WO2024036192A2 - Compositions et méthodes d'évaluation de la gravité et de traitement de la covid-19 - Google Patents

Compositions et méthodes d'évaluation de la gravité et de traitement de la covid-19 Download PDF

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WO2024036192A2
WO2024036192A2 PCT/US2023/071902 US2023071902W WO2024036192A2 WO 2024036192 A2 WO2024036192 A2 WO 2024036192A2 US 2023071902 W US2023071902 W US 2023071902W WO 2024036192 A2 WO2024036192 A2 WO 2024036192A2
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seq
conservative substitution
chain variable
variable region
nos
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Roger Johns
Qing Lin
John Skinner
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The Johns Hopkins University
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/701—Specific hybridization probes
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    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to the field of virology. More specifically, the present invention provides compositions and methods for assessing the severity of and treating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19).
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • the present inventors have extensively studied and defined pathways of lung inflammation induced by human resistin (hResistin), especially its role in amplifying inflammation, in serving as a chemokine, and in activating BTK, Th2, and HMGB1 pathways. 1 As described herein, the present inventors’ current clinical, human immune cell, and humanized animal model studies demonstrate an important role for hResistin signaling in the etiology of COVID-19. SUMMARY OF THE INVENTION The present inventors propose hResistin as a major regulator of Sars-Cov-2 inflammation in COVID-19 and a target for therapy.
  • hResistin is the most elevated analyte among dozens of tested inflammatory cytokines/chemokines in human patients with COVID-19, and that there is a logarithmic correlation between circulating hResistin level and the WHO-max disease severity index of hospitalized COVID-19 patients.
  • hResistin concentration correlated with other key proinflammatory Th1/Th2 cytokines, chemokines, and growth factors in the serum of patients with COVID-19 including IL-1 ⁇ (Table 1).
  • Immunohistology of COVID-19 in patient lung showed that hResistin expression was highly induced in the airway, pulmonary parenchyma, and inflammatory cells (FIG.4), and co-localized with BTK, a TEC kinase that we have previously shown to be a binding partner of hResistin and Resistin-like molecule alpha (RELM ⁇ ), 4 (the equivalent rodent form of hResistin).
  • RELM ⁇ Resistin-like molecule alpha
  • BTK is activated by and facilitates the chemokine activities of hResistin/RELM ⁇ and has recently been strongly implicated as a critical regulator of NLRP3 inflammasome activation.
  • SARS-CoV-2 spike protein induces hResistin and its downstream pro-inflammatory pathways, including the NLRP3 inflammasome and its active products IL-1 ⁇ and IL-18, as well as the inflammasome activators HMGB1 and BTK. This induction of the inflammasome was prevented by pre-application of the present inventors’ human therapeutic hResistin-blocking antibody (FIG.10).
  • the present inventors have shown that hResistin regulates SARS-Cov2- induced immune responses to drive lung inflammation and the subsequent cytokine storm in COVID-19 pathogenesis, serves as a predictor of severity and is a target for anti-hResistin therapy (FIG.1).
  • the inventors present evidence that their therapeutic monoclonal human monoclonal antibody directed against hResistin is efficacious in the prevention and reversal and amelioration of COVID-19 disease. Accordingly, in one aspect, the present invention provides methods for predicting disease severity in a patient with COVID-19.
  • the method comprises (a) measuring the level of Resistin in a sample obtained from the patient with COVID-19; (b) comparing the level measured in step (a) to a reference; and (c) predicting disease severity in the patient with COVID-19.
  • the present invention provides methods for risk stratification of progressing to severe disease of a patient with COVID-19.
  • the method comprises (a) measuring the level of Resistin in a sample obtained from the patient with COVID-19; (b) comparing the level measured in step (a) to a reference; and (c) stratifying the risk of the patient with COVID-19.
  • the present invention provides methods for monitoring disease progression in a patient with COVID-19.
  • the method comprises (a) measuring the level of Resistin in a first sample obtained from the patient with COVID-19; (b) measuring the level of Resistin in a second sample from the patient with COVID-19 that has been obtained after the first sample; (c) comparing the level measured in step (a) to the level measured in step (b); and (d) monitoring disease progression in the patient with COVID-19 based on the results of step (c).
  • the methods for predicting disease, risk stratifying and/or monitoring disease progression can further comprise the step of screening DNA obtained from the patient for the presence of a Resistin polymorphism associated with severe COVID- 19 and/or hospitalization.
  • a Resistin polymorphism associated with severe COVID-19 comprises rs10402265 (C>G).
  • a Resistin polymorphism associated with hospitalization comprises rs12459044 (C>G).
  • the level of Resistin can be measured using an antibody or antigen-binding fragment thereof described herein.
  • the present invention provides methods for treating COVID-19.
  • the method comprises the step of administering to the patient an isolated, recombinant antibody or antigen-binding fragment thereof that binds human Resistin.
  • the anti-Resistin antibody or antigen-binding fragment thereof can comprise a single chain variable fragment (scFv), a dimeric scFv, a Fab, a Fab’, a F(ab’)2 fragment or a full-length antibody.
  • scFv single chain variable fragment
  • Fab fragment antigen-binding fragment
  • F(ab’)2 fragment fragment antigen-binding fragment
  • the patient has severe COVID-19.
  • the hResistin therapeutic antibody comprises clone 13, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:73 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:73, and the light chain variable region comprises SEQ ID NO:77 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:77.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:74-76, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:74-76, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:78-80, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:78-80.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:72 or a conservative substitution at up to 5 amino acids of SEQ ID NO:72.
  • the hResistin therapeutic antibody comprises clone 42, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:163 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:163, and the light chain variable region comprises SEQ ID NO:167 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:167.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:164-166, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:164-166, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:168-170, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:168-170.
  • the hResistin antibody or antigen-binding fragment thereof comprises a single chain variable fragment (scFv) or antigen-binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:162 or a conservative substitution at up to 5 amino acids of SEQ ID NO:162.
  • the hResistin therapeutic antibody comprises clone 2, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:13 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:13, and the light chain variable region comprises SEQ ID NO:17 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:17.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:14-16, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:14-16, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:18-20, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:18-20.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:12 or a conservative substitution at up to 5 amino acids of SEQ ID NO:12.
  • the hResistin therapeutic antibody comprises clone 11, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:63 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:63, and the light chain variable region comprises SEQ ID NO:67 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:67.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:64-66, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:64-66, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:68-70, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:68-70.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:62 or a conservative substitution at up to 5 amino acids of SEQ ID NO:62.
  • scFv single chain variable fragment
  • the anti-Resistin antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein (a) the heavy chain variable region comprises SEQ ID NO:3 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:3, and the light chain variable region comprises SEQ ID NO:7 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:7; (b) the heavy chain variable region comprises SEQ ID NO:13 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:13, and the light chain variable region comprises SEQ ID NO:17 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:17; (c) the heavy chain variable region comprises SEQ ID NO:23 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:23, and the light chain variable region comprises SEQ ID NO:27 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:27; (d) the heavy chain variable region comprises SEQ ID NO:
  • the anti-Resistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising complementarity determining regions (CDRs) 1, 2 and 3 comprising SEQ ID NOS:4-6, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:4-6, and a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:8-10, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:8-10; (b) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:14-16, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:14-16, and a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:18-20, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:18-20; (c) a heavy chain variable region comprising
  • the anti-Resistin antibody or antigen-binding fragment thereof further comprises a heavy chain constant region comprising SEQ ID NO:172 and a light chain constant region comprising SEQ ID NO:174.
  • the anti-Resistin antibody or antigen-binding fragment thereof comprises an scfv or antigen-binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:2 or a conservative substitution at up to 5 amino acids of SEQ ID NO:2; SEQ ID NO:12 or a conservative substitution at up to 5 amino acids of SEQ ID NO:12; SEQ ID NO:22 or a conservative substitution at up to 5 amino acids of SEQ ID NO:22; SEQ ID NO:32 or a conservative substitution at up to 5 amino acids of SEQ ID NO:32; SEQ ID NO:42 or a conservative substitution at up to 5 amino acids of SEQ ID NO:42; SEQ ID NO:52 or a conservative substitution at up to 5 amino acids of SEQ ID NO:
  • the present invention provides a method for treating a viral infection in a patient comprising the step of administering to the patient an isolated, recombinant antibody or antigen-binding fragment thereof that binds human Resistin.
  • the viral infection is caused by human papillomavirus (HPV).
  • HPV human papillomavirus
  • the present invention provides RNA interference compositions.
  • a ribonucleic acid (RNA) interfering (RNAi) composition comprises about 18-25 nucleotides that is complementary to SEQ ID NO:244, wherein the RNAi composition is capable of inhibiting the expression of human Resistin.
  • RNAi composition is a small interfering RNA (siRNA), a short hairpin RNA (shRNA), double stranded RNA (dsRNA), and RNA construct or an anti-sense oligonucleotide.
  • shRNA small interfering RNA
  • shRNA short hairpin RNA
  • dsRNA double stranded RNA
  • the present invention provides an shRNA for knocking down Resistin expression comprising SEQ ID NO:246 or SEQ ID NO:247.
  • FIG.1 Schematic illustration of the role of hResistin in the pathophysiology of COVID-19.
  • FIG.2. hResistin serum levels in COVID-19 patients are corelated with disease severity.
  • hResistin levels were measured with an R-PLEX ELISA kit (F21ZO-3, Mesoscale Discovery). Data represent means ⁇ SEM. *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001.
  • FIG.3. Cross-correlation chart of hResistin serum (log) levels with patient characteristics, including severity of outcome.
  • FIG.4A Immunofluorescence images of immune cells in the COVID-19 lung parenchyma tissues. Sections were stained with anti-Mac2 (CL8942AP, Cedarlane), anti-MPO (AF3667, R&D) or anti-CD76b (ab134147, Abcam) antibodies.
  • FIG. 4B Immunofluorescence images of hResistin signals in the airway (upper panels) and pulmonary parenchyma (middle panels).
  • FIG.6A-6C Anti-hResistin/RELM ⁇ antibody ameliorates lung inflammation and body weight loss in the K18-hACE2 mice with COVID-19.
  • the SARS CoV2-infected mice were treated with saline (No Ab), isotype control IgG1 (Con IgG) or the anti- hResistin/RELM ⁇ antibody, as described in the proposal.
  • FIG.6A isotype control IgG1 (Con IgG) or the anti- hResistin/RELM ⁇ antibody, as described in the proposal.
  • FIG.7A-7C SARS CoV2 induces RELM ⁇ expression in the lung of K18-hACE2 mice.
  • FIG.7A q-RT-PCR analysis of RELM ⁇ gene expression in the mouse lung tissues with or without infection.
  • FIG.7B Images of western blotting on the RELM ⁇ protein expression.
  • FIG.8A-8B SARS CoV2 upregulates BTK, HMGB1 and NLRP3 in the mouse lung through activating hResistin/RELM ⁇ .
  • FIG.8A SARS CoV2 upregulates BTK, HMGB1 and NLRP3 in the mouse lung through activating hResistin/RELM ⁇ .
  • the SARS-CoV-2 MA model The body weight of mice infected with SARS-CoV-2 MA. Data are presented as means + STD.
  • FIG.10. SARS-CoV-2 spike protein induces HMGB1 and NLRP3 inflammasome pathways by activating hResistin in monocytes.
  • Human THP-1 cells were treated with 10 ⁇ g/mL recombinant SARS-CoV-2 spike protein (DAGC149, Creative Diagnostics) for 6 hours (dose was chosen based on the present inventors’ preliminary study). In some groups, cells were pre-treated with anti-hResistin Ab (developed by the present inventors’ lab) at 3 ⁇ g/mL (a dose that blocks activities of hResistin protein without cytotoxic effects).
  • Nonimmunized IgG1 (Con Ab, Lonza) served as an isotype control.
  • the present inventors used quantitative RT-PCR with primers (IDT, pre-designed) of the targeted molecules to measure gene expression. The relative changes were normalized against a housekeeping gene and calculated with the 2 - ⁇ CT method.
  • HMGB1 high mobility group box 1; IL-1 ⁇ , interleukin 1 ⁇ ; NLRP3, an inflammasome.
  • SARS-CoV-2 activates hResistin to activate BTK, HMGB1 and the NLRP3 inflammasome in neutrophils, another prominent source of hResistin in innate immunity and in COVID-19.
  • hResistin induces the pro-inflammatory phenotype of the HL-60- differentiated neutrophils.
  • FIG.13 hResistin induces chemotaxis of B cells through activating BTK. In the transwell migration system in hypoxic condition (left panel), human B cell line (HCC1937 BL) was stimulated with hResistin recombinant protein at 10 and 30 nM, with pretreatment of 25 uM BTK inhibitor LFMA-13.
  • FIG.14 Schematic illustration of proposed Hresistin-regulated inflammatory signaling axis. Through the in vitro cell studies, the present inventors will determine the Hresistin-driven signaling pathways in human immune cells, including: 1) the HMGB1- dependent NLRP3 priming; and 2) the BTK-dependent NLRP3 assembly/activation and IL- 1 ⁇ /IL-18 secretion.
  • FIG.15 Flow cytometry analysis of the intratracheally allotransplanted BAL cells. Normoxic WT C57BL/6 mice were used.
  • Donor BAL mouse cells were collected and labeled ex vivo with red fluorescent dye PKH26 (Sigma) and then intratracheally administer (0.6x10 6 cells in 50 ⁇ l PBS) to the recipient mice.
  • PKH26 red fluorescent dye
  • BAL cells of recipient mice were isolated and detected with flow cytometry.
  • Among the gated viable cells around 1% cells are PKH26+ BAL cells of which with more than 80% are F4/80+CD11c+ macrophages (upper panels). Cells stained with corresponding isotype controls served as negative control (lower panels).
  • FIG.16A-16F The red fluorescent dye PKH26 (Sigma) and then intratracheally administer (0.6x10 6 cells in 50 ⁇ l PBS) to the recipient mice.
  • BAL cells of recipient mice were isolated and detected with flow cytometry.
  • Among the gated viable cells around 1% cells are PKH26+ BAL cells of which with more than 80% are F4/80+CD11c+ macrophages
  • the anti-hResistin antibody inhibits hResistin-stimulated proliferation of human primary SMCs and exhibited a cross-reactive ability to block rodent RELM ⁇ actions in SMC assays.
  • FIG.16A hResistin dose dependently induced human primary SMC proliferation. Human bronchial SMCs (Lonza) were stimulated with the present inventors’ lab-made recombinant hResistin protein for 48 hours. Proliferation was quantified by 5-bromo-2’-deoxyuridine (BrdU) ELISA (Roche).
  • FIG.16B and 16C The anti-hResistin antibody
  • Anti- hResistin antibody blocked hResistin-induced proliferation of human bronchial SMCs (FIG.16B).
  • FIG.16C human pulmonary artery SMCs
  • FIG.16D-16F Anti-hResistin antibody (Ab) bind to mouse RELM ⁇ and block its induction of SMC proliferation.
  • FIG.16D Immunoprecipitation analysis of the binding of rat RELM ⁇ to Ab.
  • FIG.16E Rat RELM ⁇ protein dose dependently induced human SMC proliferation.
  • FIG.17 (supplemental to FIG.10).
  • SARS-CoV-2 spike protein upregulates TGF ⁇ and ⁇ -SMA by activating hResistin in monocytes.
  • Human THP-1 cells were treated with 10 ⁇ g/mL recombinant SARS-CoV-2 spike protein (DAGC149, Creative Diagnostics) for 6 hours (dose was chosen based on the present inventors’ preliminary study). In some groups, cells were pre-treated with anti-hResistin Ab (developed by the present inventors’ lab) at 3 ⁇ g/mL (a dose that blocks activities of hResistin protein without cytotoxic effects).
  • Nonimmunized IgG1 (Con Ab, Lonza) served as an isotype control.
  • FIG.18A-18F Potency of lead antibodies for blocking hResistin-stimulated proliferation of human smooth muscle cells (SMCs).
  • FIG.18A hResistin dose dependently induced human primary SMC proliferation. Human bronchial SMCs (Lonza) were stimulated with the present inventors’ lab-made recombinant hResistin protein for 48 hours.
  • FIG.18B and FIG. 18C Anti-hResistin antibody Ab-b blocked hResistin-induced proliferation of human SMCs.
  • the present inventors incubated 0.1-10 ⁇ g/mL Ab-b with hResistin recombinant protein for 20 minutes at room temperature before adding the mixture to human bronchial SMCs (FIG.19B).
  • FIG.18D-18F The other three lead anti-hResistin antibodies Ab-a (FIG.18D), Ab-c (FIG.18E), and Ab-d (FIG.18F) were incubated at the indicated doses with 3 ⁇ g/mL recombinant hResistin for 30 minutes at room temperature before being applied to human primary SMCs.
  • FIG.19A-19F Size exclusion high-performance liquid chromatography (SE-HPLC) analysis of the purified lead antibodies.
  • FIG.19A Plasmon resonance binding kinetics of lead antibodies to hResistin. Octet surface plasmon resonance evaluation of the kinetics of anti-hResistin antibodies Ab-a.
  • FIG.20A Ab-b (FIG.20B), Ab-c (FIG.20C) and Ab-d (FIG.20D) binding to recombinant hResistin.
  • Binding experiments were performed on a Biacore 3000. Antibodies were immobilized onto anti-Human-IgG sensors and their binding of 7 dilutions of recombinant hResistin protein were monitored in real time (FIG.20E). Association or disassociation with the surface causes a shift in wavelength of reflected light. Measuring the shift over time enabled the determination of binding kinetics. From the observed kon (ka) and koff (kd), equilibrium affinity KD (kd/ka) was determined.
  • FIG.21A-21E Lead antibody binds to an active epitope of hResistin.
  • FIG.21A Energy funnel plots were generated from Rosetta SnugDock protocol. Each point represents one candidate docked structure, the x-axis root-mean-squared-deviation of the antibody C ⁇ coordinate relative to the lowest-energy model, and the y-axis is a Rosetta score representing the energy of the interface.
  • FIG.21B shows
  • FIG.21C Monomer structure of hResistin, predicted using homology modelling from PDB structure 1RFX of mouse-resistin. 23, 49 FIG.21D. Docked pose of the antibody Ab-b with hResistin; the epitope region is highlighted in pink.
  • FIG.21E Detail of the interaction between the epitope and the CDR loops.
  • FIG.22A-22C Anti-hResistin antibodies bind to rat RELM ⁇ and block its induction of human smooth muscle cell (SMC) proliferation.
  • SMC smooth muscle cell
  • FIG.22B Rat RELM ⁇ protein dose dependently induced human SMC proliferation. Primary human bronchial SMCs were stimulated with lab-made recombinant rat RELM ⁇ protein for 48 hours.
  • FIG.22C The therapeutic antibody candidate Ab-b dose dependently inhibited SMC proliferation induced by rat RELM ⁇ .
  • Anti-hResistin antibodies (Ab) were incubated with lab-made recombinant rat RELM ⁇ protein for 20 minutes before they were applied to human primary SMCs for 48 hours.
  • FIG.23 A schematic illustration of experimental strategy for developing human antibodies that target hResistin for pulmonary hypertension (PH) treatment.
  • FIG.24 Post-stability study analysis of Ab-b after incubation under conditions of low pH, agitation, high temperature or freeze-thawing. Reduced and non-reduced Ab-b were electrophoresed. SDS-PAGE analysis shows a protein species band between 98 kDa and 198 kDa under non-reduced conditions (lanes 2, 4, 6, 8, 10, 12), which is consistent with the estimated molecular weight of the full-length antibody (146 kDa) and comparable to the predominant band seen for the inter-assay control antibody (lane 14).
  • FIG.25A-25H HPLC analysis of the protein stability of Ab-b. All samples were analyzed by SE-HPLC at 5 mg/ml on a Zorbax GF-2509.4 mm ID x 25 cm column (Agilent) as described in the Methods.
  • FIG.25G Nonimmunized human IgG1 served as an isotype control.
  • FIG.25H Monomer proportion and aggregation of Ab-b exposed to different incubation conditions were observed and summarized.
  • FIG.26A-26F cIEF analysis of the protein stability of Ab-b.
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, for example, hydroxyproline, gamma-carboxyglutamate, and O-phosphoserine, phosphothreonine.
  • amino acid analog refers to a compound that has the same basic chemical structure as a naturally occurring amino acid, i.e., a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group (e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium), but that contains some alteration not found in a naturally occurring amino acid (e.g., a modified side chain).
  • Amino acids and analogs are well known in the art. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
  • amino acid mimetic refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function in a manner similar to a naturally occurring amino acid.
  • Amino acid analogs may have modified R groups (for example, norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • an amino acid analog is a D-amino acid, a beta-amino acid, or an N- methyl amino acid.
  • antibody is meant any immunoglobulin polypeptide, or fragment thereof, having immunogen binding ability.
  • antibody fragments refer to a portion of an intact antibody.
  • antibody fragments include, but are not limited to, linear antibodies; single-chain antibody molecules; Fc or Fc’ peptides, Fab and Fab fragments, and multi-specific antibodies formed from antibody fragments.
  • the terms also refer to fragments that bind an antigen of a target molecule (e.g., Resistin) and can be referred to as “antigen-binding fragments.”
  • conjugate refers to a complex of two molecules linked together, for example, linked together by a covalent bond.
  • an antibody is linked to an effector molecule; for example, an antibody that specifically binds to Resistin covalently linked to an effector molecule.
  • the linkage can be by chemical or recombinant means.
  • the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule.
  • a peptide linker short peptide sequence
  • conjugates can be prepared from two molecules with separate functionalities, such as an antibody and an effector molecule, they are also sometimes referred to as “chimeric molecules.”
  • the terms “conjugating,” “joining,” “bonding,” “labeling” or “linking” refer to making two molecules into one contiguous molecule; for example, linking two polypeptides into one contiguous polypeptide, or covalently attaching an effector molecule or detectable marker radionuclide or other molecule to a polypeptide, such as an scFv.
  • the terms include reference to joining a ligand, such as an antibody moiety, to an effector molecule.
  • the linkage can be either by chemical or recombinant means.
  • “Chemical means” refers to a reaction between the antibody moiety and the effector molecule such that there is a covalent bond formed between the two molecules to form one molecule.
  • “Conservative” amino acid substitutions are those substitutions that do not substantially decrease the binding affinity of an antibody for an antigen (for example, the binding affinity of an antibody for Resistin).
  • a human antibody that specifically binds Resistin can include at most about 1, at most about 2, at most about 5, at most about 10, or at most about 15 conservative substitutions and specifically bind the Resistin polypeptide.
  • conservative variation also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that antibody retains binding affinity for Resistin.
  • Non-conservative substitutions are those that reduce an activity or binding to Resistin.
  • Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (I ), Lysine ( ); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).
  • effector molecule means a molecule intended to have or produce a desired effect; for example, a desired effect on a cell to which the effector molecule is targeted.
  • Effector molecules include such molecules as polypeptides, radioisotopes and small molecules.
  • Non-limiting examples of effector molecules include toxins, chemotherapeutic agents and anti-angiogenic agents. The skilled artisan will understand that some effector molecules may have or produce more than one desired effect.
  • an effector molecule is the portion of a chimeric molecule, for example a chimeric molecule that includes a disclosed antibody or fragment thereof, that is intended to have a desired effect on a cell to which the chimeric molecule is targeted.
  • epitopes or “antigenic determinant” are used interchangeably herein and refer to that portion of an antigen capable of being recognized and specifically bound by a particular antibody.
  • the antigen is a polypeptide
  • epitopes can be formed both from contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained upon protein denaturing, whereas epitopes formed by tertiary folding are typically lost upon protein denaturing.
  • An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation.
  • An antigenic determinant can compete with the intact antigen (i.e., the “immunogen” used to elicit the immune response) for binding to an antibody.
  • An “expression vector” is a nucleic acid construct, generated recombinantly or synthetically, bearing a series of specified nucleic acid elements that enable transcription of a particular gene in a host cell. Typically, gene expression is placed under the control of certain regulatory elements, including constitutive or inducible promoters, tissue-preferred regulatory elements, and enhancers.
  • fragment is meant a portion (e.g., at least about 5, 10, 25, 50, 100, 125, 150, 200, 250, 300, 350, 400, or 500 amino acids or nucleic acids) of a protein or nucleic acid molecule that is substantially identical to a reference protein or nucleic acid and retains at least one biological activity of the reference. In some embodiments the portion retains at least 50%, 75%, or 80%, or more preferably 90%, 95%, or even 99% of the biological activity of the reference protein or nucleic acid described herein.
  • a “host cell” is any prokaryotic or eukaryotic cell that contains either a cloning vector or an expression vector.
  • humanized forms of non-human (e.g., murine) antibodies are chimeric antibodies that contain minimal sequence, or no sequence, derived from non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
  • humanized antibodies can comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are generally made to further refine antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a nonhuman immunoglobulin and all or substantially all of the FR residues are those of a human immunoglobulin sequence.
  • the humanized antibody can also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. Examples of methods used to generate humanized antibodies are described in U.S.
  • human antibody as used herein means an antibody produced by a human or an antibody having an amino acid sequence corresponding to an antibody produced by a human made using any of the techniques known in the art. This definition of a human antibody includes intact or full-length antibodies, fragments thereof, and/or antibodies comprising at least one human heavy and/or light chain polypeptide such as, for example, an antibody comprising murine light chain and human heavy chain polypeptides. “Hybrid antibodies” are immunoglobulin molecules in which pairs of heavy and light chains from antibodies with different antigenic determinant regions are assembled together so that two different epitopes or two different antigens can be recognized and bound by the resulting tetramer.
  • isolated refers to material that is free to varying degrees from components which normally accompany it as found in its native state. Various levels of purity may be applied as needed according to this invention in the different methodologies set forth herein; the customary purity standards known in the art may be used if no standard is otherwise specified. Indeed, the term “purified” does not require the material to be present in a form exhibiting absolute purity, exclusive of the presence of other compounds.
  • isolated nucleic acids, peptides and proteins include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell, as well as, chemically synthesized nucleic acids.
  • An isolated nucleic acid, peptide or protein, for example an antibody can be at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% pure.
  • modulation is meant a change (increase or decrease) in the expression level or biological activity of a gene or polypeptide as detected by standard methods known in the art. As used herein, modulation includes at least about 10% change, 25%, 40%, 50% or a greater change in expression levels or biological activity (e.g., about 75%, 85%, 95% or more).
  • the term “mimetic” means an agent having a structure that is different from the general chemical structure of a reference agent, but that has at least one biological function of the reference.
  • the term “neutralizing antibody” refers to an antibody that is able to specifically bind to a target protein in such a way as to inhibit a biological function associated with that target protein. In general, any protein that can perform this type of specific blocking activity is considered a neutralizing protein; neutralizing antibodies are therefore a specific class of neutralizing protein.
  • nucleic acid refers to an oligomer or polymer of ribonucleic acid or deoxyribonucleic acid, or analog thereof.
  • oligomers consisting of naturally occurring bases, sugars, and intersugar (backbone) linkages as well as oligomers having non-naturally occurring portions which function similarly.
  • modified or substituted oligonucleotides are often preferred over native forms because of properties such as, for example, enhanced stability in the presence of nucleases.
  • Specific examples of some nucleic acids envisioned for this invention may contain phosphorothioates, phosphotriesters, methyl phosphonates, short chain alkyl or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic intersugar linkages.
  • oligonucleotides having morpholino backbone structures Seemerton, J. E. and Weller, D.
  • the phosphodiester backbone of the oligonucleotide may be replaced with a polyamide backbone, the bases being bound directly or indirectly to the aza nitrogen atoms of the polyamide backbone (P. E. Nielsen et al. Science 199: 254, 1997).
  • oligonucleotides may contain alkyl and halogen-substituted sugar moieties comprising one of the following at the 2’ position: OH, SH, SCH3, F, OCN, O(CH2)nNH2 or O(CH 2 ) n CH 3 , where n is from 1 to about 10; C 1 to C 10 lower alkyl, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF3; OCF3; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO 2 CH 3 ; ONO 2 ; NO 2 ; N 3 ; NH 2 ; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a conjugate; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligon
  • Oligonucleotides may also have sugar mimetics such as cyclobutyls in place of the pentofuranosyl group.
  • Other preferred embodiments may include at least one modified base form.
  • modified bases include 2-(amino)adenine, 2-(methylamino)adenine, 2-(imidazolylalkyl)adenine, 2- (aminoalklyamino)adenine, or other heterosubstituted alkyladenines.
  • operably linked means that a first polynucleotide is positioned adjacent to a second polynucleotide that directs transcription of the first polynucleotide when appropriate molecules (e.g., transcriptional activator proteins) are bound to the second polynucleotide.
  • recombinant is meant the product of genetic engineering or chemical synthesis.
  • positioned for expression is meant that the polynucleotide of the present invention (e.g., a DNA molecule) is positioned adjacent to a DNA sequence that directs transcription and translation of the sequence (i.e., facilitates the production of, for example, a recombinant protein of the present invention, or an RNA molecule).
  • binding refers to that binding which occurs between such paired species as antibody/antigen, aptamer/target, enzyme/substrate, receptor/agonist and lectin/carbohydrate which may be mediated by covalent or non-covalent interactions or a combination of covalent and non- covalent interactions.
  • the binding which occurs is typically electrostatic, hydrogen-bonding, or the result of lipophilic interactions.
  • “specific binding” occurs between a paired species where there is interaction between the two which produces a bound complex having the characteristics of, for example, an antibody/antigen.
  • the specific binding is characterized by the binding of one member of a pair to a particular species and to no other species within the family of compounds to which the corresponding member of the binding member belongs.
  • an antibody typically binds to a single epitope and to no other epitope within the family of proteins.
  • specific binding between an antigen and an antibody will have a binding affinity of at least 10 -6 M.
  • the antigen and antibody will bind with affinities of at least 10 -7 M, 10 -8 M to 10 -9 M, 10 -10 M, 10 -11 M, or 10 -12 M.
  • the term refers to a molecule (e.g., an antibody) that binds to a target (e.g., Resistin) with at least five- fold greater affinity as compared to any non-targets, e.g., at least 10-, 20-, 50-, or 100-fold greater affinity.
  • a target e.g., Resistin
  • substantially identical is meant a protein or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein).
  • such a sequence is at least 60%, more preferably 80% or 85%, and most preferably 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used for comparison.
  • Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis.53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs).
  • sequence analysis software for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis.53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs.
  • sequence analysis software for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis.53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs.
  • Such software matches identical or similar sequences by assign
  • Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
  • a BLAST program may be used, with a probability score between e.sup.-3 and e.sup.-100 indicating a closely related sequence.
  • transformed cell is meant a cell into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a polynucleotide molecule encoding (as used herein) a protein of the present invention.
  • B. Antibodies and Antigen-Binding Fragments Thereof The present invention provides antibodies to Resistin. In some embodiments, the antibodies are also cross-reactive with Resistin-Like Molecule Beta (RELMB).
  • An “antibody” is a polypeptide ligand including at least the complementarity determining regions (CDRs) of a light chain or heavy chain immunoglobulin variable region which specifically binds an epitope of an antigen or a fragment thereof.
  • Antibodies include intact immunoglobulins and the variants of them well known in the art, such as Fab’, F(ab)’2 fragments, single chain Fv proteins (scFv), and disulfide stabilized Fv proteins (dsFv).
  • scFv protein is a fusion protein in which a light chain variable region of an antibody and a heavy chain variable region of an antibody are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains.
  • the term “antibody” also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies) and heteroconjugate antibodies(such as, bispecific antibodies).
  • a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds.
  • Each heavy and light chain contains a constant region and a variable region (the regions are also known as domains).
  • References to “VH” or “VH” refer to the variable region of an immunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab.
  • VL refers to the variable region of an immunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.
  • the heavy and the light chain variable regions specifically bind the antigen.
  • Light and heavy chain variable regions contain a framework region interrupted by three hypervariable regions, also called complementarity- determining regions or CDRs. The extent of the framework region and CDRs have been defined (see, for example, Kabat et al., (1991) Sequences of Proteins of Immunological Interest, 5lh Edition, U.S.
  • the sequences of the framework regions of different light or heavy chains are relatively conserved within a species.
  • the framework region of an antibody that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.
  • the CDRs are primarily responsible for binding to an epitope of an antigen.
  • the precise amino acid sequence boundaries of a given CDR can be readily determined using any of a number of well-known schemes, including those described by Kabat et al. (1991), “Sequences of Proteins of Immunological Interest,” 5th Ed.
  • CDR1 is the CDR 1 from the variable domain of the heavy chain of the antibody in which it is found
  • LCDR 1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found.
  • An antibody that specifically binds an antigen of interest has a specific VH region and VL region sequence, and thus specific CDR sequences.
  • Antibodies with different specificities due to different combining sites for different antigens) have different CDRs. Although it is the CDRs that vary from antibody to antibody, only a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs).
  • a single-chain antibody (scFv) is a genetically engineered molecule containing the VH and VL domains of one or more antibody(ies) linked by a suitable polypeptide linker as a genetically fused single chain molecule.
  • Diabodies are bivalent, bispecific antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites.
  • a chimeric antibody is an antibody that contains one or more regions from one antibody and one or more regions from one or more other antibodies.
  • An antibody may have one or more binding sites. If there is more than one binding site, the binding sites may be identical to one another or may be different. For instance, a naturally-occurring immunoglobulin has two identical binding sites, a single-chain antibody or Fab fragment has one binding site, while a bispecific or bifunctional antibody has two different binding sites.
  • an antibody that specifically binds to Resistin is an antibody that binds substantially to Resistin, including cells or tissue expressing Resistin, substrate to which the Resistin is attached, or Resistin in a biological specimen. It is, of course, recognized that a certain degree of non-specific interaction may occur between an antibody or conjugate including an antibody (such as an antibody that specifically binds Resistin or conjugate including such antibody) and a non-target (such as a cell that does not express Resistin). Typically, specific binding results in a much stronger association between the antibody and protein or cells bearing the antigen than between the antibody and protein or cells lacking the antigen.
  • an antibody that binds Resistin is monoclonal.
  • the Resistin antibody is a polyclonal antibody.
  • the preparation and use of polyclonal antibodies are also known the skilled artisan.
  • the present invention also encompasses hybrid antibodies, in which one pair of heavy and light chains is obtained from a first antibody, while the other pair of heavy and light chains is obtained from a different second antibody. Such hybrids may also be formed using humanized heavy and light chains.
  • Such antibodies are often referred to as “chimeric” antibodies.
  • intact antibodies are said to contain “Fc” and “Fab” regions.
  • the Fc regions are involved in complement activation and are not involved in antigen binding.
  • An antibody from which the Fc’ region has been enzymatically cleaved, or which has been produced without the Fc’ region, designated an “F(ab ⁇ )2” fragment retains both of the antigen binding sites of the intact antibody.
  • an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region designated an “Fab’” fragment, retains one of the antigen binding sites of the intact antibody.
  • Fab ⁇ fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain, denoted “Fd.”
  • the Fd fragments are the major determinants of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity).
  • Isolated Fd fragments retain the ability to specifically bind to immunogenic epitopes.
  • Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein (1975) Nature 256:495. Using the hybridoma method, a mouse, hamster, or other appropriate host animal, is immunized as described above to elicit the production by lymphocytes of antibodies that will specifically bind to an immunizing antigen.
  • lymphocytes can be immunized in vitro. Following immunization, the lymphocytes are isolated and fused with a suitable myeloma cell line using, for example, polyethylene glycol, to form hybridoma cells that can then be selected away from unfused lymphocytes and myeloma cells.
  • a suitable myeloma cell line using, for example, polyethylene glycol, to form hybridoma cells that can then be selected away from unfused lymphocytes and myeloma cells.
  • Hybridomas that produce monoclonal antibodies directed specifically against a chosen antigen as determined by immunoprecipitation, immunoblotting, or by an in vitro binding assay such as radioimmunoassay (RIA) or enzyme-linked immunosorbent assay (ELISA) can then be propagated either in vitro culture using standard methods (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, 1986) or in vivo as ascites tumors in an animal.
  • the monoclonal antibodies can then be purified from the culture medium or ascites fluid as described for polyclonal antibodies above.
  • monoclonal antibodies can also be made using recombinant DNA methods as described in U.S. Pat. No.4,816,567.
  • the polynucleotides encoding a monoclonal antibody are isolated, such as from mature B-cells or hybridoma cell, such as by RT-PCR using oligonucleotide primers that specifically amplify the genes encoding the heavy and light chains of the antibody, and their sequence is determined using conventional procedures.
  • the isolated polynucleotides encoding the heavy and light chains are then cloned into suitable expression vectors, which when transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, monoclonal antibodies are generated by the host cells.
  • recombinant monoclonal antibodies or fragments thereof of the desired species can be isolated from phage display libraries as described (McCafferty et al., 1990, Nature, 348:552-554; Clackson et al., 1991, Nature, 352:624-628; and Marks et al., 1991, J. Mol. Biol., 222:581-597).
  • the polynucleotide(s) encoding a monoclonal antibody can further be modified in a number of different ways using recombinant DNA technology to generate alternative antibodies.
  • the constant domains of the light and heavy chains of, for example, a mouse monoclonal antibody can be substituted 1) for those regions of, for example, a human antibody to generate a chimeric antibody or 2) for a non-immunoglobulin polypeptide to generate a fusion antibody.
  • the constant regions are truncated or removed to generate the desired antibody fragment of a monoclonal antibody.
  • site-directed or high-density mutagenesis of the variable region can be used to optimize specificity, affinity, etc. of a monoclonal antibody.
  • the monoclonal antibody against Resistin is a humanized antibody.
  • Humanized antibodies are antibodies that contain minimal sequences from non-human (e.g., murine) antibodies within the variable regions. In practice, humanized antibodies are typically human antibodies with minimum to no non-human sequences.
  • a human antibody is an antibody produced by a human or an antibody having an amino acid sequence corresponding to an antibody produced by a human. Humanized antibodies can be produced using various techniques known in the art.
  • An antibody can be humanized by substituting the CDR of a human antibody with that of a non-human antibody (e.g., mouse, rat, rabbit, hamster, etc.) having the desired specificity, affinity, and capability (Jones et al., 1986, Nature, 321:522-525; Riechmann et al., 1988, Nature, 332:323-327; Verhoeyen et al., 1988, Science, 239:1534-1536).
  • the humanized antibody can be further modified by the substitution of additional residue either in the Fv framework region and/or within the replaced non-human residues to refine and optimize antibody specificity, affinity, and/or capability.
  • Human antibodies can be directly prepared using various techniques known in the art.
  • Immortalized human B lymphocytes immunized in vitro or isolated from an immunized individual that produce an antibody directed against a target antigen can be generated (See, for example, Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p.77 (1985); Boerner et al., 1991, J. Immunol., 147 (1):86-95; and U.S. Pat. No.5,750,373).
  • the human antibody can be selected from a phage library, where that phage library expresses human antibodies (Vaughan et al., 1996, Nature Biotechnology, 14:309-314; Sheets et al., 1998, PNAS, 95:6157-6162; Hoogenboom and Winter, 1991, J. Mol. Biol., 227:381; Marks et al., 1991, J. Mol. Biol., 222:581). Humanized antibodies can also be made in transgenic mice containing human immunoglobulin loci that are capable upon immunization of producing the full repertoire of human antibodies in the absence of endogenous immunoglobulin production. This approach is described in U.S. Pat.
  • antibody fragments can be isolated from the antibody phage libraries discussed above.
  • the antibody fragment can also be linear antibodies as described in U.S. Pat. No.5,641,870, for example, and can be monospecific or bispecific. Other techniques for the production of antibody fragments will be apparent.
  • the present invention further embraces variants and equivalents which are substantially homologous to the chimeric, humanized and human antibodies, or antibody fragments thereof, set forth herein. These can contain, for example, conservative substitution mutations, i.e., the substitution of one or more amino acids by similar amino acids.
  • conservative substitution refers to the substitution of an amino acid with another within the same general class such as, for example, one acidic amino acid with another acidic amino acid, one basic amino acid with another basic amino acid or one neutral amino acid by another neutral amino acid. What is intended by a conservative amino acid substitution is well known in the art.
  • the hResistin therapeutic antibody comprises clone 13, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:73 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:73, and the light chain variable region comprises SEQ ID NO:77 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:77.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:74-76, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:74-76, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:78-80, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:78-80.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:72 or a conservative substitution at up to 5 amino acids of SEQ ID NO:72.
  • the hResistin therapeutic antibody comprises clone 42, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:163 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:163, and the light chain variable region comprises SEQ ID NO:167 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:167.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:164-166, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:164-166, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:168-170, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:168-170.
  • the hResistin antibody or antigen-binding fragment thereof comprises a single chain variable fragment (scFv) or antigen-binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:162 or a conservative substitution at up to 5 amino acids of SEQ ID NO:162.
  • the hResistin therapeutic antibody comprises clone 2, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:13 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:13, and the light chain variable region comprises SEQ ID NO:17 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:17.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:14-16, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:14-16, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:18-20, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:18-20.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:12 or a conservative substitution at up to 5 amino acids of SEQ ID NO:12.
  • the hResistin therapeutic antibody comprises clone 11, as described in U.S. Patent No.10,822,407.
  • the hResistin antibody comprises an anti-Resistin antibody or antigen-binding fragment thereof comprising a heavy chain variable region and a light chain variable region, wherein the heavy chain variable region comprises SEQ ID NO:63 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:63, and the light chain variable region comprises SEQ ID NO:67 or a conservative substitution at up to 5 amino acid positions of SEQ ID NO:67.
  • the hResistin antibody or antigen-binding fragment thereof comprises (a) a heavy chain variable region comprising CDRs 1, 2 and 3 comprising SEQ ID NOS:64-66, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:64-66, and (b) a light chain variable region comprising CDRs 1, 2, and 3 comprising SEQ ID NOS:68-70, respectively, or a conservative substitution at up to 2 amino acids of one or more of SEQ ID NOS:68-70.
  • the hResistin antibody or antigen- binding fragment thereof comprises a single chain variable fragment (scFv) or antigen- binding fragment thereof that binds Resistin, wherein the scFv comprises SEQ ID NO:62 or a conservative substitution at up to 5 amino acids of SEQ ID NO:62.
  • scFv single chain variable fragment
  • the antibody comprises a variable heavy chain comprising SEQ ID NO:3, SEQ ID NO:13, SEQ ID NO:23, SEQ ID NO:33, SEQ ID NO:43, SEQ ID NO:53, SEQ ID NO:63, SEQ ID NO:73, SEQ ID NO:83, SEQ ID NO:93, SEQ ID NO:103, SEQ ID NO:113, SEQ ID NO:123, SEQ ID NO:133, SEQ ID NO:143, SEQ ID NO:153, SEQ ID NO:163, or fragments thereof.
  • the antibody comprises a variable heavy chain that is at least 90% identical to SEQ ID NO:3, SEQ ID NO:13, SEQ ID NO:23, SEQ ID NO:33, SEQ ID NO:43, SEQ ID NO:53, SEQ ID NO:63, SEQ ID NO:73, SEQ ID NO:83, SEQ ID NO:93, SEQ ID NO:103, SEQ ID NO:113, SEQ ID NO:123, SEQ ID NO:133, SEQ ID NO:143, SEQ ID NO:153, SEQ ID NO:163, or fragments thereof.
  • the antibody comprises a light chain comprising SEQ ID NO:7, SEQ ID NO:17, SEQ ID NO:27, SEQ ID NO:37, SEQ ID NO:47, SEQ ID NO:57, SEQ ID NO:67, SEQ ID NO:77, SEQ ID NO:87, SEQ ID NO:97, SEQ ID NO:107, SEQ ID NO:117, SEQ ID NO:127, SEQ ID NO:137, SEQ ID NO:147, SEQ ID NO:157, SEQ ID NO:167, or fragments thereof.
  • the antibody comprises a light chain that is at least 90% identical to SEQ ID NO:7, SEQ ID NO:17, SEQ ID NO:27, SEQ ID NO:37, SEQ ID NO:47, SEQ ID NO:57, SEQ ID NO:67, SEQ ID NO:77, SEQ ID NO:87, SEQ ID NO:97, SEQ ID NO:107, SEQ ID NO:117, SEQ ID NO:127, SEQ ID NO:137, SEQ ID NO:147, SEQ ID NO:157, SEQ ID NO:167, or fragments thereof.
  • variable domain of the heavy chain comprises one or more complementarity determining regions (CDRs) selected from the group consisting of SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:4, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:104, SEQ ID NO:
  • CDRs complementarity
  • variable domain of the heavy chain comprises one or more complementarity determining regions (CDRs) that are at least 90% identical to a CDR selected from the group consisting of SEQ ID NO:4, SEQ ID NO:15, SEQ ID NO:6, SEQ ID NO:14, SEQ ID NO:5, SEQ ID NO:16, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:74, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:4, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:
  • variable domain of the light chain comprises one or more CDRs selected from the group consisting of SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:40, SEQ ID NO
  • variable domain of the light chain comprises one or more CDRs that are at least 90% identical to a CDR selected from the group consisting of SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:68, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:80, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:108, SEQ ID NO:9,
  • the present invention provides a scfv that binds human Resistin, wherein the scfv is encoded by SEQ ID NO:1, SEQ ID NO:11, SEQ ID NO:21, SEQ ID NO:31, SEQ ID NO:41, SEQ ID NO:51, SEQ ID NO:61, SEQ ID NO:71, SEQ ID NO:81, SEQ ID NO:91, SEQ ID NO:101, SEQ ID NO:111, SEQ ID NO:121, SEQ ID NO:131, SEQ ID NO:141, SEQ ID NO:151, SEQ ID NO:161 or fragments thereof.
  • the scfv is encoded by nucleotide sequence that is at least 90% identical to SEQ ID NO:1, SEQ ID NO:11, SEQ ID NO:21, SEQ ID NO:31, SEQ ID NO:41, SEQ ID NO:51, SEQ ID NO:61, SEQ ID NO:71, SEQ ID NO:81, SEQ ID NO:91, SEQ ID NO:101, SEQ ID NO:111, SEQ ID NO:121, SEQ ID NO:131, SEQ ID NO:141, SEQ ID NO:151, SEQ ID NO:161 or fragments thereof.
  • the present invention also provides a scfv that binds human Resistin, wherein the scfv comprises SEQ ID NO:2, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:52, SEQ ID NO:62, SEQ ID NO:72, SEQ ID NO:82, SEQ ID NO:92, SEQ ID NO:102, SEQ ID NO:112, SEQ ID NO:122, SEQ ID NO:132, SEQ ID NO:142, SEQ ID NO:152, SEQ ID NO:162 or fragments thereof.
  • the scfv comprises an amino acid sequence that is at least 90% identical to SEQ ID NO:2, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:52, SEQ ID NO:62, SEQ ID NO:72, SEQ ID NO:82, SEQ ID NO:92, SEQ ID NO:102, SEQ ID NO:112, SEQ ID NO:122, SEQ ID NO:132, SEQ ID NO:142, SEQ ID NO:152, SEQ ID NO:162 or fragments thereof.
  • the antibodies of the present invention can further comprise a constant domain comprising SEQ ID NO:172, SEQ ID NO:174 or a fragment thereof.
  • the antibodies can further comprise a constant domain that is at least 90% identical to SEQ ID NO:172, SEQ ID NO:174 or a fragment thereof.
  • the present invention also provides a Resistin antibody comprising a heavy chain selected from the group consisting of SEQ ID NO:176, SEQ ID NO:180, SEQ ID NO:184, SEQ ID NO:188, SEQ ID NO:192, SEQ ID NO:196, SEQ ID NO:200, SEQ ID NO:204, SEQ ID NO:208, SEQ ID NO:212, SEQ ID NO:216, SEQ ID NO:220, SEQ ID NO:224, SEQ ID NO:228, SEQ ID NO:232, SEQ ID NO:236, and SEQ ID NO:240.
  • a Resistin antibody comprises a light chain selected from the group consisting of SEQ ID NO:178, SEQ ID NO:182, SEQ ID NO:186, SEQ ID NO:190, SEQ ID NO:194, SEQ ID NO:198, SEQ ID NO:202, SEQ ID NO:206, SEQ ID NO:210, SEQ ID NO:214, SEQ ID NO:218, SEQ ID NO:222, SEQ ID NO:226, SEQ ID NO:230, SEQ ID NO:234, SEQ ID NO:238, and SEQ ID NO: 242.
  • the present invention provides a Resistin antibody comprising (a) a heavy chain selected from the group consisting of SEQ ID NO:176, SEQ ID NO:180, SEQ ID NO:184, SEQ ID NO:188, SEQ ID NO:192, SEQ ID NO:196, SEQ ID NO:200, SEQ ID NO:204, SEQ ID NO:208, SEQ ID NO:212, SEQ ID NO:216, SEQ ID NO:220, SEQ ID NO:224, SEQ ID NO:228, SEQ ID NO:232, SEQ ID NO:236, and SEQ ID NO:240 and (b) a light chain selected from the group consisting of SEQ ID NO:178, SEQ ID NO:182, SEQ ID NO:186, SEQ ID NO:190, SEQ ID NO:194, SEQ ID NO:198, SEQ ID NO:202, SEQ ID NO:206, SEQ ID NO:210, SEQ ID NO:214, SEQ ID NO:218, SEQ ID NO:222, SEQ ID NO:
  • the present invention provides Resistin antibodies that are also cross-reactive with Resistin Like Molecule Beta (RELM ⁇ ).
  • Resistin scfv are also cross-reactive with RELM ⁇ .
  • the antibodies and/or fragments thereof are recombinant.
  • RNA Interference Compositions for Targeting Resistin mRNA the expression of Resistin may be inhibited by the use of RNA interference techniques (RNAi).
  • RNAi is a remarkably efficient process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA in animals and plant cells.
  • RNAi can be triggered, for example, by nucleotide (nt) duplexes of small interfering RNA (siRNA), micro-RNAs (miRNA), functional small-hairpin RNA (shRNA), or other dsRNAs which are expressed in-vivo using DNA templates with RNA polymerase III promoters.
  • a ribonucleic acid (RNA) interfering (RNAi) composition comprises about 18-25 nucleotides that is complementary to SEQ ID NO:244, wherein the RNAi composition is capable of inhibiting the expression of human Resistin.
  • RNAi composition is a small interfering RNA (siRNA), a short hairpin RNA (shRNA), double stranded RNA (dsRNA), and RNA construct or an anti-sense oligonucleotide.
  • shRNA small interfering RNA
  • shRNA short hairpin RNA
  • dsRNA double stranded RNA
  • shRNA shRNA for knocking down Resistin expression comprising SEQ ID NO:246 or SEQ ID NO:247.
  • RNA and DNA which can be a gene or a portion thereof, a cDNA, a synthetic polydeoxyribonucleic acid sequence, or the like, and can be single stranded or double stranded, as well as a DNA/RNA hybrid.
  • RNA interference refers to the silencing or decreasing of gene expression by siRNAs. It is the process of sequence-specific, post- transcriptional gene silencing in animals and plants, initiated by siRNA that is homologous in its duplex region to the sequence of the silenced gene.
  • the gene may be endogenous or exogenous to the organism, present integrated into a chromosome or present in a transfection vector that is not integrated into the genome.
  • the expression of the gene is either completely or partially inhibited.
  • RNAi inhibits the gene by compromising the function of a target RNA, completely or partially.
  • Both plants and animals mediate RNAi by the RNA-induced silencing complex (RISC); a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger.
  • RISC RNA-induced silencing complex
  • RISC a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger.
  • RISC is known to contain short RNAs derived from the double-stranded RNA trigger. The short RNA sequences are homologous to the target gene that is being suppressed.
  • shRNA or “short hairpin RNA” refers to a sequence of ribonucleotides comprising a single-stranded RNA polymer that makes a tight hairpin turn on itself to provide a “double- stranded “or duplexed region.
  • shRNA can be used to silence gene expression via RNA interference.
  • shRNA hairpin is cleaved into short interfering RNAs (siRNA) by the cellular machinery and then bound to the RNA-induced silencing complex (RISC). The complex inhibits RNA as a consequence of the complexed siRNA hybridizing to and cleaving RNAs that match the siRNA that is bound thereto.
  • siRNA short interfering RNAs
  • siRNA refers to a short interfering RNA.
  • small interfering RNA and “siRNA” refer to short interfering RNA or silencing RNA, which are a class of short double-stranded RNA molecules that play a variety of biological roles. Most notably, siRNA is involved in the RNA interference (RNAi) pathway where the siRNA interferes with the expression of a specific gene.
  • RNAi RNA interference
  • siRNAs comprise a duplex, or double-stranded region, of about 18-25 nucleotides long; often siRNAs contain from about two to four unpaired nucleotides at the 3’ end of each strand.
  • At least one strand of the duplex or double- stranded region of a siRNA is substantially homologous to or substantially complementary to a target RNA molecule.
  • the strand complementary to a target RNA molecule is the “antisense strand”; the strand homologous to the target RNA molecule is the “sense strand”, and is also complementary to the siRNA antisense strand.
  • siRNAs may also contain additional sequences; non-limiting examples of such sequences include linking sequences, or loops, as well as stem and other folded structures.
  • an antisense refers to a polynucleotide or oligonucleotide molecule that is substantially complementary or 100% complementary to a particular polynucleotide or oligonucleotide molecule (RNA or DNA), i.e., a “sense” strand, or portion thereof.
  • RNA or DNA polynucleotide or oligonucleotide molecule
  • an antisense molecule may be complementary in whole or in part to a molecule of messenger RNA, miRNA, pRNA, tRNA, rRNA of hnRNA, or a sequence of DNA that is either coding or non-coding.
  • Polynucleotides of the present invention may be of any suitable length.
  • RNAi compositions/molecules to be used to regulate gene expression.
  • Such molecules are typically from about 5 to 100, 5 to 50, 5 to 45, 5 to 40, 5 to 35, 5 to 30, 5 to 25, 5 to 20, or 10 to 20 nucleotides in length.
  • the molecule may be about 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 45 or 50 nucleotides in length.
  • Such polynucleotides may include from at least about 15 to more than about 120 nucleotides, including at least about 16 nucleotides, at least about 17 nucleotides, at least about 18 nucleotides, at least about 19 nucleotides, at least about 20 nucleotides, at least about 21 nucleotides, at least about 22 nucleotides, at least about 23 nucleotides, at least about 24 nucleotides, at least about 25 nucleotides, at least about 26 nucleotides, at least about 27 nucleotides, at least about 28 nucleotides, at least about 29 nucleotides, at least about 30 nucleotides, at least about 35 nucleotides, at least about 40 nucleotides, at least about 45 nucleotides, at least about 50 nucleotides, at least about 55 nucleotides, at least about 60 nucleotides, at least about 65 nucleotides, at least about 70 nucleo
  • the terms “complementary” or “complement” refer to a nucleic acid comprising a sequence of consecutive nucleobases or semi consecutive nucleobases (e.g., one or more nucleobase moieties are not present in the molecule) capable of hybridizing to another nucleic acid strand or duplex even if less than all the nucleobases do not base pair with a counterpart nucleobase.
  • a “complementary” nucleic acid comprises a sequence in which about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100%, and any range derivable therein, of the nucleobase sequence is capable of base-pairing with a single or double stranded nucleic acid molecule during hybridization.
  • the term “complementary” refers to a nucleic acid that may hybridize to another nucleic acid strand or duplex in stringent conditions, as would be understood by one of ordinary skill in the art.
  • the term “homologous” or “% identity” as used herein means a nucleic acid (or fragment thereof) or a protein (or a fragment thereof) having a degree of homology to the corresponding natural reference nucleic acid or protein that may be in excess of 70%, or in excess of 80%, or in excess of 85%, or in excess of 90%, or in excess of 91%, or in excess of 92%, or in excess of 93%, or in excess of 94%, or in excess of 95%, or in excess of 96%, or in excess of 97%, or in excess of 98%, or in excess of 99%.
  • the percentage of homology or identity as described herein is typically calculated as the percentage of amino acid residues found in the smaller of the two sequences which align with identical amino acid residues in the sequence being compared, when four gaps in a length of 100 amino acids may be introduced to assist in that alignment (as set forth by Dayhoff, in Atlas of Protein Sequence and Structure, Vol.5, p.124, National Biochemical Research Foundation, Washington, D.C. (1972)).
  • the percentage homology as described above is calculated as the percentage of the components found in the smaller of the two sequences that may also be found in the larger of the two sequences (with the introduction of gaps), with a component being defined as a sequence of four, contiguous amino acids.
  • sequence identity or homology can be determined by comparing the sequences when aligned so as to maximize overlap and identity while minimizing sequence gaps.
  • sequence identity may be determined using any of a number of mathematical algorithms.
  • a non-limiting example of a mathematical algorithm used for comparison of two sequences is the algorithm of Karlin & Altschul, Proc. Natl. Acad. Sci. USA 1990, 87, 2264-2268, modified as in Karlin & Altschul, Proc. Natl. Acad. Sci. USA 1993, 90, 5873-5877.
  • % identity represents the number of amino acids or nucleotides which are identical at corresponding positions in two sequences of a protein or nucleic acids, respectively. For example, two amino acid sequences each having 100 residues will have 95% identity when 95 of the amino acids at corresponding positions are the same. Similarly, two nucleic acid sequences each having 100 bases will have 95% identity when 95 of the bases at corresponding positions are the same.
  • Another example of a mathematical algorithm used for comparison of sequences is the algorithm of Myers & Miller, CABIOS 1988, 4, 11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • a PAM120 weight residue table When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Yet another useful algorithm for identifying regions of local sequence similarity and alignment is the FASTA algorithm as described in Pearson & Lipman, Proc. Natl. Acad. Sci. USA 1988, 85, 2444-2448. Another algorithm is the WU-BLAST (Washington University BLAST) version 2.0 software (WU-BLAST version 2.0 executable programs for several UNIX platforms).
  • This program is based on WU-BLAST version 1.4, which in turn is based on the public domain NCBI-BLAST version 1.4 (Altschul & Gish, 1996, Local alignment statistics, Doolittle ed., Methods in Enzymology 266, 460-480; Altschul et al., Journal of Molecular Biology 1990, 215, 403-410; Gish & States, Nature Genetics, 1993, 3: 266-272; Karlin & Altschul, 1993, Proc. Natl. Acad. Sci. USA 90, 5873-5877; all of which are incorporated by reference herein).
  • the default amino acid comparison matrix is BLOSUM62, but other amino acid comparison matrices such as PAM can be utilized.
  • the terms “modified” and “modification” when used in the context of the constituents of a nucleotide monomer, i.e., sugar, nucleobase and intemucleoside linkage (backbone), refer to non-natural changes to the chemical structure of these naturally occurring constituents or the substitutions of these constituents with non-naturally occurring ones, i.e., mimetics.
  • the “unmodified” or “naturally occurring” sugar ribose (of RNA) can be modified by replacing the hydrogen at the 2’-position of ribose with a methyl group.
  • the naturally occurring intemucleoside linkage of nucleic acids is a 3’ to 5’ phosphodiester linkage that can be modified, in one embodiment, by replacing one of the non-bridging oxygen atoms of the phosphate linker with a sulfur atom to create a phosphorothioate linkage.
  • Modified oligonucleotides are structurally distinguishable, but functionally interchangeable with naturally occurring or synthetic unmodified oligonucleotides and usually have enhanced properties such as increased resistance to degradation by exonucleases and endonucleases, or increased binding affinity.
  • modifications to the oligonucleotides of the present invention encompass substitutions or changes in internucleoside linkages, sugar moieties, or nucleobases.
  • non-natural or “unnatural” refers to an oligonucleotide which comprises at least one modification in an internucleoside linkage, a sugar, and/or a nucleobase thereof, wherein such modified intemucleoside linkage, modified sugar, and/or modified nucleobase is not found naturally in DNA or RNA (unless specifically defined otherwise herein)
  • Non-naturally occurring intemucleoside linkages of the oligonucleotides of the present invention include those that contain a phosphorus atom and also those that do not contain a phosphorus atom.
  • phosphoms -containing modified oligonucleotide backbones are known in the art and may be used in the oligonucleotides of the present invention.
  • Examples of phosphoms -containing intemucleoside linkages of non-natural (modified) oligonucleotide backbones which may occur in the presently disclosed oligonucleotides include, but are not limited to, phosphorothioate, phosphorodithioate, phosphoramidite, phosphorodiamidate, morpholino, phosphotriester, aminoalkylphosphotriester, phosphonate, chiral phosphorothioates, methyl and other alkyl phosphonates including 3’-alkylene phosphonate, 5’-alkylene phosphonate and chiral phosphonate, phosphinate, phosphoramidates including 3’-amino phosphoramidate and aminoalkylphosphoramidate, thionophosphoramidate,
  • U.S. patents that teach the preparation of such phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos.3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,194,599; 5,565,555; 5,527,899; 5,721,218; 5,672,697 and 5,625,050.
  • the intemucleoside linkages are without phosphorus atoms and may instead comprise short chain alkyl or cycloalkyl intemucleoside linkages, mixed heteroatom and alkyl or cycloalkyl intemucleoside linkages, or one or more short chain heteroatomic or heterocyclic intemucleoside linkages.
  • the non-naturally occurring intemucleoside linkages are uncharged and in others, the linkages are achiral.
  • the non-naturally occurring intemucleoside linkages are uncharged and achiral, such as peptide nucleic acids (PNAs).
  • oligonucleotides of the present invention may be defined by a complementary correspondence to a sequence or SEQ ID NO disclosed herein, or segment thereof, and may comprise, independently, one or more modifications to a sugar moiety, an intemucleoside linkage, or a nucleobase.
  • oligonucleotide backbones include siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; riboacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CPU component parts.
  • both the sugar moiety and the intemucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with non- natural groups.
  • One such oligomeric compound is referred to as a peptide nucleic acid (PNA).
  • PNA peptide nucleic acid
  • the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone.
  • the nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
  • the oligonucleotide can be further modified so as to be conjugated to an organic moiety such as a biogenic molecule that is selected to improve stability, distribution and/or cellular uptake of the oligonucleotide, e.g., cholesterol, forming the nucleic acid compound of the present invention.
  • an organic moiety can be attached, e.g., to the 3’ or 5’ end of the oligonucleotide, and/or at the 2’ position of the sugar moiety of a nucleotide of the oligonucleotide, such as the 2’ ribose position.
  • the nucleic acid compound can further be in isolated form or can be part of a pharmaceutical composition, such as a pharmaceutical composition formulated for parental administration.
  • the pharmaceutical compositions can contain one or more nucleic acid compounds, and in some embodiments can contain two or more inhibitory nucleic acid compounds, each one directed to a different target gene.
  • C. Delivery The RNAi composition or oligonucleotide composition can be delivered in any of a variety of forms, including in liposomes and via expression vectors.
  • the composition can be endogenously expressed from transcription units inserted into DNA or RNA vectors.
  • the recombinant vectors can be DNA plasmids or viral vectors for example.
  • Viral vectors suitable for producing the oligonucleotide composition capable of reducing Resistin expression or activity can be constructed based on, but not limited to, adeno-associated vims, retrovirus, lentivirus, adenovirus, or alphavirus.
  • the recombinant vectors which contain a nucleic acid for expressing the oligonucleotide composition can be delivered as described above and can persist in target cells.
  • viral vectors can be used that provide for transient expression of the oligonucleotides. Such vectors can be repeatedly administered as necessary.
  • the delivery vehicles (vectors) for the oligonucleotide composition optionally comprise an expression construct which includes an enhancer sequence, a promoter sequence, and other sequences necessary for expression of the products of the Resistin oligonucleotide sequence.
  • the promoter is cell-specific.
  • the term “cell-specific” means that the particular promoter selected for the recombinant vector can direct expression of the selected transgene only in a particular cell type.
  • vectors which may be used include, but are not limited to, adeno-associated virus vectors, an attenuated or gutless adenoviral vectors, lentiviral vectors, retroviral vectors, herpes virus vectors, and Sindbis virus vectors, papilloma virus vectors, as well as plasmids or synthetic (non-viral) vectors, and/or nanoparticles.
  • the vectors may be either monocistronic, bicistronic, or multicistronic.
  • a recombinant vector (e.g., lenti-, AAV) sequence can be packaged as a “particle” for subsequent infection (transduction) of a cell, ex vivo, in vitro or in vivo.
  • a recombinant vector sequence is encapsulated or packaged into an AAV particle
  • the particle can also be referred to as a “rAAV.”
  • Such particles include proteins that encapsulate or package the vector genome.
  • Particular examples include viral envelope proteins, and in the case of AAV, capsid proteins.
  • Any suitable route of administration of the oligonucleotide-containing vector may be employed.
  • parenteral subcutaneous, subretinal, suprachoroidal, intramuscular, intravenous, transdermal
  • Dosage formulations include injections, implants, or other known and effective gene therapy delivery methods.
  • Delivery of the oligonucleotide-expressing vectors can be systemic, such as by intravenous or intra-muscular administration, direct administration to a site, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.
  • the therapeutic and/or pharmaceutical compositions in non-limiting embodiments, contain viral particles per dose in a range of, for example, from about 10 4 to about 10 11 particles, from about 10 5 to about 10 10 particles, or from about 10 6 to about 10 9 particles.
  • vector genomes are provided in in a range of, for example, from about 10 4 to about 10 14 vector genomes, from about 10 5 to about 10 13 vector genomes, from about 10 6 to about 10 13 vector genomes, from about 10 7 to about 10 13 vector genomes, from about 10 8 to about 10 13 vector genomes, or from about 10 9 to about 10 13 vector genomes. Because nucleases that cleave the phosphodiester linkages are expressed in almost every cell, unmodified nucleic acid molecules such as the inhibitory oligonucleotide compositions of the present invention may be modified to resist degradation, as described above for example.
  • oligonucleotides may be conjugated to the oligonucleotides to improve their ability to resist degradation, target certain cells, or to cross barriers like cell membranes or the blood brain barrier.
  • examples of such molecules include lipids such as, but not limited to, stearic acid, palmitic acid, docosanoic acid, docosahexanoic acid, docosahexaenoic acid, cholesterol, tocopherol, and other C12-C22 saturated or unsaturated fatty acids; peptides such as but not limited to, cell-penetrating peptides (CPPs) such as penetratin, HIV-1 Tat peptides, pVEC-Cadherin 615-634, polyarginines (6-12), and transportan, linear and cyclic RGD- containing peptides, and SPACE peptide; receptor- specific ligands; aptamers (synthetic oligoribonucleotides); antibodies or antibody fragments; C
  • the molecule may be conjugated to the oligonucleotide composition by any suitable means, such as via linker or a cleavable bond such as but not limited to disulfide, thioether, pH sensitive (e.g., hydrazone or carboxymethylmaleic anhydride), or ethylene glycol.
  • the oligonucleotides or nucleic acid compositions of the present invention may be delivered in the form of nanoparticles and microparticles which encapsulate the nucleic acid compounds within liposomes of cationic lipids or within PEG, for example.
  • These delivery systems can enhance intracellular delivery either by protecting the nucleic acid compound from nuclease degradation and/or by promoting absorptive endocytosis. Further, in particular embodiments, the addition of dioleylphosphatidylethanolamine to liposome delivery systems results in the destabilization of endosomal membranes and promotion of release of the oligonucleotide after endocytosis.
  • the nucleic acid compounds can be administered to cells by a variety of other methods known to those of skill in the art, including, but not limited to, ionophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors.
  • the nucleic acid compounds can be delivered via the nanoparticle system shown in U.S. Patent Application Publication 2019/0255088.
  • the liposomes may comprise amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous solution.
  • Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent Nos.4,235,871; 4,501,728; 4,837,028; and 4,737,323.
  • the nanoparticles which contain the nucleic acid compounds of the present invention may comprise a pharmaceutically acceptable carrier such as, but not limited to, poly(ethylene-co-vinyl acetate), PVA, partially hydrolyzed poly(ethylene-co-vinyl acetate), poly(ethylene-co-vinyl acetate-co-vinyl alcohol), a cross-linked poly/ethylene-co- vinyl acetate), a cross-linked partially hydrolyzed poly (ethylene-co -vinyl acetate), a cross- linked poly(ethylene-co-vinyl acetate-co-vinyl alcohol), poly-D,L-lactic acid, poly-L-lactic acid, polyglycolic acid, PGA, copolymers of lactic acid and glycolic acid, polycaprolactone, polyvalerolactone, poly (anhydrides), copolymers of polycaprolactone with polyethylene glycol, copolymers of polylactic acid with polyethylene glycol, polyethylene glycol; fibrin, Gelf
  • Copolymers can comprise from about 1% to about 99% by weight of a first monomer unit such as ethylene oxide and from 99% to about 1% by weight of a second monomer unit such as propylene oxide.
  • Blends of a first polymer such as gelatin and a second polymer such as poly-L-lactic acid or polyglycolic acid can comprise from about 1% to about 99% by weight of the first polymer and from about 99% to about 1% of the second polymer.
  • the nucleic acid compositions can be delivered directly by systemic administration such as using oral formulations or stereotactic injection into prostate or prostate tumor, typically in saline with chemical modifications to enable uptake, or other methods described elsewhere herein.
  • the oligonucleotide of the nucleic acid compound has a phosphorothioate backbone
  • the oligonucleotide binds to serum proteins, slowing excretion by the kidney.
  • the aromatic nucleobases also interact with other hydrophobic molecules in serum and on cell surfaces.
  • siRNA delivery systems involve complexing the RNA with cationic and neutral lipids, although encouraging results have also been obtained using peptide transduction domains and cationic polymers. Including PEGylated lipids in the formulation prolongs the circulating half-life of the particles.
  • one type of optimization of single-stranded DNA or RNA oligonucleotides is the use of chemical modifications to increase the nuclease resistance such as the introduction of phosphorothioate (“PS”) linkages in place of the phosphodiester bond.
  • PS linkages also improved binding to serum proteins in vivo, increasing half-life and permitting greater delivery of active compound to tissues.
  • Chemical modifications to subunits of the nucleotides can also improve potency and selectivity by increasing binding affinity of oligonucleotides for their complementary sequences.
  • nucleoside sugars examples include 2’-0-methyl (2’-O-Me), 2’-fluoro (2’-F), and 2’-0-methoxyethyl (2’-MOE) RNA, and others as discussed elsewhere herein.
  • LNA locked nucleic acid
  • BNA bridged nucleic acid
  • the therapeutic agents can be complexed, conjugated, encapsulated or otherwise associated with a dendrimer.
  • Dendrimers are three-dimensional, hyperbranched, monodispersed, globular and polyvalent macromolecules including surface end groups. Due to their unique structural and physical features, dendrimers have shown unprecedented potential as nano-carriers for various biomedical applications including targeted drug/gene delivery, imaging and diagnosis. See U.S. Patent Nos.10,918,820 and 10,369,124, as well as U.S. Patent Application Publication No.20220080056, No. 20220071923, No.20210353823, No.20210252153, No.20200171200, No.20200022938, No.20190142964, No.20170232120, No.20170173172, No.20170119899, No.20170119897, and No.20170043027.
  • dendrimer includes, but is not limited to, a molecular architecture with an interior core and layers (or “generations”) of repeating units which are attached to and extend from this interior core, each layer having one or more branching points, and an exterior surface of terminal groups attached to the outermost generation.
  • dendrimers have regular dendrimeric or “starburst” molecular structures.
  • dendrimers have a diameter from about 1 nm up to about 50 nm, more preferably from about 1 nm to about 20 nm, from about 1 nm to about 10 nm, or from about 1 nm to about 5 nm. In some embodiments, the diameter is between about 1 nm to about 2 nm.
  • the dendrimers have a diameter effective to cross the blood brain barrier (“BBB”) and to be retained in target cells for a prolonged period of time.
  • Exemplary dendrimers include, but are not limited to, polyamidoamine (PAMAM), polyester, polylysine, polypropylamine (POPAM), poly(propylene imine) (PPI), iptycene, aliphatic poly(ether), and/or aromatic polyether dendrimers.
  • PAMAM polyamidoamine
  • POPAM polypropylamine
  • PPI poly(propylene imine)
  • iptycene aliphatic poly(ether), and/or aromatic polyether dendrimers.
  • the dendrimers can have carboxylic, amine and/or hydroxyl terminations. Dendrimers can be any generation including, but not limited to, generation 1, generation 2, generation 3, generation 4, generation 5, generation 6, generation 7, generation 8, generation 9, or generation 10.
  • dendrimers are PAMAM dendrimers used as a platform and modified with surface groups for increased number of hydroxyl groups.
  • the dendrimers include a plurality of hydroxyl groups.
  • Some exemplary high-density hydroxyl groups-containing dendrimers include commercially available polyester dendritic polymer such as hyperbranched 2,2-Bis(hydroxyl- methyl)propionic acid polyester polymer (for example, hyperbranched bis-MPA polyester- 64-hydroxyl, generation 4), dendritic polyglycerols.
  • the high-density hydroxyl groups-containing dendrimers are oligo ethylene glycol (OEG)-like dendrimers.
  • Each dendrimer of a dendrimer complex may be of similar or different chemical nature than the other dendrimers (e.g., the first dendrimer may include a PAMAM dendrimer, while the second dendrimer may include a POPAM dendrimer).
  • the first or second dendrimer may further include an additional agent.
  • the multiarm PEG polymer includes a polyethylene glycol having at least two branches bearing sulfhydryl or thiopyridine terminal groups; however, PEG polymers bearing other terminal groups such as succinimidyl or maleimide terminations can be used.
  • the PEG polymers in the molecular weight range of 10 kDa to 80 kDa can be used.
  • the molecular weight of the dendrimers can be varied to prepare polymeric nanoparticles that form particles having properties, such as drug release rate, optimized for specific applications.
  • the dendrimers can have a molecular weight of between about 150 Da and 1 MDa.
  • the polymer has a molecular weight of between about 500 Da and about 100 kDa, more preferably between about 1 kDa and about 50 kDa, most preferably between about 1 kDa and about 20 kDa.
  • the present invention provides a method for treating a disease, disorder or condition mediated by human Resistin in a patient comprising the step of administering to the patient an anti-Resistin antibody or antigen-binding fragment thereof described herein.
  • the disease, disorder or condition is mediated by a virus.
  • the virus is a coronavirus.
  • the coronavirus is SARS-CoV-2 (COVID-19).
  • the present invention can be used to treat other viral conditions such as human papillomavirus (HPV).
  • the disease, disorder or condition is one or more of pulmonary hypertension, cardiac hypertrophy and failure, asthma, lung inflammation, sepsis, acute lung injury, respiratory distress syndrome, pulmonary fibrosis, scleroderma, arteriosclerosis, chronic obstructive lung disease/emphysema, normal and abnormal wound healing, cancer, cell proliferation, stem cell growth and differentiation, diabetic retinopathy, and insulin resistance.
  • subject or patient is meant a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, or feline.
  • a subject or patient is a human subject or patient.
  • an effective amount is meant the amount of a required compound to ameliorate the symptoms of a disease relative to an untreated patient.
  • the effective amount of active compound(s) used to practice the present invention for therapeutic treatment of COVID-19 varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount.
  • the terms “treat”, “treatment”, “treating”, or “amelioration” when used in reference to a disease, disorder or medical condition refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to reverse, alleviate, ameliorate, inhibit, lessen, slow down or stop the progression or severity of a symptom, a condition, a disease, or a disorder.
  • the term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition, a disease, or a disorder. Treatment is generally “effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is “effective” if the progression of a disease, disorder or medical condition is reduced or halted.
  • treatment includes not just the improvement of symptoms or markers, but also a cessation or at least slowing of progress or worsening of symptoms that would be expected in the absence of treatment. Also, “treatment” may mean to pursue or obtain beneficial results, or lower the chances of the individual developing the condition, disease, or disorder even if the treatment is ultimately unsuccessful.
  • Those in need of treatment include those already with the condition, disease, or disorder as well as those prone to have the condition, disease, or disorder or those in whom the condition, disease, or disorder is to be prevented.
  • preventative treatment means maintaining or improving a healthy state or non-diseased state of a healthy subject or subject that does not have a disease.
  • preventative treatment or “health surveillance” “also means to prevent or to slow the appearance of symptoms associated with a condition, disease, or disorder.
  • preventative treatment also means to prevent or slow a subject from obtaining a condition, disease, or disorder.
  • administering refers to the placement an agent or a treatment as disclosed herein into a subject by a method or route which results in at least partial localization of the agent or treatment at a desired site.
  • “Route of administration” may refer to any administration pathway known in the art, including but not limited to aerosol, nasal, via inhalation, oral, anal, intra-anal, peri-anal, transmucosal, transdermal, parenteral, enteral, topical or local.
  • Parenteral refers to a route of administration that is generally associated with injection, including intratumoral, intracranial, intraventricular, intrathecal, epidural, intradural, intraorbital, infusion, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrathecal, intrauterine, intravascular, intravenous, intraarterial, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal.
  • the compositions may be in the form of solutions or suspensions for infusion or for injection, or as lyophilized powders.
  • the pharmaceutical compositions can be in the form of tablets, gel capsules, sugar-coated tablets, syrups, suspensions, solutions, powders, granules, emulsions, microspheres or nanospheres or lipid vesicles or polymer vesicles allowing controlled release.
  • the pharmaceutical compositions can be in the form of aerosol, lotion, cream, gel, ointment, suspensions, solutions or emulsions.
  • “administering” can be self-administering. For example, it is considered as “administering” that a subject consumes a composition as disclosed herein.
  • coronaviruses and SARS-CoV-2 (COVID-19)
  • coronaviruses refers to a group of related viruses that cause diseases in mammals and birds. In humans, coronaviruses cause respiratory tract infections that can range from mild to lethal. Mild illnesses include some cases of the common cold, while more lethal varieties can cause “SARS”, “MERS”, and “COVID-19”.
  • Coronaviruses (CoV) are large, enveloped, positive-sense RNA viruses. Human coronaviruses are typically associated with respiratory tract disease.
  • Coronaviruses that can infect humans include human coronavirus (HCoV)-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV, SARS-CoV-1, and SARS-CoV-2. Coronaviruses are divided into 3 genera: Alphacoronavirus, betacoronavirus, and gammacoronavirus.
  • Betacoronaviruses SARS-CoV-2, SARS-CoV-1, and MERS-CoV are associated with severe disease in humans (Zubair, JAMA Neurology published online May 29, 2020, DOI: 10.1001/jamaneurol.2020.2065: Neuropathogenesis and Neurologic Manifestations of the Coronaviruses in the Age of Coronavirus Disease 2019 A Review).
  • the viral envelope of coronavirus is formed by a lipid bilayer wherein the membrane (M), envelope (E) and spike (S) structural proteins are anchored.
  • nucleocapsid (N) protein Inside the envelope, multiple copies of the nucleocapsid (N) protein form the nucleocapsid, which is bound to the positive-sense single-stranded RNA genome in a continuous beads-on-a-string type conformation.
  • Its genome comprises Orfs la and lb encoding the replicase/transcriptase polyprotein, followed by sequences encoding the spike (S)-envelope protein, the envelope (E)- protein, the membrane (M)-protein and the nucleocapsid (N)- protein. Interspersed between these reading frames are the reading frames for the accessory proteins which differ between the different virus strains.
  • Human Coronavirus NL63 HoV-NL63
  • Human Coronavirus 229E HoV-229E
  • a-CoV Human Coronavirus HKU1 (HCoV-HKU1)
  • b-CoV Human Coronavirus OC43 (HCoV-OC43)
  • MERS-CoV Middle East respiratory syndrome-related Coronavirus
  • SARS- CoV Severe acute respiratory syndrome Coronavirus
  • b-CoV Severe acute respiratory syndrome Coronavirus 2
  • SARS-CoV-2 Severe acute respiratory syndrome Coronavirus
  • COVID 19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), formerly known as nCoV-19 (novel Corona virus 2019). Because the strain was first discovered in Wuhan, China, it is sometimes referred to as the Wuhan virus. SARS-Cov-2 is highly contagious in humans, and the World Health Organization (WHO) has designated the still ongoing pandemic of COVID- 19 a Public Health Emergency of International Concern. The earliest case of infection currently known is thought to have been found on 17 November 2019.
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • WHO World Health Organization
  • the SARS-Cov-2 sequence was first published on January 10, 2020 (Wuhan-Hu-1, GenBank accession number MN908947). Subsequent to the first outbreak in Wuhan, the virus spread to all provinces of China and to more than 150 other countries in Asia, Europe, North America, South America, Africa, and Oceania. Symptoms include high-fever, sore throat, dry cough, and exhaustion. In severe cases, pneumonia may develop.
  • the term “disease severity” characterizes the impact that a disease process has on the utilization of resources, comorbidities, and mortality. The disease severity reflects the degree of illness and risk of disease manifested by patients, based either on clinical data from the medical records or on hospital discharge/billing data.
  • disease progression refers to the course of a disease.
  • the term reflects a disease or physical ailment whose course in most cases is the worsening, growth, or spread of the disease. This may happen until death, serious debility, or organ failure occurs.
  • Some progressive diseases can be halted and reversed by treatment. Many can be slowed by medical therapy. Still, others cannot be altered by current treatments.
  • Symptoms of a disease are implication of the disease noticeable by the tissue, organ or organism having such disease—such as COVID-19—and include, but are not limited to, fever, chills, cough, shortness of breath or difficulty breathing, fatigue, muscle or body aches, headache, new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting and diarrhea of the tissue, an organ or an individual.
  • “Signs” or “signals” of a disease include but are not limited to the change or alteration such as the presence, absence, increase or elevation, decrease or decline, of specific indicators such as biomarkers or molecular markers, or the development, presence, or worsening of symptoms.
  • Emergency warning signs of COVID-19 include, but are not limited to, trouble breathing, persistent pain or pressure in the chest, new confusion, inability to wake or stay awake and pale, gray or blue-colored skin, lips or nail beds, depending on skin tone.
  • hospital admission or “hospitalization” is well understood by the skilled person and refers to the process of admitting a patient to a hospital involving a stay at hospital for at least one night or more. Staying in the hospital is necessary because the individuals are too sick to stay at home, require nursing care, and/or is receiving medications and undergoing tests and/or surgery that can only be performed in the hospital setting. Typically, but not necessarily a patient is admitted to hospital due to the development, presence, or progression of a disease.
  • a patient may be admitted to hospital in cases where a mild form of a disease becomes more severe and more intense monitoring and/or treatment of the patient is required.
  • intensive care unit is known in the art.
  • the term refers to a health care unit that treats patients with life-threatening conditions which require constant support from equipment and medication in order to maintain normal bodily functions.
  • the term “mortality” as used herein, refers to the state or condition of being mortal or being a patient with COVID-19 to death. The mortality rate is the percentage of deaths associated with a disease or medical treatment.
  • monitoring as used herein, preferably, relates to assessing the disease progression as referred to herein elsewhere.
  • COVID-19 can mean infection by, but not limited to, SARS- CoV-2 Alpha (B.1.1.7 and Q lineages); Beta (B.1.351 and descendent lineages); Gamma (P.1 and descendent lineages); Epsilon (B.1.427 and B.1.429); Eta (B.1.525); Iota (B.1.526); Kappa (B.1.617.1); 1.617.3; Mu (B.1.621, B.1.621.1); and Zeta (P.2).
  • infection includes Delta (B.1.617.2 and AY lineages).
  • infection includes Omicron (B.1.1.529 and BA lineages).
  • a subject or patient having COVID-19 can be treated with other known COVID-19 treatments or therapies.
  • the concomitant therapeutic intervention includes, but is not limited to, azithromycin, remdesivir, systemic glucocorticoid, tocilizumab, convalescent plasma, hydroxychloroquine, monoclonal antibodies against SARS-CoV-2, baricitinib, anticoagulant, and combinations thereof.
  • systemic glucocorticoid comprises dexamethasone, prednisone, methylprednisolone, or combinations thereof.
  • Antiviral therapy can be used and includes, but is not limited to, remdesivir; chloroquine or hydroxychloroquine and/or azithromycin; interferons; ivermectin; lopinavir/ritonavir and other HIV protease inhibitors; molnupiravir; nitazoxanide; and ritonavir-boosted nirmatrelvir.
  • Anti-SARS-CoV-2 antibody products include convalescent plasma and anti-SARS- CoV-2 monoclonal antibodies.
  • Anti-SARS-CoV-2 monoclonal antibodies include, but are not limited to, bamlanivimab plus etesevimab; casirivmag plus imdevimab; sotrovimab; and tixagevimab pus cilgavimab.
  • Immunodulators include, but are not limited to, colchicine; corticosteroids; fluvoxamine; granulocyte-macrophage colony-stimulating factor inhibitors; interleukin-1 inhibitors; interleukin-6 inhibitors; janus kinase inhibitors and burton’s tyrosine kinase inhibitors.
  • Antithrombotic therapy includes anticoagulant and antiplatelet therapy.
  • Supplements include vitamin C, vitamin D and zinc. Treatment can further include, but is not limited to, progesterone receptor agonists.
  • the progesterone receptor agonist include, but are not limited to, progesterone, levonorgestrel, etonogestrel, hydroxyprogesterone caproate, ulipristal acetate, medroxyprogesterone acetate, norethindrone, desogestrel, chlormadinone acetate, progesterone, dienogest, drospirenone, dydrogesterone, everolimus, hydroxyprogesterone, lynestrenol, medrogestone, medroxyprogesterone, megestrol acetate, nomegestrol acetate, norgestrel, promegestone, vilaprisan, danazol, methylestrenolone, VOLT-02, EC-313, MDC- WWM, and combinations thereof IV.
  • Resistin polymorphisms can be used as a marker of COVID-19 in a subject.
  • Resistin polymorphisms can be used a marker or predictor of COVID-19 severity in a subject.
  • Resistin polymorphisms can be used a predictor of hospitalization.
  • Resistin polymorphisms include, but are not limited to, rs10402265, C>G (disease severity) and rs12459044, C>G (hospitalization).
  • Other polymorphisms can be used to predict, for example, ICU admission or treatment. For example, patients selected for ICU are expected to have complications of their clinical outcome within 24 and 72 hours.
  • a subject can be one who has been previously diagnosed with or identified as suffering from or having a condition, disease, or disorder in need of treatment (e.g., COVID- 19) or one or more complications related to the condition, disease, or disorder, and optionally, have already undergone treatment for the condition, disease, disorder, or the one or more complications related to the condition, disease, or disorder.
  • a condition, disease, or disorder in need of treatment e.g., COVID- 19
  • one or more complications related to the condition, disease, or disorder e.g., COVID- 19
  • optionally, have already undergone treatment for the condition, disease, disorder, or the one or more complications related to the condition, disease, or disorder.
  • a subject can also be one who has not been previously diagnosed as having a condition, disease, or disorder or one or more complications related to the condition, disease, or disorder.
  • a subject can be one who exhibits one or more risk factors for a condition, disease, or disorder, or one or more complications related to the condition, disease, or disorder, or a subject who does not exhibit risk factors.
  • a “subject in need” of treatment for a particular condition, disease, or disorder can be a subject suspected of having that condition, disease, or disorder, diagnosed as having that condition, disease, or disorder, already treated or being treated for that condition, disease, or disorder, not treated for that condition, disease, or disorder, or at risk of developing that condition, disease, or disorder.
  • the subject is selected from the group consisting of a subject suspected of having a disease, a subject that has a disease, a subject diagnosed with a disease, a subject that has been treated for a disease, a subject that is being treated for a disease, and a subject that is at risk of developing a disease.
  • the subject is selected from the group consisting of a subject suspected of having COVID-19, a subject that has COVID-19, a subject diagnosed with COVID-19, a subject that has severe COVID-19, a subject suspected of having severe COVID-19, a subject that has been treated for COVID-19, a subject that is being treated for COVID-19, and a subject that is at risk of developing COVID-19.
  • At risk of is intended to mean at increased risk of, compared to a normal subject, or compared to a control group, e.g., a patient population.
  • a subject carrying a particular marker may have an increased risk for a specific condition, disease or disorder, and be identified as needing further testing.
  • Increased risk or “elevated risk” mean any statistically significant increase in the probability, e.g., that the subject has the disorder.
  • the risk is increased by at least 10%, at least 20%, and even at least 50% over the control group with which the comparison is being made.
  • a subject can be at risk of developing severe COVID-19. “Sample” is used herein in its broadest sense.
  • biological sample denotes a sample taken or isolated from a biological organism.
  • a sample or biological sample may comprise a bodily fluid including blood, serum, plasma, tears, aqueous and vitreous humor, spinal fluid; a soluble fraction of a cell or tissue preparation, or media in which cells were grown; or membrane isolated or extracted from a cell or tissue; polypeptides, or peptides in solution or bound to a substrate; a cell; a tissue, a tissue print, a fingerprint, skin or hair; fragments and derivatives thereof.
  • samples or biological samples include cheek swab; mucus; whole blood, blood, serum; plasma; urine; saliva, semen; lymph; fecal extract; sputum; other body fluid or biofluid; cell sample; and tissue sample etc.
  • the term also includes a mixture of the above-mentioned samples or biological samples.
  • sample also includes untreated or pretreated (or pre-processed) biological samples.
  • a sample or biological sample can comprise one or more cells from the subject.
  • Subject samples or biological samples usually comprise derivatives of blood products, including blood, plasma and serum.
  • the sample is a biological sample.
  • the sample is blood.
  • the sample is plasma.
  • the sample is blood, plasma, serum, or urine. In certain embodiments, the sample is a serum sample. In particular embodiments, the sample is a urine sample.
  • body fluid or “bodily fluids” are liquids originating from inside the bodies of organisms.
  • Bodily fluids include amniotic fluid, aqueous humour, vitreous humour, bile, blood (e.g., serum), breast milk, cerebrospinal fluid, cerumen (earwax), chyle, chyme, endolymph and perilymph, exudates, feces, female ejaculate, gastric acid, gastric juice, lymph, mucus (e.g., nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil), serous fluid, semen, sputum, synovial fluid, sweat, tears, urine, vaginal secretion, and vomit.
  • blood e.g., serum
  • breast milk e.g., breast milk
  • cerebrospinal fluid cerumen (earwax)
  • cerumen earwax
  • chyle chyle
  • endolymph endo
  • Extracellular bodily fluids include intravascular fluid (blood plasma), interstitial fluids, lymphatic fluid and transcellular fluid.
  • Biological sample also includes a mixture of the above-mentioned body fluids.
  • Biological samples may be untreated or pretreated (or pre-processed) biological samples. Sample collection procedures and devices known in the art are suitable for use with various embodiment of the present invention.
  • sample collection procedures and devices include but are not limited to: phlebotomy tubes (e.g., a vacutainer blood/specimen collection device for collection and/or storage of the blood/specimen), dried blood spots, Microvette CB300 Capillary Collection Device (Sarstedt), HemaXis blood collection devices (microfluidic technology, Hemaxis), Volumetric Absorptive Microsampling (such as CE-IVD Mitra microsampling device for accurate dried blood sampling (Neoteryx), HemaSpotTM-HF Blood Collection Device, a tissue sample collection device; standard collection/storage device (e.g., a collection/storage device for collection and/or storage of a sample (e.g., blood, plasma, serum, urine, etc.); a dried blood spot sampling device.
  • phlebotomy tubes e.g., a vacutainer blood/specimen collection device for collection and/or storage of the blood/specimen
  • dried blood spots e.g.
  • the Volumetric Absorptive Microsampling (VAMS 1M ) samples can be stored and mailed, and an assay can be performed remotely.
  • the term “reference” means a standard or control condition.
  • binding assay is meant a biochemical assay wherein the Resistin biomarker is detected by binding to an agent, such as an antibody, through which the detection process is carried out. The detection process may involve fluorescent or radioactive labels, and the like. The assay may involve immobilization of the biomarker, or may take place in solution.
  • Immunoassay is an assay that uses an antibody to specifically bind an antigen (e.g., a marker such as Resistin).
  • the immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen.
  • immunoassays include ELISA (enzyme-linked immunosorbent assay), immunoprecipitation, SISCAPA (stable isotope standards and capture by anti-peptide antibodies), Western blot, etc.
  • the term “statistically significant” or “significantly” refers to statistical evidence that there is a difference. It is defined as the probability of making a decision to reject the null hypothesis when the null hypothesis is actually true. The decision is often made using the p- value.
  • detection may be used in the context of detecting biomarkers, detecting peptides, detecting proteins, or of detecting a condition, detecting a disease or a disorder (e.g., when positive assay results are obtained).
  • detecting and “diagnosing” are considered synonymous when mere detection indicates the diagnosis.
  • marker or “biomarker” are used interchangeably herein, and in the context of the present invention refer to a protein or peptide (for example, protein or peptide associated with COVID-19 as described herein) is differentially present in a sample taken from patients having a specific disease or disorder as compared to a control value, the control value consisting of, for example average or mean values in comparable samples taken from control subjects (e.g., a person with a negative diagnosis, normal or healthy subject).
  • Biomarkers may be determined as specific peptides or proteins which may be detected by, for example, antibodies or mass spectroscopy.
  • a mass spectroscopy or other profile of multiple antibodies may be used to determine multiple biomarkers, and differences between individual biomarkers and/or the partial or complete profile may be used for diagnosis.
  • the biomarkers may be detected by antibodies, mass spectrometry, or combinations thereof.
  • the term “differentially present” or “change in level” refers to differences in the quantity and/or the frequency of a marker present in a sample taken from patients having a specific disease or disorder as compared to a control subject.
  • a marker can be present at an elevated level or at a decreased level in samples of patients with the disease or disorder compared to a control value (e.g., determined from samples of control subjects).
  • a marker can be detected at a higher frequency or at a lower frequency in samples of patients compared to samples of control subjects.
  • a marker can be differentially present in patients having severe COVID-19 as compared to a control subject including patients having non-severe COVID-19 or no COVID-19.
  • a marker, compound, composition or substance is differentially present in a sample if the amount of the marker, compound, composition or substance in the sample (a patient having severe COVID-19) is statistically significantly different from the amount of the marker, compound, composition or substance in another sample (a patient having non-severe COVID-19 or no COVID-19), or from a control value (e.g., an index or value representative of non-severe COVID-19 or no COVID-19).
  • a compound is differentially present if it is present at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 110%, at least about 120%, at least about 130%, at least about 150%, at least about 180%, at least about 200%, at least about 300%, at least about 500%, at least about 700%, at least about 900%, or at least about 1000% greater or less than it is present in the other sample (e.g., control), or if it is detectable in one sample and not detectable in the other.
  • a marker, compound, composition or substance is differentially present between samples if the frequency of detecting the marker, etc.
  • a biomarker is differentially present between the two sets of samples if it is detected at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 100% more frequently or less frequently observed in one set of samples (e.g., a patient having severe COVID-19) than the other set of samples (e.g., a patient having non-severe COVID-19 or no COVID-19).
  • cut-off points, etc. that represent a statistically significant difference to determine whether the marker is differentially present.
  • the term “one or more of” refers to combinations of various biomarkers. The term encompasses 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15 ,16 ,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40... N, where “N” is the total number of biomarker proteins in the particular embodiment.
  • the term also encompasses, and is interchangeably used with, at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15 ,16 ,17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40... N.
  • biomarkers herein includes the phrase “one or more of” the biomarkers and, in particular, includes the “at least 1, at least 2, at least 3” and so forth language in each recited embodiment of a biomarker panel.
  • Detectable moiety or a “label” refers to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means.
  • useful labels include 32 P, 35 S, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin-streptavidin, digoxigenin, haptens and proteins for which antisera or monoclonal antibodies are available, or nucleic acid molecules with a sequence complementary to a target.
  • the detectable moiety often generates a measurable signal, such as a radioactive, chromogenic, or fluorescent signal, that can be used to quantify the amount of bound detectable moiety in a sample.
  • the detectable moiety is a stable isotope.
  • the stable isotope is selected from the group consisting of 15 N, 13 C, 18 O and 2 H.
  • Resistin can be detected and/or measured by immunoassay. Immunoassay requires biospecific capture reagents/binding agent, such as antibodies, to capture the biomarkers. Many antibodies are available commercially.
  • Antibodies also can be produced by methods well known in the art, e.g., by immunizing animals with the biomarkers.
  • Biomarkers can be isolated from samples based on their binding characteristics. Alternatively, if the amino acid sequence of a polypeptide biomarker is known, the polypeptide can be synthesized and used to generate antibodies by methods well-known in the art.
  • Biospecific capture reagents useful in an immunoassay can also include lectins. The biospecific capture reagents can, in some embodiments, bind all forms of the biomarker, e.g., PSA and its post-translationally modified forms (e.g., glycosylated form).
  • the biospecific capture reagents bind the specific biomarker and not similar forms thereof.
  • an anti-Resistin antibody or antigen-binding fragment thereof described here is used to detect/measure Resistin.
  • the present invention contemplates traditional immunoassays including, for example, sandwich immunoassays including ELISA or fluorescence-based immunoassays, immunoblots, Western Blots (WB), as well as other enzyme immunoassays. Nephelometry is an assay performed in liquid phase, in which antibodies are in solution. Binding of the antigen to the antibody results in changes in absorbance, which is measured.
  • a biospecific capture reagent for the biomarker e.g., Resistin
  • an MS probe such as a pre-activated protein chip array.
  • the biomarker is then specifically captured on the biochip through this reagent, and the captured biomarker is detected by mass spectrometry.
  • the expression levels of the protein biomarkers employed herein are quantified by immunoassay, such as enzyme-linked immunoassay (ELISA) technology.
  • the levels of expression of Resistin is determined by contacting the biological sample with an antibody, or antigen binding fragment thereof, that selectively bind to the Resistin biomarker; and detecting binding of the antibody, or antigen binding fragment thereof, to the Resistin biomarker.
  • the binding agents employed in the disclosed methods and compositions are labeled with a detectable moiety.
  • a binding agent and a detection agent are used, in which the detection agent is labeled with a detectable moiety.
  • the term antibody is used in describing binding agents or capture molecules.
  • the level of a Resistin biomarker in a sample can be assayed by contacting the biological sample with an antibody, or antigen binding fragment thereof, that selectively binds to the target protein (referred to as a capture molecule or antibody or a binding agent), and detecting the binding of the antibody, or antigen-binding fragment thereof, to the protein.
  • the detection can be performed using a second antibody to bind to the capture antibody complexed with its target biomarker.
  • a target biomarker can be an entire protein, or a variant or modified form thereof.
  • Kits for the detection of proteins as described herein can include pre-coated strip/plates, biotinylated secondary antibody, standards, controls, buffers, streptavidin-horse radish peroxidise (HRP), tetramethyl benzidine (TMB), stop reagents, and detailed instructions for carrying out the tests including performing standards.
  • the present disclosure also provides methods for detecting proteins (including, e.g., Resistin) in a sample obtained from a subject, wherein the levels of expression of the proteins in a biological sample are determined simultaneously.
  • methods comprise: (a) contacting a biological sample obtained from the subject with a plurality of binding agents that each selectively bind to one or more biomarker proteins for a period of time sufficient to form binding agent-biomarker complexes; and (b) detecting binding of the binding agents to the one or more biomarker proteins.
  • detection thereby determines the levels of expression of the biomarkers in the biological sample; and the method can further comprise (c) comparing the levels of expression of the one or more biomarker proteins in the biological sample with predetermined threshold values, wherein levels of expression of at least one of the biomarker proteins above or below the predetermined threshold values indicates, for example, the subject has COVID-19, the severity of COVID-19, and/or is/will be responsive to COVID-19 therapy.
  • binding agents that can be effectively employed in such methods include, but are not limited to, antibodies or antigen-binding fragments thereof, aptamers, lectins and the like.
  • any other suitable agent e.g., a peptide, an aptamer, or a small organic molecule
  • a biomarker of the present invention is optionally used in place of the antibody in the above described immunoassays.
  • an aptamer that specifically binds a biomarker and/or one or more of its breakdown products might be used.
  • Aptamers are nucleic acid-based molecules that bind specific ligands. Methods for making aptamers with a particular binding specificity are known as detailed in U.S. Patents No.5,475,096; No.5,670,637; No.
  • the assay performed on the biological sample can comprise contacting the biological sample with one or more capture agents (e.g., antibodies, lectins, peptides, aptamer, etc., combinations thereof) to form a biomarker:capture agent complex.
  • capture agents e.g., antibodies, lectins, peptides, aptamer, etc., combinations thereof. The complexes can then be detected and/or quantified.
  • a subject can then be identified as having severe COVID-19 based on a comparison of the detected/quantified/measured levels of biomarkers to one or more reference controls as described herein.
  • the biomarker levels can also be utilized with other biomarker measurements.
  • a first, or capture, binding agent such as an antibody that specifically binds the Resistin protein biomarker of interest, is immobilized on a suitable solid phase substrate or carrier.
  • the test biological sample is then contacted with the capture antibody and incubated for a desired period of time.
  • a second, detection, antibody that binds to a different, non-overlapping, epitope on the biomarker (or to the bound capture antibody) is then used to detect binding of the polypeptide biomarker to the capture antibody.
  • the detection antibody is preferably conjugated, either directly or indirectly, to a detectable moiety. Examples of detectable moieties that can be employed in such methods include, but are not limited to, cheminescent and luminescent agents; fluorophores such as fluorescein, rhodamine and eosin; radioisotopes; colorimetric agents; and enzyme-substrate labels, such as biotin.
  • the assay is a competitive binding assay, wherein labeled protein biomarker is used in place of the labeled detection antibody, and the labeled biomarker and any unlabeled biomarker present in the test sample compete for binding to the capture antibody.
  • the amount of biomarker bound to the capture antibody can be determined based on the proportion of labeled biomarker detected.
  • Solid phase substrates, or carriers, that can be effectively employed in such assays are well known to those of skill in the art and include, for example, 96 well microtiter plates, glass, paper, and microporous membranes constructed, for example, of nitrocellulose, nylon, polyvinylidene difluoride, polyester, cellulose acetate, mixed cellulose esters and polycarbonate.
  • Suitable microporous membranes include, for example, those described in US Patent Application Publication no. US 2010/0093557 A1.
  • Methods for the automation of immunoassays are well known in the art and include, for example, those described in U.S. Patent Nos.5,885,530, 4,981,785, 6,159,750 and 5,358,691.
  • the presence of several different protein biomarkers in a test sample can be detected simultaneously using a multiplex assay, such as a multiplex ELISA.
  • Multiplex assays offer the advantages of high throughput, a small volume of sample being required, and the ability to detect different proteins across a board dynamic range of concentrations.
  • such methods employ an array, wherein multiple binding agents (for example capture antibodies) specific for multiple biomarkers are immobilized on a substrate, such as a membrane, with each capture agent being positioned at a specific, pre- determined, location on the substrate.
  • a substrate such as a membrane
  • Methods for performing assays employing such arrays include those described, for example, in US Patent Application Publication nos. US2010/0093557A1 and US2010/0190656A1, the disclosures of which are hereby specifically incorporated by reference.
  • Multiplex arrays in several different formats based on the utilization of, for example, flow cytometry, chemiluminescence or electron-chemiluminesence technology, can be used.
  • Flow cytometric multiplex arrays also known as bead-based multiplex arrays, include the Cytometric Bead Array (CBA) system from BD Biosciences (Bedford, Mass.) and multi- analyte profiling (xMAP®) technology from Luminex Corp. (Austin, Tex.), both of which employ bead sets which are distinguishable by flow cytometry.
  • CBA Cytometric Bead Array
  • xMAP® multi- analyte profiling
  • Luminex Corp. Austintin, Tex.
  • a multiplex ELISA from Quansys Biosciences (Logan, Utah) coats multiple specific capture antibodies at multiple spots (one antibody at one spot) in the same well on a 96-well microtiter plate. Chemiluminescence technology is then used to detect multiple biomarkers including Resistin at the corresponding spots on the plate.
  • the Resistin biomarker of the present invention may be detected by means of an electrochemicaluminescent assay developed by Meso Scale Discovery (Gaithersburg, MD). Electrochemiluminescence detection uses labels that emit light when electrochemically stimulated. Background signals are minimal because the stimulation mechanism (electricity) is decoupled from the signal (light).
  • Labels are stable, non-radioactive and offer a choice of convenient coupling chemistries. They emit light at ⁇ 620 nm, eliminating problems with color quenching. See U.S. Patents No.7,497,997; No. 7,491,540; No.7,288,410; No.7,036,946; No.7,052,861; No.6,977,722; No.6,919,173; No. 6,673,533; No.6,413,783; No.6,362,011; No.6,319,670; No.6,207,369; No.6,140,045; No. 6,090,545; and No.5,866,434. See also U.S. Patent Applications Publication No.
  • Resistin can be detected by other suitable methods.
  • Detection paradigms that can be employed to this end include optical methods, electrochemical methods (voltametry and amperometry techniques), atomic force microscopy, and radio frequency methods, e.g., multipolar resonance spectroscopy.
  • Resistin can be captured and concentrated using nano particles.
  • the proteins can be captured and concentrated using Nanotrap® technology (Ceres Nanosciences, Inc. (Manassas, VA)).
  • Nanotrap® technology (Ceres Nanosciences, Inc. (Manassas, VA)).
  • the Nanotrap platform reduces pre-analytical variability by enabling biomarker enrichment, removal of high-abundance analytes, and by preventing degradation to highly labile analytes in an innovative, one-step collection workflow. Multiple analytes sequestered from a single sample can be concentrated and eluted into small volumes to effectively amplify, up to 100- fold or greater depending on the starting sample volume (Shafagati, 2014; Shafagati, 2013; Longo, et al., 2009), resulting in substantial improvements to downstream analytical sensitivity.
  • Biochips generally comprise solid substrates and have a generally planar surface, to which a capture reagent (also called an adsorbent or affinity reagent) is attached. Frequently, the surface of a biochip comprises a plurality of addressable locations, each of which has the capture reagent bound there.
  • Protein biochips are biochips adapted for the capture of polypeptides. Many protein biochips are described in the art. These include, for example, protein biochips produced by Ciphergen Biosystems, Inc. (Fremont, CA.), Invitrogen Corp. (Carlsbad, CA), Affymetrix, Inc.
  • the present invention comprises a microarray chip.
  • the chip comprises a small wafer that carries a collection of binding agents bound to its surface in an orderly pattern, each binding agent occupying a specific position on the chip.
  • the set of binding agents specifically bind to Resistin and one or more other biomarkers.
  • a few micro-liters of blood, serum or plasma are dropped on the chip array.
  • Protein biomarkers present in the tested specimen bind to the binding agents specifically recognized by them.
  • Subtype and amount of bound mark is detected and quantified using, for example, a fluorescently-labeled secondary, subtype- specific antibody.
  • an optical reader is used for bound biomarker detection and quantification.
  • a system can comprise a chip array and an optical reader.
  • a chip is provided.
  • reaction conditions e.g., component concentrations, desired solvents, solvent mixtures, temperatures, pressures and other reaction ranges and conditions that can be used to optimize the product purity and yield obtained from the described process. Only reasonable and routine experimentation will be required to optimize such process conditions.
  • the present inventors hypothesize that hResistin regulates SARS-Cov2-induced immune responses to drive lung inflammation and the subsequent cytokine storm in COVID- 19 pathogenesis, and serves as a predictor of severity and a target for anti-Hesistin therapy (FIG.1).
  • the goals of this project are to provide a better understanding of the role and mechanism of hResistin in the pathobiology of SARS-CoV-2 viral infection that lead to its morbidity and mortality, ascertain its ability to predict severity of disease, and evaluate the present inventors’ human therapeutic antibody against hResistin as a novel form of therapy for COVID-19 in animal models.
  • the present inventors intend to clarify the role of hResistin in COVID-19 lung inflammation with the following examples: 1.
  • EXAMPLE 1 To investigate the role of hResistin in human COVID-19. COVID-19 is assessed in patient lung tissues and PBMCs.
  • hResistin Expression/localization of hResistin are determined and correlated with other key related signals, specific immune cells, and disease severity.
  • COVID-19 is assessed in serum.
  • hResistin and associated cytokine variables are evaluated longitudinally from admission to discharge or death in correlation with progression of severity of disease to predict outcome.
  • the potential of using hResistin expression and polymorphisms as biomarkers for COVID-19 disease severity is further assessed. 2.
  • EXAMPLE 2 To determine the role of hResistin and its therapeutic antibody using COVID-19 animal models in vivo. The therapeutic effects of hResistin blocking antibody in preventing and reversing mouse models of COVID-19 are determined further.
  • EXAMPLE 3 To define the role of hResistin in mechanisms of SARS-CoV2- induced inflammation in human cells. The hResistin-regulated immune responses to SARS- CoV-2 in human primary cells are investigated. In addition, the mechanism of hResistin in mediating the SARS-Cov2 response, largely via the priming and activation of the NLRP inflammasome, is biochemically demonstrated in immune cells from COVID-19 patients.
  • APPROACH General statistical issues: All data included in the preliminary findings and the proposed results will be reported as mean ⁇ SEM.
  • Sex as a biological variable Whether biological sex affects COVID-19 pathogenesis remains unclear. Some studies indicate that the infection risk of SARS-CoV-2 has no significant association with sex, but the mortality risk for SARS-CoV-2 infections appears to be higher risk in males than in females. 18 Therefore, the present inventors will include both sexes with equal numbers in the vertebrate animal studies (Example 2) for this proposal. In the human studies (Example 1), in addition to the analysis performed on the entire dataset, the present inventors will also conduct an analysis in subgroups, with consideration of race and sex. EXAMPLE 1: THE ROLE OF HRESISTIN IN HUMAN COVID-19.
  • RELM ⁇ the rodent homolog of hResistin
  • HIMF hypoxia-induced mitogenic factor
  • the present inventors obtained a standardized set of serum specimens from the Johns Hopkins ICTR Biospecimen Repository.
  • the set of specimens (or “box”) provided for these Phase I pilot projects was intended for exploratory biomarker research.
  • the present inventors used a COVID-19 disease-severity box, consisting of 4 groups of up to 20 gender-matched specimens from patients whose peak disease severity matches one of the four WHO COVID- 19 stages (see brief description of FIG.2).
  • the specimen acquisition time was 48-72 hours before the patient reached the designated clinical severity stage.
  • This kit combined 20 analytes associated with immune response to viral infection, including G-CSF, GM-CSF, IFN- ⁇ 2a, IFN- ⁇ , IFN- ⁇ , IL-1RA, IL-1 ⁇ , IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12p70, IP-10, MCP1, MIP-1 ⁇ , TNF- ⁇ , and VEGF-A.
  • hResistin level is higher than any of these inflammatory cytokines/chemokines in all four WHO COVID-19 stages. Intriguingly, the present inventors found a cross correlation of other key inflammatory cytokines/chemokines with log hResistin concentration and with severity of outcomes (Table 1).
  • hResistin was highly induced in the airway and pulmonary parenchyma of COVID-19 patients and colocalized with its binding partner BTK (FIG.4). 4 It was also associated with local accumulation of macrophages, neutrophils, and B cells (FIG.4). Table 1. Correlation between hResistin concentration and disease severity with cytokines and chemokines. Upper/lower 95% confidence bounds displayed as subscripts.
  • hResistin 1 severity 2 3 3 0 7 8 hResistin was log-transformed Disease severity is maximum ordinal WHO outcome scale score during hospitalization Assessment of COVID-19 in Lung Tissues and PBMCs: Expression/Localization of hResistin and Correlation with Other Key Related Signals and Specific Immune Cells Lung Tissue: The present inventors will further investigate airway tissue and lung parenchyma from deceased COVID-19 patients. The tissue is from a biorepository at Johns Hopkins.
  • the present inventors will conduct immunofluorescence analysis by mounting tissues on slides and treating them with primary antibodies specific for hResistin, 37 BTK (total and phosphorylated), 4 and signaling factors of Damage-Associated Molecular Pattern (DAMP) (HMGB1, RAGE, S100A11 and TLR4) 2, 3, 19, 36, 38, 39 and inflammasome (NLRP3, IL-1 ⁇ , IL-18, and caspase-1) 13 (Abcam). Then, slides will be incubated with appropriate fluorochrome-coupled secondary antibodies (Jackson ImmunoResearch) and counterstained with DAPI (P36935, Life Technologies). The present inventors will perform correlation analysis of hResistin with these COVID-related signaling receptors, adaptors, or mediators.
  • DAMP Damage-Associated Molecular Pattern
  • the present inventors will also determine the relation between the expression and localization of these targeted molecules with markers of immune cells, including macrophages (Mac2), neutrophils (MPO), and B (CD79b) category cells.
  • Mac2 macrophages
  • MPO neutrophils
  • B (CD79b) category cells markers of immune cells
  • hResistin and BTK 3, 4 FOG.4
  • hResistin will be co-stained with the above-listed immune cell markers in COVID-19 lungs based on the literature-reported hResistin/RELM ⁇ expression in these immune cells in lung inflammatory diseases. 1,40, 41 Quantitative analysis will be performed on these colocalized cells as the present inventors have done previously.
  • PBMCs Primary human mononuclear cells
  • PBMCs Primary human mononuclear cells
  • BTK BTK
  • DAMP HMGB1/RAGE/TLR4
  • inflammasome NLRP3/IL-1 ⁇ /caspase-1
  • Flow cytometry will be used to label the monocytes, neutrophils and B cells in these PBMCs with markers as above-stated, and the expression of hResistin and downstream molecules in these inflammatory cells will be examined by multi- staining analysis.
  • Serum samples will be drawn to minimize the time between the serum sample draw and changes in the patient’s ordinal WHO outcome scale (if applicable) and at roughly quartiles of hospital length of stay for patients who maintain the same WHO outcome scale value for their entire hospitalization.
  • Statistical analysis plan 1) Assessing the correlation between hResistin levels and disease severity. Boxplots of hResistin and cytokines stratified by the ordinal WHO outcome scale value closest to the time of the serum sample will be constructed, and linear regression models will be used to compare the mean hResistin and cytokines across the categories of the ordinal WHO outcome scale; statistical comparisons will be based on robust variance estimates to account for the correlation between the repeated serum samples within a patient.
  • the linear regression models will be extended to adjust for patient demographics, including age, sex and race, clinical characteristics and other clinical/biomarker variables.
  • hResistin Assuming a linear change in hResistin (log-transformed) per day leading to the maximum disease severity category, the present inventors will have 80% power to detect effect sizes of 0.6 and greater in comparing patients with no to minimum oxygen to those who die.
  • the present inventors will use the repeated serum samples/hResistin measures to obtain initial estimates of the discriminatory power of hResistin for the maximum disease severity category using the same approach.
  • Polymorphism could account for the differential severity of response in COVID-19 patients and the likelihood of secondary complications such as heart failure, cardiomyopathy, PH, and other lung diseases.
  • the present inventors hypothesize that polymorphisms of RETN may predict severity of disease and cardiopulmonary complications in COVID-19 patients.
  • RETN intronic variant was associated with COVID severity: The present inventors examined genetic variants in RETN gene identified through the GWAS on 718 patients in the Hopkins COVID PMAP cohort using the Infinium Multi-Ethnic Global BeadChip for array genotyping.
  • RETN promoter variant was associated with hospitalization phenotype of COVID: To further explore exome sequence data for RETN gene region that captured genetic variation not assayed by array genotyping, the present inventors examined exome-wide sequencing data for 450,045 individuals from the UK Biobank.
  • This additional evidence suggests the possibility that this common variant rs12459044 located in the proximal promoter of RETN can potentially increase RETN transcription/expression and, consequently, increase risk of hospitalization from SARS-CoV-2 infection.
  • the present inventors propose to establish the role of RETN as a genetic and biological marker for susceptibility and severity of COVID in the Hopkins COVID PMAP cohort.
  • the present inventors will expand the present inventors’ RETN biomarker studies with additional serum samples from COVID patients enrolled in the Hopkins cohort.
  • the present inventors expect to confirm hResistin levels as a predictor for disease severity (see statistical analysis plan above for details).
  • the present inventors will acquire genotypes for RETN variants by additional genotyping in the full set of DNA samples from 718 patients and confirm their association with disease severity.
  • the present inventors will examine the correlation between the risk genotypes of RETN variants and serum levels of hResistin, as well as COVID severity measurements.
  • the present inventors expect to observe upregulation of DAMP, BTK, and inflammasome signaling in COVID-19–positive clinical specimens compared with the respective control expression and will quantify these by Western analysis.
  • the present inventors anticipate that the levels of these markers will correlate with hResistin level, inflammatory cell infiltration, and disease severity. If similar to the present inventors’ hypoxic lung studies, BTK will co-localize with upregulated hResistin, consistent with the present inventors’ published work that they are binding partners.
  • the present inventors anticipate that serum levels of hResistin will correlate with disease severity, variant genotypes, or haplotypes.
  • the present inventors may alternatively examine the correlation of hResistin with phenotypic and metabolic characteristics of these cells as previously described.
  • the present inventors expect to identify associations between common and rare RETN polymorphisms and COVID-19 patient severity classification.
  • expressed variation in the transcriptome and epigenome which potentially alters the proteome, may mediate the relationship between genotype, phenotype, and environment.
  • the present inventors will dissect key downstream inflammatory pathways of hResistin in innate and adaptive immunity in COVID-19.
  • the immuno-modulatory mechanism underlying the beneficial effects of anti-hResistin/RELM ⁇ antibody will be interrogated in vivo.
  • SARS-CoV-2 infection can trigger a cytokine storm whereby pro-inflammatory cytokines are overproduced by the immune system, resulting in multiorgan damage, especially in the cardiopulmonary system. 7, 10, 34 Inflammatory infiltrate of neutrophils and macrophages to the infection site initiates innate immunity and instructs B cells for adaptive immunity. 12, 35, 36
  • the mechanisms underlying SARS-CoV-2-induced inflammation are still unclear.
  • hResistin as an etiological factor in hypoxia-induced vascular inflammation.
  • the present inventors also recently developed and validated therapeutic monoclonal antibodies against hResistin. 29, 37 These human antibodies exhibited a cross-reactive ability to block rodent RELM ⁇ (the functional rodent analog of hResistin) actions in smooth muscle cell assays and in animal models of PH, exhibiting anti-inflammation and anti-remodeling effects.
  • RELM ⁇ the functional rodent analog of hResistin
  • the present inventors further dissect the roles of hResistin/RELM ⁇ play in initiating the cytokine storm in vivo.
  • the present inventors have successfully created COVID-19 animal models using K18-hACE2 transgenic mice in the Johns Hopkins BSL-3 Animal Facilities.
  • This mouse model exhibits severe pathological lung inflammation and weight loss (FIG.6C).
  • SARS-CoV-2 markedly induced expression of RELM ⁇ in the infected lung (FIG.7).
  • Administration of anti-hResistin/RELM ⁇ antibody rescued body weight loss (FIG.6C) and ameliorated lung inflammation (FIG.6A-B) in these COVID-19 mice.
  • K18-hACE2 mouse model these humanized transgenic mice are provided to JH investigators by the JHU Department of Molecular and Comparative Pathobiology and studied in BSL3 facilities. The infection of these humanized mice with SARS-CoV-2 causes severe disease in the lung and other organs with symptoms similar to those of human COVID-19. 39 The present inventors will inoculate K18-hACE2 mice with 10 ⁇ L of 10 7 TCID 50/mL SARS-CoV-2 virus (USA-WA1/2020, NR#52281). Control animals will receive equivalent inoculations with dilution media alone.
  • the present inventors will record body weight and mortality, as well as the following physiologic observations: lethargy, respiratory rate, evidence of rib and diaphragm retraction indicating difficulty breathing, and oxygen saturation by tail oximeter. According to preliminary observations, the K18 hACE2 transgenic mice succumb to SARS-CoV-2 infection by day 5, consistent with published studies. 40 2)
  • the SARS-CoV-2 MA model 52 Wild-type (WT) C57BL/6J mice will be infected with mouse-adapted (MA) SARS-CoV-2 (a recombinant virus that can use mouse ACE2 for entry into cells).
  • WT Wild-type
  • MA mouse-adapted SARS-CoV-2
  • This COVID-19 model also has been created in the present inventors’ JH RAR BSL-3 animal facilities and is provided for JH investigators.
  • mice model and the WT C57BL/6J mice to be infected with SARS-CoV-2 MA model will each be divided into five groups (n ⁇ 6 per group): 1) non-infected (control animals); 2) SARS-CoV-2 (or SARS- CoV-2 MA) infection alone; 3) SARS-CoV-2 infection with control IgG1 (Lonza); and 4-5) SARS-CoV-2 infection with the present inventors’ anti-hResistin antibody before (prevention) or after (reversal) infection. Injection of anti-hResistin antibody or isotype control IgG1 will begin 1 week before infection (group 4, prevention) or four days after infection (group 5, reversal).
  • Antibodies (4 mg/kg) will be administered intraperitoneally (i.p.) twice a week, as optimized in the present inventors’ previous study, 29 until the end of the observation (death or full recovery).
  • An additional group of RELM ⁇ -deficient mice infected with SARS-CoV-2 MA will be included in parallel as a more complete means of blocking RELM ⁇ .
  • Micro-CT imaging of the lungs The present inventors will acquire 3-D CT images of the lungs of these mice with COVID-19 in the JHU molecular imaging core and then perform qualitative and semi-quantitative image analysis of the lung abnormalities using a CT severity score adapted from a human scoring system.
  • mice after mice are anesthetized with ketamine/xylazine, the present inventors will insert and tie an 18-G tracheostomy tube and then quickly inflate the mouse lungs for 9 sec with a 0.8 mL gas sample containing Ne and CO to measure the diffusing capacity for CO, as described elsewhere. 55
  • the diffusing capacity measurement will take about 1 minute, whereupon the mice will be sacrificed and the lungs will be subjected to bronchoalveolar lavage (BAL).
  • BAL bronchoalveolar lavage
  • the recovered fluid is spun down for further analysis of inflammatory cells. After the BAL dynamic measurements, the lungs will be inflated with formalin at a pressure of 25 cm H2O, tied while inflated, and immersed in formalin for at least 24 hours.
  • the present inventors plan to examine the mouse lung function on days 0, 1, 3, and 5 post- infection in both mouse models, and on days 14 and 28 only in the mice infected with SARS- CoV-2 MA. Tissue collection and analysis: As the mechanistic studies parallel the present inventors’ observations of body weight, lung abnormalities, and survival, the present inventors will collect, serum, lung, heart, and spleen on days 0, 1, 3, and 5 post-infection in both models, and on days 14 and 28 in the mice infected with SARS-CoV-2 MA.
  • the collected tissues will be separated into 3 parts: 1) in RNAlater for mRNA extraction; 2) snap- frozen and stored at ⁇ 80°C for WB analysis; 3) fixed in 10% formalin.
  • the JHU pathology core will process these samples for slicing and H&E staining.
  • Circulating RELM ⁇ in serum will be analyzed with an ELISA kit from MesoScale. Expression and localization of RELM ⁇ in lung/heart/spleen will be tested by PCR, WB, and tissue immunofluorescence (IHC) with the anti-RELM ⁇ antibody (R&D).
  • the present inventors will follow the published scoring methods 50 to evaluate pathological severity of lung tissues and the therapeutic effects of anti-hResistin antibody in infected mice.
  • the present inventors will determine the virus titers in these infected mice by qRT- PCR assay of the lung tissues.
  • Experiments will be conducted by JH RAR in the BSL3 facility according to methods reported by other groups. 50, 53, 60 In those published studies, the mean viral loads in airway and lung were consistently the highest among all tested organ tissues. 50, 53, 60 Chemokine/cytokine profiling.
  • the lung tissues of these mouse models treated with or without anti- RELM ⁇ antibody are collected, and extracted mRNA will be tested by Qiagen RT2 ProfilerTM PCR Array for Mouse Th1 & Th2 Responses (PAMM-034Z), Mouse Chemokines & Receptors (PAMM-022Z) and Mouse Growth Factors (PAMM- 041Z) to determine the key Th1/Th2 cytokines, chemokines and growth factors regulated by RELM ⁇ in the pulmonary inflammatory responses to SARS-CoV2
  • the present inventors will use the mouse tissues collected Example 2 to determine the gene (qRT-PCR) and protein expression (WB) levels of RELM ⁇ , BTK (total and phosphorylated protein), 4 DAMP signaling proteins (HMGB1, RAGE,
  • the preo-IL-1 ⁇ will appear as two bands with MW of 35 and 29 (vs. mature form with MW of 17), and the predicted MW of pro-caspase-1 will be 45 (vs. the mature form that has two bands with MW of 20 and 20).
  • the present inventors will use IHC staining of slide-mounted lung and heart tissues, to analyze the colocalization of these RELM ⁇ downstream molecules with the markers of immune cells, including MAC2 and F4/80 for macrophages, Ly6G and MPO for neutrophils, and B220 and CD79B for B cells.
  • ELISA kits will test the levels of HMGB1 (NBP2-62782, NOVUS), BTK (LS-F10965, LSBio), and NLRP3 (ab279417, Abcam) in collected serum and BAL fluid. Validating these hResistin/RELM ⁇ downstream pathways in infected lung will be critical to elucidate the mechanisms that underlie the therapeutic effects of the anti-hResistin/RELM ⁇ antibody. Administration of anti-hResistin/RELM ⁇ antibody is expected to have therapeutic effects in the two COVID-19 mouse models. In the K18-hACE2 mice, blocking hResistin/RELM ⁇ should prolong survival or prevent death.
  • anti-hResistin/RELM ⁇ antibody is anticipated to attenuate lung inflammation and suppress the signaling of BTK, DAMP, and inflammasome in lung.
  • RELM ⁇ gene deficiency would have beneficial and immunomodulatory effects similar to that of the antibody in COVID-19 development.
  • the present inventors also expect anti-hResistin antibody administration or RELM ⁇ gene depletion to downregulate BTK, HMGB1, and NLRP3 in heart, BAL fluid, and serum.
  • the present inventors may also test other key cytokines and chemokines in these fluids with the V-PLEX Mouse Cytokine 19-Plex Kit from MesoScale.
  • the collected spleen may also be examined by histology, FACS, or WB for these hResistin/RELM ⁇ downstream immune signaling pathways.
  • the present inventors may also test another DAMP protein, S100A11.
  • S100A11 As a RAGE ligand, S100A11 has been shown to mediate the RELM ⁇ -induced cell migration in the present inventors’ previous study.
  • TLR4 is also reportedly an HMGB1 receptor and implicated in the HMGB1-regulated inflammasome.
  • the present inventors have used BALB/c mice deficient in RELM ⁇ and found that genetic ablation of RELM ⁇ in these BALB/c mice prevented ovalbumin-induced inflammation and tissue remodeling in lung and heart. 63 Therefore, the present inventors may also infect BALB/c mice with SARS-CoV-2 MA. If the SARS-CoV-2 MA model in BALB/c mice causes more severe COVID-19 disease with multiorgan damage resulting in chronic tissue remodeling in lung, heart, and other organs, the present inventors will employ it as an alternative model to study hResistin/RELM ⁇ signaling, especially its role in lung vascular and cardiac remodeling in COVID-19.
  • EXAMPLE 3 IN VITRO CELL STUDIES TO DISSECT HRESISTIN-REGULATED INFLAMMATION IN COVID-19
  • Example 3 will use in vitro cell assays to examine the detailed molecular and cellular biology of hResistin-induced inflammation in COVID-19. Published work and the present inventors’ data show that hResistin can promote migration of immune cells to sites of injury/inflammation by amplifying TH2 inflammation and causing M2 polarization; activate HMGB1 and other DAMP proteins; and activate the NLRP3 inflammasome.
  • hResistin hResistin
  • HMGB1 macrophages
  • B cells B cells
  • FIG.4 the present inventors’ data suggest that hResistin/RELM ⁇ plays an important role NLRP3 inflammasome complex activation in SARS-CoV2 infection.
  • Both hResistin and RELM ⁇ are key regulators of immune cells in diseases with Th2 inflammation.
  • Macrophages are also the main cellular sources of hResistin.
  • Neutrophils and B cells are also key immune cells in COVID-19 pathogenesis.
  • hResistin is produced by neutrophils in the serum of COVID-19 patients.
  • 41 B cells also can be the main cellular source of RELM ⁇ in the mouse model with Th2 inflammation.
  • 40 These three types of inflammatory cells are used in this Example to further investigate the role of hResistin in COVID-19 inflammation.
  • Stimulation of THP-1 monocytes with SARS-CoV-2 spike protein caused significant upregulation of hResistin production (FIG.10).
  • SARS-CoV-2 spike protein also enhanced the expression of inflammasome markers (IL-1 ⁇ /NLRP3), including IL-1 ⁇ expression by more than 100-fold, DAMP (HMGB1), and M2 subset (CD206) (FIG.10).
  • the present inventors found that the spike protein-induced DAMP, inflammasome, and M2 activation were all dependent on hResistin signaling (FIG. 10). In other experiments, the present inventors differentiated HL-60 to neutrophils. 68, 69 Treatment of these neutrophils with hResistin-recombinant protein 2 upregulated NLRP3, IL- 1 ⁇ , and HMGB1 (FIG.11). Moreover, treatment with hResistin protein upregulated BTK and HMGB1 signaling in human B cells (FIG.12). Under hypoxic conditions, hResistin protein induced B cell chemotaxis by activating BTK in vitro (FIG.13).
  • hResistin-Regulated Immune Responses to SARS-CoV-2 in Human Primary Inflammatory Cells Primary human immune cells and in vitro treatment: The present inventors will use human primary monocytes/macrophages, neutrophils, and B cells. CD14+ monocytes from peripheral blood (2W-400, Lonza) will be cultured with 25 ng/mL recombinant human M- CSF (78057, STEMCELL) to produce macrophages, as the present inventors have done previously.
  • the present inventors will sort (by flow cytometry) the monocytes and neutrophils from PBMCs of COVID-19 patients (obtained in Example 1), and treat the sorted cells with these inhibitors and activators for comparison.
  • Inflammasome activation consists of two step processes—to be ‘primed’ and then activated.
  • the PAMP or DAMP signaling facilitates the priming through NF- ⁇ B, resulting in the production of inflammasome components NLRP3, pro-caspase-1, pro-IL-18 and pro-IL-1 ⁇ .
  • HMGB1, Toll-like receptor 4 (TLR4) and NF- ⁇ B IKKB 12
  • WB The gene expression of NLRP3 inflammasome components, including NLRP3, caspase-1, IL-1 ⁇ and IL-18, will be examined with q-RT-PCR. Protein levels of the pro-form of these above-listed components, including pro-caspase-1 and pro-IL-1 ⁇ , will be tested by WB.
  • BTK regulates the intracellular translocation of NLRP3 to the dispersed trans-Golgi network (dTGN) 71 for ASC engagement.
  • dTGN dispersed trans-Golgi network
  • the present inventors will investigate whether hResistin mediates the SARS CoV2-induced NLRP3 oligomerization, ASC polymerization, full assembly and secretion of IL-1 ⁇ and IL-18. 5 The present inventors will first determine hResistin-regulated BTK phosphorylation (Tyr223 4 and Tyr551 61 ) in the human macrophages, neutrophils and B cells treated with SARS CoV-2 spike protein and anti- hResistin protein by WB.
  • the NLRP3 tyrosine phosphorylation induced by hResistin signaling will be examined in the three types of immune cells by Co-IP with anti-p- Y antibody.
  • the present inventors will test the NLRP3 oligomers by Native PAGE and visualize the NLRP3 speck formation by confocal microscopy.
  • the present inventors will conduct co-immunoprecipitation assays in human immune cells treated with or without anti-hResistin blocking antibody and with or without BTK inhibitors.
  • the present inventors will also use the THP-1 cells with gene deficiency of NLRP3 for these studies. Results will be compared with those of COVID-immune cells.
  • the THP-1 cells will be transfected with the AAV-mediated plasmids expressing BTK or its domains of PH, SH2/3, or TK. 72 Then Co-IP and WB will be performed as previously described.
  • SARS-CoV-2 will upregulate hResistin expression and activate hResistin signaling and its downstream BTK, DAMP (HMGB1/TRL4), and NLRP3 inflammasome components (both pro- and mature forms of NLRP3, caspase-1, IL-1 ⁇ and IL-18) in human immune cells.
  • This signaling will be prevented by pretreatment with anti-hResistin antibody confirming the dependence of SARS- CoV-2 on hResistin in its activation of the NLRP3 inflammasome, the major pathway causing its massive inflammatory response in COVID-19.
  • hResistin will induce the phosphorylation of BTK, and the present inventors’ further studies using cells with overexpression of BTK domains (PH, SH2/3, or TK) will identify the hResistin binding sites of BTK in the SARS CoV2-stimulated human immune cells 72 .
  • BTK BTK domains
  • hResistin would also induce the NLRP3 tyrosine phosphorylation, leading to the assembly and full activation (including subcellular translocation, oligomerization and ASC interaction) of NLRP3 inflammasome in these human immune cells from non-COVID and from COVID patients.
  • hResistin would also mediate the SARS CoV2-induced IL-1 ⁇ /IL-18 secretion from these cells.
  • the inflammasome activation would be more potent in the cells from COVID-19 patients than from non-COVID donors.
  • the present inventors also expect the activation levels of hResistin-mediated SARS CoV2-induced inflammasome in the COVID-derived cells are corelated with disease severity levels of these patients.
  • Lin Q Fan C, Gomez-Arroyo J, Van Raemdonck K, Meuchel LW, Skinner JT, Everett AD, Fang X, Macdonald AA, Yamaji-Kegan K, Johns RA. Himf (hypoxia-induced mitogenic factor) signaling mediates the hmgb1 (high mobility group box 1)-dependent endothelial and smooth muscle cell crosstalk in pulmonary hypertension. Arterioscler Thromb Vasc Biol.2019;39:2505-2519. 3. Lin Q, Fan C, Skinner JT, Hunter EN, Macdonald AA, Illei PB, Yamaji- Kegan K, Johns RA.
  • Bittner ZA Liu X, Mateo Tortola M, Tapia-Abellan A, Shankar S, Andreeva L, Mangan M, Spalinger M, Kalbacher H, Duwell P, Lovotti M, Bosch K, Dickhofer S, Marcu A, Stevanovic S, Herster F, Cardona Gloria Y, Chang TH, Bork F, Greve CL, Loffler MW, Wolz OO, Schilling NA, Kummerle-Deschner JB, Wagner S, Delor A, Grimbacher B, Hantschel O, Scharl M, Wu H, Latz E, Weber ANR. Btk operates a phospho-tyrosine switch to regulate nlrp3 inflammasome activity.
  • Fizz1/relma a novel hypoxia- induced mitogenic factor in lung with vasoconstrictive and angiogenic properties. Circ Res. 2003;92:1065-1067.
  • Angelini DJ, Su Q Yamaji-Kegan K, Fan C, Skinner JT, Champion HC, Crow MT, Johns RA.
  • Hypoxia-induced mitogenic factor (himf/fizz1/relma) induces the vascular and hemodynamic changes of pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol. 2009;296:L582-593.
  • Angelini DJ, Su Q Yamaji-Kegan K, Fan C, Skinner JT, Poloczek A, El- Haddad H, Cheadle C, Johns RA.
  • hypoxia-induced mitogenic factor (himf/fizz1/relma) in chronic hypoxia- and antigen-mediated pulmonary vascular remodeling. Respir Res. 2013;14:1.
  • Johns RA Th2 inflammation, hypoxia-induced mitogenic factor/ketz1, and pulmonary hypertension and vascular remodeling in schistosomiasis. Am J Respir Crit Care Med.2010;181:203-205.
  • Johns RA Takimoto E, Meuchel LW, Elsaigh E, Zhang A, Heller NM, Semenza GL, Yamaji-Kegan K.
  • Hypoxia-inducible factor 1alpha is a critical downstream mediator for hypoxia-induced mitogenic factor (fizz1/relmalpha)-induced pulmonary hypertension.
  • hypoxia-induced mitogenic factor has proangiogenic and proinflammatory effects in the lung via vegf and vegf receptor-2.
  • Hypoxia-induced mitogenic factor increases lung inflammation and activates pulmonary microvascular endothelial cells via an il-4-dependent mechanism. J Immunol.2010;185:5539-5548.
  • Yamaji-Kegan K Takimoto E, Zhang A, Weiner NC, Meuchel LW, Berger AE, Cheadle C, Johns RA.
  • Bruton tyrosine kinase inhibitors as potential therapeutic agents for covid-19: A review. Metabol Open.2021;11:100116. 19. Birra D, Benucci M, Landolfi L, Merchionda A, Loi G, Amato P, Licata G, Quartuccio L, Triggiani M, Moscato P. Covid 19: A clue from innate immunity. Immunol Res.2020;68:161-168. 20.
  • Rodrigues TS de Sa KSG, Ishimoto AY, Becerra A, Oliveira S, Almeida L, Goncalves AV, Perucello DB, Andrade WA, Castro R, Veras FP, Toller-Kawahisa JE, Nascimento DC, de Lima MHF, Silva CMS, Caetite DB, Martins RB, Castro IA, Pontelli MC, de Barros FC, do Amaral NB, Giannini MC, Bonjorno LP, Lopes MIF, Santana RC, Vilar FC, Auxiliadora-Martins M, Luppino-Assad R, de Almeida SCL, de Oliveira FR, Batah SS, Siyuan L, Benatti MN, Cunha TM, Alves-Filho JC, Cunha FQ, Cunha LD, Frantz FG, Kohlsdorf T, Fabro AT, Arruda E, de Olive
  • Inflammasomes are activated in response to sars-cov-2 infection and are associated with covid-19 severity in patients. J Exp Med.2021;218. 21. Vora SM, Lieberman J, Wu H. Inflammasome activation at the crux of severe covid-19. Nat Rev Immunol.2021;21:694-703. 22. Zhao N, Di B, Xu LL. The nlrp3 inflammasome and covid-19: Activation, pathogenesis and therapeutic strategies. Cytokine Growth Factor Rev.2021;61:2-15. 23. Freeman TL, Swartz TH. Targeting the nlrp3 inflammasome in severe covid- 19. Front Immunol.2020;11:1518. 24.
  • Resistin-like molecule beta is a bactericidal protein that promotes spatial segregation of the microbiota and the colonic epithelium. Proc Natl Acad Sci U S A.2017;114:11027-11033. 31. Son YM, Ahn SM, Jang MS, Moon YS, Kim SH, Cho KK, Han SH, Yun CH. Immunomodulatory effect of resistin in human dendritic cells stimulated with lipoteichoic acid from staphylococcus aureus.
  • Steppan CM Bailey ST, Bhat S, Brown EJ, Banerjee RR, Wright CM, Patel HR, Ahima RS, Lazar MA.
  • the hormone resistin links obesity to diabetes. Nature. 2001;409:307-312.
  • Fan C Fu Z, Su Q, Angelini DJ, Van Eyk J, Johns RA.
  • S100a11 mediates hypoxia-induced mitogenic factor (himf)-induced smooth muscle cell migration, vesicular exocytosis, and nuclear activation. Mol Cell Proteomics.2011;10:M110000901.
  • Lin Q Price SA, Skinner JT, Hu B, Fan C, Yamaji-Kegan K, Johns RA.
  • High-mobility group box-1 mediates toll-like receptor 4-dependent angiogenesis.
  • B cells produce the tissue-protective protein relmalpha during helminth infection, which inhibits il-17 expression and limits emphysema. Cell Rep. 2018;25:2775-2783 e2773. 41.
  • Jafarzadeh A Jafarzadeh A, Chauhan P, Saha B, Jafarzadeh S, Nemati M. Contribution of monocytes and macrophages to the local tissue inflammation and cytokine storm in covid-19: Lessons from sars and mers, and potential therapeutic interventions. Life Sci. 2020;257:118102. 0]49. Chen R, Huang Y, Quan J, Liu J, Wang H, Billiar TR, Lotze MT, Zeh HJ, Kang R, Tang D. Hmgb1 as a potential biomarker and therapeutic target for severe covid-19. Heliyon.2020;6:e05672. 50.
  • Oladunni FS Park JG, Pino PA, Gonzalez O, Akhter A, Allue-Guardia A, Olmo-Fontanez A, Gautam S, Garcia-Vilanova A, Ye C, Chiem K, Headley C, Dwivedi V, Parodi LM, Alfson KJ, Staples HM, Schami A, Garcia JI, Whigham A, Platt RN, 2nd, Gazi M, Martinez J, Chuba C, Earley S, Rodriguez OH, Mdaki SD, Kavelish KN, Escalona R, Hallam CRA, Christie C, Patterson JL, Anderson TJC, Carrion R, Jr., Dick EJ, Jr., Hall- Ursone S, Schlesinger LS, Alvarez X, Kaushal D, Giavedoni LD, Turner J, Martinez-Sobrido L, Torrelles JB.
  • Sars-cov-2 receptor ace2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell. 2020;181:1016-1035 e1019.
  • EXAMPLE 4 DEVELOPMENT OF ANTI-HUMAN RESISTIN MONOCLONAL ANTIBODIES Proteins in the resistin-like molecule (RELM) family are critically involved in the pathogenesis of a variety of inflammation-related pathologies. The present inventors’ previous rodent work strongly suggested that human resistin (hResistin) is mechanistically important to the etiology of human vascular inflammatory diseases and constitutes a therapeutic target.
  • hResistin human resistin
  • the anti-hResistin monoclonal antibodies were generated through phage screening of a human library, validated for their in vitro anti-proliferative function against hResistin in primary human pulmonary smooth muscle cells (SMCs), and further screened for immunogenicity, manufacturability, stability, and toxic effects. Their purity, antigen binding affinities and structural modeling were also validated. These human antibodies inhibited hResistin-stimulated proliferation of human primary SMCs and exhibited a cross-reactive ability to block rodent RELM actions in SMC assays.
  • Resistin-like molecule (RELM) signaling is an important component of the type II inflammatory response to tissue injury in the lung and other organs, 1, 2 and may be critically involved in inflammasome signaling and its downstream responses.
  • the present inventors laboratory discovered a molecule in the lungs of mice exposed to a chronic hypoxia-induced PH model and named it hypoxia-induced mitogenic factor [HIMF, which is also known as resistin-like molecule (RELM) ⁇ or FIZZ1) because it was upregulated in the hypoxic lung and showed potent mitogenic effects.
  • HIMF hypoxia-induced mitogenic factor
  • RELM resistin-like molecule
  • FIZZ1 resistin-like molecule
  • RELM ⁇ also has been shown to play a critical role in the development of Th2 inflammatory models induced by ovalbumin sensitization, schistosomiasis, and HIV-related stimuli.
  • 1, 3, 4, 6-9 Human resistin (hResistin) is expressed by myeloid cells, especially macrophages, and its expression pattern shows a greater similarity to that of murine HIMF/RELM ⁇ than to that of murine resistin.
  • the present inventors’ mechanistic study of gene-modified mouse lines recently revealed that hResistin induces pulmonary vascular remodeling and PH development by mediating the endothelial and smooth muscle cell crosstalk and macrophage activation dependent on activation of damage-associated molecular pattern (DAMP) signaling.
  • DAMP damage-associated molecular pattern
  • the present inventors have found that the elevation of resistin in peripheral blood of patients with idiopathic PH and or scleroderma-associated PH correlates with severity of PH hemodynamic changes (unpublished observations). Additionally, research into the immuno-regulatory properties of RELM ⁇ and hResistin has expanded to other related pulmonary pathologies including fibrosis and cancer in lung. 2 The cardiac-specific effects of hResistin on modulating inflammation in heart also have been revealed in the present inventors’ recent study. 13, 14 Moreover, the hResistin-induced vascular lesions and inflammation might also lead to atherosclerosis, thrombosis, diabetes, pathological angiogenesis, cancers, and other vascular inflammatory diseases.
  • hResistin might contribute to the etiology of the related human vascular inflammatory diseases and that it might serve as a biomarker and therapeutic target for these diseases.
  • the present inventors began preclinical testing to identify specific agents that could inhibit the onset or progression of PH in humans by impeding the activity of hResistin.
  • the present inventors previously observed that trans-tracheal administration of short hairpin (sh) RNA against rodent HIMF/RELM ⁇ prevented much of the vascular remodeling and hemodynamic changes that occur during development of hypoxia-induced PH. 4
  • recombinant elimination of rodent HIMF/RELM ⁇ had anti-PH effects.
  • hResistin As the role of hResistin in a wide variety of human diseases, especially the cardiothoracic and vascular pathologies, expands rapidly, 2 the potential application of a therapeutic antibody against hResistin widens and becomes increasingly important. Thus, the present inventors hypothesize that suppressing the actions of hResistin with a blocking antibody will delay, prevent, or reverse progress of PH. Because hResistin is significantly expressed only under pathologic conditions, 15 successful targeting of this protein to treat PH is likely to prove highly specific actions and to have few side effects.
  • the present inventors evaluated their effectiveness and their feasibility for use in humans with preclinical in vitro and vivo assays and validated their cross-reactivity for blocking rodent RELM ⁇ .
  • the present inventors’ results indicate that monoclonal anti-hResistin therapeutic antibodies have potential efficacy against PH and other related inflammatory pathologies in lung and other organs in rodents and humans.
  • Materials and Methods Anti-hResistin Antibody Development Antibodies were developed in cooperation with the present inventors’ commercial partners Creative Biolabs (Shirley, NY). Lonza (London, England) and Wuxi AppTec (Cambridge, MA,USA and Shanghai, China) provided scale-up production.
  • recombinant proteins of 3 ⁇ g/mL hResistin or 0.3 ⁇ g/mL rat RELM ⁇ were incubated with antibodies for 20 minutes before they were applied to human bronchial SMCs.
  • the present inventors lab has published the proliferative and chemotactic actions of RELM ⁇ and hResistin on human pulmonary SMCs, bone marrow stem cells, leukocytes, and human mesenchymal stem cells 16-18 and hResistin-induced activation of human lung ECs and SMCs. 19, 20 These studies showed proof of principle for using cell proliferation and migration assays to assess antibody efficacy in isolated cell studies.
  • the present inventors have tried a variety of relevant human cell lines (PA-SMCs, B- SMCs, PMV-ECs, human lung fibroblasts, and the human THP-1 cell lines) to test the effect of antibody blockade of hResistin on a variety of parameters including expression of specific proteins/genes (endothelin, IL-6, IL-8, MCP-1, TIMP-1 urokinase plasminogen activator [uPA], collagen 1A1, collagen 3A, NF-kB, CAP1 adenylyl cyclase activation) and physiologic responses such as cell migration and cell proliferation.
  • specific proteins/genes endothelin, IL-6, IL-8, MCP-1, TIMP-1 urokinase plasminogen activator [uPA], collagen 1A1, collagen 3A, NF-kB, CAP1 adenylyl cyclase activation
  • physiologic responses such as cell migration and cell proliferation.
  • this potency assay thus also represented the biological effect and therapeutic activity of the present inventors’ generated antibodies.
  • This cell assay was performed following the Guidance for Industry: Potency for cellular and gene therapy products issued by FDA in 2011 (the Part IV. Potency Assay Design and Validation). In this study, all the reagents, materials, standards, controls and calibrated equipment, as well as the training of operators, were adequately qualified. Sample randomization and quantitative analysis of the BrdU read-out with appropriate statistical methods, as well as sufficient number of replicates, demonstrated the accuracy, precision, specificity and consistency of this bioassay.
  • the present inventors chose this dose to evaluate the antibody capabilities (FIG.19A-19C).
  • PDGF at 20 ng/mL served as a positive control.
  • the present inventors further ranked the 17 antibodies (selected from the initial 80 clones as mentioned in the above section of Selection and Initial Screening) by potency and specificity in blocking function.
  • the present inventors then chose four as lead antibody candidates based on their blocking potentials.
  • the present inventors further labelled them as Ab-a, Ab-b, Ab-c, and Ab-d.
  • Ab-b was the most potent (FIG.19B and 19D-19F). It exhibited marked blocking efficacy in human primary SMC bioassays as shown in FIG. 19B (bronchial) and 1C (pulmonary vascular). The human cell-based bioassay thus allowed us to rank, choose, and validate the continued efficacy of lead antibodies against hResistin, and formed the basis the following testing in PH animal models. Binding Characteristics of the Lead Antibodies. These four above-selected lead antibodies were further synthesized by Lonza in small (1.2 L culture) and large (6 L culture) batches in CHO cells for use in in vivo assays.
  • Single and double gene GS vectors using Lonza’s GS XceedTM Gene Expression System were constructed and transfected into CHOK1SV GS-KO cells to express those antibodies. Stable recombinant cells were propagated for the fed-batch overgrowth cultures. Protein titre in supernatant samples was determined by Octet. Purification of antibodies in medium was carried out by Protein A affinity chromatography, to yield between 11.5 and 187 mg of purified material for the small scale evaluation cultures (Table VI), and between 350 mg to 2,028 mg for the large scale material supply (Table VII).
  • Ab-b expressed from fast stable pool at 7L scale was evaluated bioreactor production on CHO cell culture process platform by Wuxi AppTec, another one of the present inventors’ CRO’s.
  • the yield of Ab-b was 1.17g/L final titers with a purity of 96.07% after purification and less than 1EU/mg for endotoxin, demonstrating the promise of successful manufacturability.
  • the product quality was further validated by SE- HPLC analysis, and the generated antibodies exhibited high purity and low aggregate levels (FIG.19, and Table VIII). Endotoxin levels in the large-scale (1-2 grams) purified antibodies were below 0.53 EU/mg.
  • the present inventors thus employed structural modeling with RosettaAntibody and SnugDock 21 to further analyze the binding sites on hResistin interacting with Ab-b.
  • RosettaAntibody and SnugDock 21 On the hResistin protein, as reported previously, 22 two active site epitope regions were predicted: residue 50-65 and 78-93. The present inventors thus focused the present inventors’ docking on these two regions.
  • FIG. 21A Using a local docking run, the present inventors separately docked both the epitope regions of hResistin with the antibody Ab-b (FIG. 21A). Docking indicated that the putative epitope regions are binding sites for the hResistin protein when present in monomer state (FIG. 21A) which is the most functional form of hResistin exhibiting pro- proliferative capabilities (data not shown). Structural modeling further suggested that the lead antibody Ab-b interacts with the active binding epitopes in the globular head region of hResistin (FIG. 21B-5E) 23 , thereby blocking the pro-mitogenic effects of hResistin.
  • Rodent RELM ⁇ dose-dependently stimulated the proliferation of human bronchial SMCs at a minimum dose of 0.3 ⁇ g/mL (FIG.22B).
  • anti-hResistin human antibodies blocked the SMC proliferation induced by rodent RELM ⁇ (FIG.22C), indicating that rat RELM ⁇ can activate human RELM responses.
  • the present inventors went on to examine whether antibody application could be therapeutically efficacious in the rodent PH models (FIG.23), a critical step in moving these antibodies toward human use. Assessment of systematic and organ-specific toxicity of anti-hResistin antibody.
  • the present inventors lead antibodies had anti- proliferative properties in human cell assays and were able to block the activities of rodent RELM ⁇ which also was able to induce the proliferative phenotype in human SMCs. These results indicates that antibody in vivo application could be therapeutically efficacious in the future rodent PH models, a critical step in moving these antibodies toward human use (FIG. 23). Because hResistin and rodent RELM have incomplete homology and the lead antibody was at most 50% as effective against the rodent isoform in vitro as it was against hResistin, the present inventors expect that the antibody will be even more potent in humans than in rats.
  • RELMs activate damage-associated-molecular-pattern (DAMP) molecules, including HMGB1 11, 12 and S100A11, 17 and are responsible for impairments in mitochondrial function 13 and BMPR2 signaling 11 .
  • RELMs may also alter miRNAs in hypoxic lung tissue.
  • RELM signaling is a regulator for stem cell proliferation, differentiation, mobilization, and recruitment related to PH. 16, 18
  • the anti-RELM antibodies that the present inventors generated may have the potential to integrate these immune-, gene- and cell-based treatment strategies for a comprehensive anti-PH therapy.
  • PH in humans is a complex and multifactorial disease that is often identified at a late stage, combination therapy would allow distinct pathogenic pathways to be targeted simultaneously, leading to additive or synergistic beneficial effects.
  • the present inventors may combine the present inventors’ antibodies with other current investigational approaches such as treatments that target tyrosine kinase, 42 G- protein-coupled chemokine receptor, 42 microRNAs, 36 endothelin signaling, 42 IL-6, 25 or DAMPs. 43, 44 All of these pathways are involved in the inflammation-mediating properties of RELMs and thus would reinforce the functions of anti-RELM antibodies. 17, 19, 24, 45, 46 These projects will propel the therapeutic antibody studies forward for human development and use in clinical phase trials.
  • the present inventors have completed the tissue cross- reactivity testing with normal human tissues, and results indicated that the present inventors’ monoclonal antibody has no toxicologic significance in that model, 47 .
  • This provides initial human support for the safety seen in the present inventors’ rodent micro- and macro- pathology studies and in vivo utilization studies.
  • the present inventors are also performing the bioanalytic assay and pharmacokinetics studies. Development of such novel therapeutics may generate a more comprehensive understanding of the PH disease mechanisms and open the door for precision medicine.
  • the mechanistic insights might also be useful for improving outcomes of a variety of other vasculature-related disorders, especially cancers.
  • the present inventors antibodies may have additional benefits for patients with some cancers. Moreover, given the roles of hResistin in a variety of pulmonary, cardiac, and other related inflammatory pathologies including atherosclerosis, thrombosis, diabetes, pathological angiogenesis, cancers, etc., as mentioned above, 2 the present inventors’ developed antibody also can be a novel potential therapeutic for these diseases.
  • hypoxia-induced mitogenic factor recruits bone marrow-derived cells to the murine pulmonary vasculature.
  • S100a11 mediates hypoxia-induced mitogenic factor (himf)-induced smooth muscle cell migration, vesicular exocytosis, and nuclear activation. Mol Cell Proteomics.2011;10:M110000901.
  • Kolosova IA Angelini D, Fan C, Skinner J, Cheadle C, Johns RA. Resistin- like molecule a stimulates proliferation of mesenchymal stem cells while maintaining their multipotency.
  • Hypoxia-inducible factor 1alpha is a critical downstream mediator for hypoxia-induced mitogenic factor (fizz1/relmalpha)-induced pulmonary hypertension.
  • Rothman AM Arnold ND, Chang W, Watson O, Swift AJ, Condliffe R, Elliot CA, Kiely DG, Suvarna SK, Gunn J, Lawrie A. Pulmonary artery denervation reduces pulmonary artery pressure and induces histological changes in an acute porcine model of pulmonary hypertension. Circ Cardiovasc Interv.2015;8:e002569. 35. Chen SL, Zhang H, Xie DJ, Zhang J, Zhou L, Rothman AM, Stone GW. Hemodynamic, functional, and clinical responses to pulmonary artery denervation in patients with pulmonary arterial hypertension of different causes: Phase ii results from the pulmonary artery denervation-1 study.
  • hResistin Production of recombinant hResistin in T-REx 293 cells was induced by tetracycline (1 ⁇ g/mL) in DMEM supplemented with 5% fetal bovine serum, 100 ⁇ g/mL hygromycin B, and 7.5 ⁇ g/mL blasticidin. hResistin then was purified from the cell culture medium with anti-FLAG M2 antibody agarose (Sigma, St. Louis, MO) column chromatography. Phage display approach to initial screening of the generated antibodies. The present inventors initiated an antibody search using hResistin to select scFv binders from a phage display human scFv library. An initial 80 clones were chosen from the screen.
  • Soluble ELISA was used to select hResistin scFv clones that bound to their target positively. These selected scFv fragments were subsequently made into full human IgG1 antibodies for use in initial lead selection studies. ELISA evaluation for potency and selectivity. A sandwich-type ELISA approach was created to evaluate the binding efficacy of each anti-hResistin antibody. The antigen concentration and the antibody concentration were varied to assist in selecting the initial antibodies for further screening. In silico screening. In silico evaluations included deamidation risk, oxidation risk, isoelectric point, and immunogenicity.
  • aggregation and post-translational modifications such as glycosylation, deamidation, oxidation and variation of the N- and C-termini.
  • the antibody aggregation platform was developed using machine learning algorithms based on sequence and structural features of antibodies as described. 2 Asparagine deamidation, aspartate isomerisation and fragmentation, and C- terminal lysine processing were predicted by detecting the targeted and succeeding residues. Analyses of possible influences from structural features were also performed. The isoelectric point was calculated based on the number of charged residues in the primary amino-acid sequence using EMBOSS pKa values.
  • N-glycosylation the motif N-X-S/T where X is any residue except Proline generally served to detect sites.
  • a boosting decision tree ensemble algorithm was trained on experimentally determined glycosylation sites in order to predict O-glycosylation.
  • N-terminal Glycine-Proline motifs were detected to predict cyclization.
  • Methionine and Tryptophan residues were identified for the prediction of oxidation.
  • N-terminal Glutamine or Glutamate residues were detected for pyroglutamate formation analysis. Stable pooled production, purification and product analysis of antibodies.
  • heavy and light chain genes were synthesized by Life Technologies and sub-cloned into Lonza Biologics GS XceedTM gene expression system vectors.
  • Stable pooled transfections of CHOK1SV GS-KO cells with the established double gene vector DNA plasmids were carried out via electroporation using the Gene Pulse XCell.
  • recombinant cells were cultured in CD-CHO media supplemented with 50 ⁇ M MSX and SP4, and propagated for the fed-batch overgrowth cultures.
  • Protein A purification of the clarified supernatant was performed using HiTrap MabSelect SuRE columns in tandem (GE Healthcare) on an AKTA purifier. Eluted fractions were immediately pH adjusted by neutralizing with 2x PBS buffer, pH 7.4 and titrated to approximately pH 7.2–7.6 by the addition of dilute sodium hydroxide solution.
  • Antibody protein yield was determined by 280 nm absorbance on a Nanodrop instrument. Samples of clarified cell culture supernatant were also analyzed on an Octet QKe using Protein A Biosensors (ForteBio, 18-5010). 200 ⁇ L aliquots of supernatant samples were loaded into a 96-well plate and quantified against an eight-point standard curve. Fast Stable Pool production. Ab-b was generated from fast stable pool cultured in 7L bioreactors based on WuXi Biologics Chinese Hamster Ovary (CHO) cell culture process. Cells in pools showed acceptable cell growth rates in exponential phase and reached equivalent peak viable cell densities, ranged in 20–25 ⁇ 10 6 cells/mL.
  • hResistin antibodies were then passed over the captured antigen at varying concentrations. Chip regeneration was carried out with carbonate buffer (pH 11.55, 50 mM) or CAPS buffer (pH 11.4, 0.1 M). Binding of antigen (hResistin) to the antibodies was monitored in real time. From the observed apparent on-rates (ka) and off-rates (kd), the equilibrium affinity KD (kd/ka) was determined. The binding curves were referenced with negative (human IgG) and positive (R&D goat anti-hResistin polyclonal Ab) controls, and the data were fitted to the Biacore 1000 analysis software. Endotoxin measurement.
  • Endotoxin levels of the purified proteins at 1 mg/mL concentration were measured with the Endosafe-PTS instrument, a cartridge-based method based on the Limulus Amebocyte Lysate (LAL) assay (Charles River, Frederick, MD). Structural modeling for the assessment of antibody-protein binding.
  • the ClusPro online server was used to check whether the present inventors’ predictive epitope regions (residues 50-65 and 78-93) 3 can be identified. 4, 5 Using the known crystal structure for resistin in mice as a basis (PDB ID 1RFX, 58% sequence identity), 6, 7 the present inventors modeled the three-dimensional structure of a monomeric hResistin. antibody three-dimensional structure was predicted from sequence by using RosettaAntibody.
  • Antibody was concentrated to 5 mg/mL using Amicon centrifugal filters with a molecular weight cut off of 30kDa (UFC903024, Merck). 500 ⁇ l of the concentrated product was aliquoted per test condition (Table IX) into glass vials for each condition to be tested. After a 14 day incubation period the stability of Ab-b in each condition was assessed via SDS-PAGE, SE-HPLC and cIEF. SE-HPLC analysis was performed as mentioned above. Capillary IEF analysis was performed using the Maurice Capillary Electrophoresis (iCE) system (Protein Simple).
  • samples were diluted in sample buffer to a final concentration of 1mg/mL (and a final salt concentration ⁇ 50 mM).
  • the sample buffer was prepared by mixing deionised water with 1% methyl cellulose, Pharmalyte 3-10, 500mM arginine and pI markers, to give a final volume of 200 ⁇ l.
  • Running conditions were as follows: 1 min at 1500V followed by 4.5min at 3000V for each sample.
  • Data analysis was performed using Compass for iCE (Protein Simple).
  • hResistin/RELM (Lonza, customized): In vitro blockade: 0.1-10 ⁇ g/mL.
  • FLAG M2 (Sigma, F1804): WB: 1 mg/mL.
  • BrdU kit
  • ELISA 0.075 U/mL.
  • WB western blot; ELISA, enzyme-linked immunosorbent assay.
  • brackets refer to self- epitopes. Based on the critical epitope counts, the affected HLA allotypes and DRB1 risk score, the ten antibodies can be ranked by increased immunogenic risk as follows: Ab #1 ⁇ #5 ⁇ [#2, #4] ⁇ #10 ⁇ [#3, #6] ⁇ [#7, #8, #9].
  • Table VI Yields and titres of 1.2L fed batch cultures for the anti-hResistin antibodies A ntibodies Concentration Yield Titre Monomer Endotoxin ( mg/mL) Volume (ml) (mg) (mg/L) (%) (EU/mg) A ntibodies Concentration Yield Titre Monomer Endotoxin ( mg/mL) Volume (ml) (mg) (mg/L) (%) (EU/mg) y p g Antibodies Injection Total Fragments Total Aggregates Total Monomer Ab 1 366 9633 Table IX. Stability Study Conditions Condition Temperature Duration Table X. Serum CBC parameters of the antibody-treated rats CBC Vehicle (Con)-injected Ab-b-injected Con vs. Ab Item Mean SEM Range Mean SEM Range p value
  • Table XI Serum chemistry parameters of the antibody-treated rats Chemistry Vehicle (Con)-injected Ab-b-injected Con vs. Ab Item Mean SEM Range Mean SEM Range p value Table XII. Gross evaluation of the antibody-treated rats Item Vehicle (Con)-injected Ab-b-injected Gross BCS 4/5 (5 rats; 3 unremarkable) BCS 4/5 (4 rats; one unremarkable) . Organ Weights (g) Vehicle (Con)-injected Ab-b-injected Con vs.

Abstract

La présente invention concerne le domaine de la virologie. Plus spécifiquement, la présente invention concerne des compositions et des méthodes pour évaluer la gravité et traiter le coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2) ou la COVID-19. Dans des modes de réalisation particuliers, une méthode de traitement de la COVID-19 chez un patient comprend l'étape d'administration au patient d'un anticorps recombinant isolé ou d'un fragment de liaison à l'antigène de celui-ci qui se lie à la Résistine humaine.
PCT/US2023/071902 2022-08-09 2023-08-09 Compositions et méthodes d'évaluation de la gravité et de traitement de la covid-19 WO2024036192A2 (fr)

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