ebrahimi does not teach the histone being H3.1.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314).
It would have been obvious to one of ordinary skill in the art at the time of the instant application to modify Ebrahimi’s method of measuring cell free nucleosomes to detect an infection with Albright’s teachings of H3.1 being used to detect infections. Albright teaches that H3.1 incorporation required viral DNA replication (see page 10318). Albright further teaches Histones of the H3 class are found to be associated with viral genomes during lytic infection and latency (see page 10311). One of ordinary skill in the art would have been motivated to use the histone H3.1 taught by Albright with Ebrahimi’s methods of measuring cell free nucleosomes to detect infections because as Albright teaches, H3.1 is known to be associated with infectious diseases. The artisan would have reasonable expectation of success based on the cumulative
disclosure of these prior art references at the time the instant application was filed.
Claims 15-16 are rejected under 35 U.S.C. 103 as being unpatentable over Ebrahimi and Albright et al., as applied to claims 1-7, 14, and 17-19 above, in view of Trumpie et al., “Lateral flow (immuno)assay: its strengths, weaknesses, opportunities and threats. A literature survey.” Analytical and bioanalytical chemistry vol. 393,2 (2009): 569-82. doi:10.1007/s00216-008-2287-2.
The teachings of Ebrahimi and Albright as it pertains to claims 1-7, 14, and 17-19 are discussed in the 35 USC 103 rejection above. Ebrahimi does not teach a two-site immunoassay method that employs an immobilized antibody and a labelled antibody, wherein either the immobilized antibody or labelled antibody is the anti-histone H3.1 antibody and the other antibody is an anti-nucleosome antibody which specifically binds to an epitope present in intact nucleosomes.
Albright teaches H3.1 is expressed in in lytic and latent infections (see abstract, see page 10314). Albright teaches the use of H3.1 antibodies (see 10313 “During the course of our work, ChIP-grade antibodies that recognize H3.1/2 or H3.3 became commercially available. The H3.1/2 antibody recognizes a linear epitope found in both H3.1 and H3.2 while the H3.3 antibody recognizes an epitope unique to H3.3.”). Further, it is known in the art that histone antibodies (H3.1, H3.2, and H3.3, as taught by Albright) are anti-nucleosome antibodies. Thus, Albright teachers H3.1 being expressed in infections, H3.1 antibodies, and anti-nucleosome antibodies.
Albright does not teach a two-site immunoassay method that employs an immobilized antibody and a labelled antibody, wherein either the immobilized antibody or labelled antibody is the anti-histone H3.1 antibody and the other antibody is an anti-nucleosome antibody which specifically binds to an epitope present in intact nucleosomes.
Trumpie teaches lateral flow immunoassays that contain two sites and employ an immobilized antibody and a labelled antibody (see page 570 teaching two sites, see pages 570-571 teaching an immobilized antibody and a labelled antibody) (instant claim 15). Trumpie teaches contacting the sample with an immobilized antibody, then contacting the sample bound to the antibody with the labelled antibody and detecting or quantifying the labelled antibody in the sample (see page 571 under “Lateral flow immunoassay”) (instant claim 16).
It would have been obvious to one of ordinary skill in the art at the time of the instant application to modify the lateral flow taught by Trumpie with the methods of measuring cell free nucleosomes to detect infections taught by Ebrahimi, with the antibodies taught by Albright. Trumpie provides motivation for using a lateral flow immunoassay by teaching that lateral flow immunoassays are fast and low cost, require a low sample volume, allow for point-of-care testing, and is sensitive for proteins, haptens, and nucleic acid amplicons (see table 5). One of ordinary skill in the art would consider using Trumpie’s methods of lateral flow, with the antibodies taught by Albright. The artisan would have reasonable expectation of success based on the cumulative disclosure of these prior art references at the time the instant application was filed.
Claim Rejections - 35 USC § 103-Response to Arguments
The arguments filed on 09/05/2025 have been considered by the examiner.
On pp. 7-9 applicant argues that Ebrahimi does not teach histone isoform H3.1. Ebrahimi teaches (i) contacting a body fluid sample obtained from the subject with a binding agent to detect or measure the level of cell free nucleosomes; (ii) repeating step (i) on one or more occasions; and (iii)using any changes in level of cell free nucleosomes to monitor the progression of the infection in the subject. Albright teaches histone isoform H3.1 and anti-H3.1 antibodies.
Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claim 1-7, 14, and 16-19 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1-9, 11-18 and 22 of copending Application No. 17802500 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
While there are minor differences in wording, the scope of the claims are identical. For
example, the instant claims use the wording “the method as defined in” prior claims, whereas
the reference claims recite “the method of” prior claims. This is only a difference in wording and
not one in scope.
Regarding instant claim 1, ‘500 teaches a method of monitoring the progress of a
disease in a subject suffering from an infection, comprising:(i) contacting a body fluid sample
obtained from the subject with a binding agent to detect or measure the level of cell free
nucleosomes or a component thereof; (ii) repeating step (i) on one or more occasions; and (iii)
using any changes in the level of cell free nucleosomes or component thereof to monitor the
progression of the infection in the subject (claim 1 of ‘500) and the histone isoform being H3.1 (claim 11 of ‘500).
Regarding instant claim 2, ‘500 teaches a method of assigning a risk of an adverse
outcome to a subject suffering from an infection, comprising:(i) contacting a body fluid sample
obtained from the subject with a binding agent to detect or measure the level of cell free
nucleosomes or a component thereof; and (ii) using the level of cell free nucleosomes detected
to assign the likelihood of an adverse outcome to said subject, wherein a subject identified with
a high likelihood of an adverse outcome is assigned for medical intervention (claim 2 of ‘500), and the histone isoform being H3.1 (claim 11 of ‘500).
Regarding instant claim 3, ‘500 teaches wherein the infection is a viral, bacterial, fungal or microbial infection (claim 3 of ‘500).
Regarding instant claim 4, ‘500 teaches wherein the infection is a respiratory tract
infection (claim 4 of ‘500).
Regarding instant claim 5, ‘500 teaches wherein the respiratory tract infection is selected from the group consisting of influenza, pneumonia and severe acute respiratory syndrome (SARS) (claim 5 of ‘500).
Regarding instant claim 6, ‘500 teaches wherein the subject is suffering from sepsis or
septic shock (claim 6 of ‘500).
Regarding instant claim 7, ‘500 teaches wherein the body fluid sample is a blood, serum or plasma sample (claim 7 of ‘500).
Regarding instant claim 14, ‘500 teaches wherein the level of cell free nucleosomes or
component thereof is detected or measured using an immunoassay, immunochemical, mass
spectroscopy, chromatographic, chromatin immunoprecipitation or biosensor method (claim 14
of ‘500).
Regardin