DETAILED ACTION
The amendment and RCE filed on 07/27/2026has been entered and fully considered. Claims 1-5, 7, 10-11, 13-14, 17-18, 20, 23, 30, 32-33, 35-36 and 39-40 are pending. Claims 18, 20, 23, 32-33, 35-36 and 39 have been withdrawn from consideration. Claims 1-5, 7, 10-11, 13-14, 17, 30 and 40 are considered on merits, of which claim 40 is newly added.
Response to Amendment
In response to amendment, the examiner modifies rejection over the prior art established in the previous Office action.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 2, 5, 7, and 40 are rejected under 35 U.S.C. § 103 as being unpatentable over Mills et al. (Methods, 2015) (Mills) in view of Melani et al. (MABS, 2019) (Melani).
Regarding claim 1, Mills teaches “[a] method for immunoglobulin repertoire profiling.” Mills explains that B cells express “a diverse repertoire of immunoglobulins,” that humans produce a normal polyclonal immunoglobulin repertoire, and that an individual monoclonal immunoglobulin may be detected above that polyclonal repertoire. Mills further teaches that the molecular mass of an immunoglobulin is determined by its clonal amino-acid sequence and can therefore act as a surrogate marker for the corresponding clone (abstract).
Regarding “reducing a mixture of immunoglobulins in a sample, the sample optionally further comprising a standard immunoglobulin, thereby obtaining a second sample comprising a mixture of light chains and heavy chains or light chains and Fd domains,” Mills teaches enriching human serum for immunoglobulins and then performing “reduction to separate light chains from heavy chains.”(abstract). Mills specifically treats patient serum containing a polyclonal immunoglobulin population with DTT or TCEP to break interchain disulfide bonds, thereby producing a dissociated mixture of light chains and heavy chains (page 60, par 1).
Mills does not expressly teach ionizing that reduced mixture while the mixture still contains both light and heavy chains because Mills subsequently separates the light chains by liquid chromatography. Melani, however, expressly teaches the missing feature. Melani chemically reduces disulfide bonds to yield free light and heavy chains (page 1352, par 2) and states that the reduced “polypeptide mixture was sprayed” into an Orbitrap mass spectrometer (page 1352, par 3). Melani more specifically reports that “[a] mixture of reduced Lc and Hc … was directly sprayed into an Orbitrap Eclipse™ Tribrid™ mass spectrometer.” Thus, Melani ionizes the same reduced sample while it remains a mixture of light and heavy chains. Melani also teaches the alternative recited in the claim, explaining that enzymatic cleavage followed by reduction can yield light chains, Fc/2 portions, and Fd domains.
Regarding “ionizing the second sample with an ionizer,” Melani teaches spraying the reduced light-chain/heavy-chain mixture with a Nanospray Flex static electrospray source at a spray voltage of 1.5–2.5 kV (page 1352, par 3).
Regarding “detecting a multiplicity of ions generated by the ionization of the second sample with a current detector,” Melani teaches that the directly sprayed mixture produces respective light-chain and heavy-chain charge-state envelopes and is detected using an Orbitrap Eclipse mass spectrometer (page 1352, par 3). An Orbitrap operates as both a mass analyzer and detector, with split outer electrodes detecting the image current produced by oscillating ions. Thus, Melani’s Orbitrap constitutes the claimed current detector and detects a multiplicity of light-chain and heavy-chain ions.
Regarding “determining ion masses for each of the multiplicity of ions detected with the current detector with a mass analyzer,” Melani teaches determining the m/z values and deconvoluted masses of the light and heavy chains using the Orbitrap mass analyzer. Melani reports an observed light-chain mass of 23,127.31 Da and a heavy-chain G1F mass of 51,068.59 Da (page 1353, par 0).
Regarding “generating a mass-domain spectrum from the ion masses with the mass analyzer,” Melani teaches mass deconvolution of the directly acquired spectrum using UniDec. Melani’s Figure 1b is a deconvoluted mass-domain spectrum generated from the directly sprayed reduced light-chain/heavy-chain mixture.
Regarding “determining one or more metrics capturing the heterogeneity or relative abundance of individual immunoglobulins,” Mills teaches reconstructed peak-area calculations for quantification, comparison of the relative abundances of polyclonal kappa and lambda populations, and detection of individual monoclonal peaks above a heterogeneous polyclonal background (page 63, par 0; page 64, par 0). Melani likewise determines relative abundance directly from mass-domain peak intensities, reporting that the directly sprayed mixture produced approximately 90% light-chain intensity and 10% heavy-chain intensity and further reporting relative abundances of individual heavy-chain glycoforms (page 1352, par 7).
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Mills by directly spraying at least an aliquot of Mills’ reduced serum immunoglobulin mixture into an Orbitrap mass spectrometer, as taught by Melani, before or in addition to Mills’ liquid-chromatographic light-chain analysis. Melani expressly teaches that gas-phase FAIMS separation can replace liquid-phase prefractionation and make middle-down antibody analysis faster, less expensive, and more robust (page 1354, par 1). The modification would have predictably provided complementary light-chain and heavy-chain mass and abundance information from the same reduced mixture, thereby providing a more complete profile of the immunoglobulin repertoire.
The proposed combination does not require eliminating Mills’ chromatography or rendering Mills inoperable for detecting low-abundance monoclonal light chains. Mills’ chromatographic analysis may be retained for its stated sensitivity, while Melani’s direct mixture scan is added before that analysis to obtain the claimed mixed-chain mass-domain readout. Melani experimentally demonstrates that both chain classes remain detectable in the direct scan and that FAIMS may thereafter improve their gas-phase resolution.
Regarding Claim 2,
Regarding “wherein an Ion Titer (IT), a degree of clonality (DoC), a spectral correlation coefficient, or any combination thereof is determined,” the limitation is written in the alternative, such that teaching a degree of clonality is sufficient.
Mills determines whether a discrete monoclonal peak is present above the broad polyclonal light-chain distribution and quantifies the monoclonal peak using reconstructed peak area. Mills therefore determines the degree to which the repertoire signal is concentrated in an individual clone rather than distributed throughout the polyclonal background (page 63, par 0), which corresponds to a degree-of-clonality metric under the broadest reasonable interpretation of claim 2.
Melani further teaches calculating relative peak intensities for individual light-chain and heavy-chain proteoforms (page 1352, par 7), thereby supplying the peak-intensity data from which such a clonality or ion-titer metric is determined.
Regarding claim 5,
Regarding “further comprising fractionating the sample prior to reduction,” Mills teaches fractionating or enriching patient serum with Melon Gel before treatment with DTT (page 58, par 3). Mills alternatively teaches affinity fractionation using CaptureSelect kappa/lambda matrices, followed by treatment with TCEP (page 58, par 9). Thus, Mills expressly fractionates the sample before reduction.
Regarding Claim 7,
Regarding “wherein the mixture of different immunoglobulins in the sample are chemically modified prior to ionization,” Mills chemically modifies the immunoglobulins by treating them with DTT or TCEP, thereby reducing and cleaving their interchain disulfide bonds before ionization (Fig. 2, page 60, par 1). Melani likewise denatures the immunoglobulins in guanidinium chloride and chemically reduces the disulfide bonds with TCEP before electrospray ionization (page 1352, par 2).
Regarding Claim 40,
Regarding “wherein the mass-domain spectrum is a direct readout of the mixture of light chains and heavy chains of the second sample comprising peaks across a light chain region and peaks across a heavy chain region,” Melani directly sprays the reduced light-chain/heavy-chain mixture into the Orbitrap without liquid-phase prefractionation (page 1352, par 3). Melani’s directly acquired spectrum contains both the light-chain charge-state envelope and the heavy-chain charge-state envelope, and the corresponding deconvoluted spectrum contains a light-chain mass region and a heavy-chain mass region. Melani reports that the deconvoluted direct-mixture spectrum contains approximately 90% light-chain peak intensity and approximately 10% heavy-chain peak intensity (page 1352, par 7).
Accordingly, Melani expressly provides the direct mixed-chain readout that Applicant identifies as absent from Mills.
Claims 3-4 are rejected under 35 U.S.C. § 103 as being unpatentable over Mills in view of Melani, as applied to claims 1 and 2 above, and further in view of Murray et al. (US 2020/0003784) (Murray).
Regarding Claim 3, Mills and Melani teach the method of claim 2 but do not expressly name the claimed mathematical expression an “Ion Titer.”
Regarding “a sum of mass-domain peak intensities across a light chain region and mass-domain peak intensities across a heavy chain region or Fd region,” Melani generates a deconvoluted mass-domain spectrum containing respective light-chain and heavy-chain regions and determines the fraction of total peak intensity attributable to each region (page 1352, par 7). The peak intensities across those regions are therefore expressly available for summation.
Regarding use of a standard, Mills teaches adding known amounts of the standard immunoglobulin rituximab to pooled human serum, measuring the corresponding deconvoluted peak areas, and using linear regression to relate peak area to the known immunoglobulin concentration.
Murray further teaches that a “surrogate internal standard can be used such that the mass of the internal standard does not overlap with the mass of the protein being quantitated,” (par [0019]), and that immunoglobulin quantities and ratios are determined using peak areas of multiply charged ion peaks or deconvoluted molecular-mass distributions (par [009]). Murray also teaches dividing the calculated peak area of one molecular-mass distribution by the calculated peak area of another distribution and comparing relative abundances with a control or reference sample (par [0021]).
It would have been obvious to one of ordinary skill to sum Melani’s light-chain and heavy-chain region intensities as the analyte signal and normalize that combined signal to the nonoverlapping mass-region signal of a known standard immunoglobulin, as suggested by Mills and Murray. Dividing the standard-region intensity by the known value or concentration of the standard converts the standard response into a response-per-unit calibration factor; dividing the analyte response by that calibration factor predictably produces an immunoglobulin titer. The motivation would have been to compensate for injection-to-injection and ionization variability and to provide a reproducible quantitative measurement of total immunoglobulin signal.
Regarding Claim 4,
Regarding “the degree of clonality (DoC) is determined by a ratio between a sum of mass-domain peak intensities across a light chain region and a sum of mass-domain peak intensities across a peak window,” Mills teaches a broad polyclonal light-chain mass distribution and identifies an individual monoclonal immunoglobulin by a discrete peak occurring within or above that polyclonal distribution. Mills separately measures the area of the individual monoclonal peak (page 63, par 0).
Murray teaches integrating molecular-mass distributions and expressing their respective peak areas as ratios. Murray expressly states that the kappa/lambda ratio is the calculated peak area for one light-chain molecular-mass distribution divided by the calculated peak area for the other distribution (par [0034][0097][0117]).
It would have been obvious to apply Murray’s known integrated-peak-area ratio calculation to Mills’ total light-chain region and Mills’ selected monoclonal peak window. Such a ratio predictably measures the extent to which the light-chain signal is concentrated in or associated with a selected clonal peak window and therefore provides a numerical degree-of-clonality measurement. The particular designation “DoC” does not impart structural or procedural novelty to the otherwise known peak-area ratio.
Claims 10, 11, and 30 are rejected under 35 U.S.C. § 103 as being unpatentable over Mills in view of Melani, as applied to claim 1 above, and further in view of Lee2016 et al. (Nature Medicine, 2016) (Lee2016).
Regarding Claim 10,
Regarding “wherein the sample has been collected from a candidate donor and wherein the donor is identified from the one or more metrics capturing the heterogeneity or relative abundance of individual immunoglobulins,” Lee2016 analyzes serum samples from four human donors and determines the composition and relative quantities of individual antibody clonotypes in each donor’s serum IgG repertoire (page 1457, par 2). Lee2016 presents each donor’s repertoire as relative-abundance histograms and heat maps and constructs custom B-cell-receptor sequence databases for each donor (page 1457, par 4).
It would have been obvious to use the donor-specific heterogeneity and relative-abundance metrics taught by Mills, Melani, and Lee2016 to identify the candidate donor whose repertoire contains a desired monoclonal immunoglobulin, clonotype, relative abundance, or repertoire profile. Lee2016 expressly associates each quantitative repertoire profile with its respective donor and therefore suggests identifying or selecting donors based on those measurements.
Regarding Claim 11,
Regarding “further comprising obtaining a target immunoglobulin from the donor,” Lee2016 teaches isolating influenza-specific serum IgG from each donor using separate antigen-affinity chromatography columns (page 1457, par 2). Lee2016 therefore physically obtains target immunoglobulins having a desired antigen specificity from the donor’s serum.
Mills likewise teaches affinity purification of immunoglobulins from donor serum using CaptureSelect reagents and reports that the method isolates immunoglobulins regardless of heavy-chain type (page 58, par 8).
It would have been obvious to obtain the target immunoglobulin from the donor identified by the repertoire-profile measurements because Lee2016 expressly uses affinity purification to recover the individual antigen-specific antibodies whose repertoire abundances are being measured.
Regarding Claim 30,
Regarding “isolating one or more cells from the sample comprising the target proteoform or a complex thereof,” Lee2016 collects peripheral blood from each donor, extracts peripheral blood mononuclear cells from the blood using a Ficoll gradient, and isolates B cells as individual cells inside emulsion droplets (Online Methods). The same donor blood provides the serum immunoglobulins analyzed by Ig-seq and the B cells used for BCR sequencing (page 1462, par 4).
Regarding “sequencing a nucleic acid from the isolated cells,” Lee2016 extracts RNA from the isolated cells, prepares libraries encoding immunoglobulin variable regions, and sequences those libraries using an Illumina MiSeq platform. Lee2016 also performs paired heavy- and light-chain sequencing from individual isolated B cells. (Online Methods).
Regarding “wherein the sequenced nucleic acid corresponds to the target proteoform or a complex thereof,” Lee2016 uses the B-cell-receptor sequences to construct a custom database for each donor and uses that database to identify the heavy-chain peptides and corresponding endogenous light-chain sequences of the serum antibodies detected proteomically (Online Methods).
It would have been obvious to add Lee2016’s paired B-cell isolation and sequencing workflow to the mixed-chain mass-spectrometric method of Mills and Melani to identify the nucleic-acid sequence encoding an immunoglobulin proteoform detected in the donor’s serum. The combination would predictably supplement a measured proteoform mass and abundance with its corresponding heavy- and light-chain sequence identity.
Claims 13-14, and 17 are rejected under 35 U.S.C. § 103 as being unpatentable over Mills in view of Melani and Lee2016, as applied to claims 1, 10, and 11 above, and further in view of the prescribing information for GAMMAGARD S/D, Immune Globulin Intravenous (Human).
Regarding Claim 13,
Mills, Melani, and Lee2016 teach profiling a donor’s immunoglobulin repertoire, identifying a donor and target immunoglobulin, and obtaining the target immunoglobulin from the donor, but do not expressly teach preparing that immunoglobulin as a pharmaceutically acceptable product.
Regarding “contacting the target immunoglobulin obtained [from] the donor with a pharmaceutically acceptable excipient, diluent, carrier, stabilizer, anticoagulant, or any combination thereof,” GAMMAGARD S/D is a sterile, freeze-dried preparation of purified IgG derived from pools of human plasma. The product is reconstituted with Sterile Water for Injection and contains stabilizing agents and additional components including human albumin, glycine, glucose, polyethylene glycol, sodium chloride, and polysorbate 80. (U.S. Food and Drug Administration)
It would have been obvious to contact the donor-derived target immunoglobulin obtained according to Lee2016 with a pharmaceutically acceptable aqueous diluent and stabilizing excipients, as taught by GAMMAGARD S/D, to produce a stable immunoglobulin formulation suitable for storage and administration. The references concern the complementary stages of obtaining human immunoglobulins, characterizing them, and formulating them into an administrable immunoglobulin product, and the formulation components perform their known stabilizing and diluting functions.
Regarding Claim 14,
Regarding “administering an effective amount of the proteome product prepared by the method according to claim 13 to the subject,” GAMMAGARD S/D is indicated for treatment of multiple antibody-responsive conditions, including primary immunodeficiency, and is administered intravenously at therapeutically effective dosages. For example, the label recommends 300–600 mg/kg every three to four weeks for primary immunodeficiency and provides additional effective dosage regimens for CLL, ITP, and Kawasaki syndrome. (U.S. Food and Drug Administration)
It would have been obvious to administer an effective amount of the formulated donor-derived immunoglobulin product because the expressly stated purpose of the known IVIG formulation is therapeutic administration to subjects needing immunoglobulin treatment.
Regarding Claim 17,
Regarding “[a] proteome product prepared by the method according to claim 13,” GAMMAGARD S/D is the resulting purified, donor-plasma-derived IgG product contacted with sterile diluent and stabilizing excipients described above. The product therefore possesses the same broadly claimed characteristics as the product prepared according to claim 13. (U.S. Food and Drug Administration)
Accordingly, the product of claim 17 would have been obvious for the same reasons stated for claim 13.
Response to Arguments
Applicant’s arguments with respect to claim(s) 1 have been considered but are moot in view of new ground of rejection.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander can be reached at 571-272-1254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/XIAOYUN R XU, Ph.D./Primary Examiner, Art Unit 1797
Prosecution Insights