WO2018136625A2 - Compositions and methods for treating diseases characterized by reactive microglia mediated synapse loss - Google Patents

Compositions and methods for treating diseases characterized by reactive microglia mediated synapse loss Download PDF

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WO2018136625A2
WO2018136625A2 PCT/US2018/014223 US2018014223W WO2018136625A2 WO 2018136625 A2 WO2018136625 A2 WO 2018136625A2 US 2018014223 W US2018014223 W US 2018014223W WO 2018136625 A2 WO2018136625 A2 WO 2018136625A2
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subject
antibody
mice
microglia
ifnar
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PCT/US2018/014223
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French (fr)
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WO2018136625A3 (en
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Michael C. Carroll
Allison Rosen BIALAS
Jessy PRESUMEY
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Children's Medical Center Corporation
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2866—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/42—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum viral
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding

Definitions

  • SLE Systemic lupus erythematosus
  • CNS central nervous system
  • CNS lupus typically presents at lupus diagnosis or within the first year. Without being bound by theory, this suggests that early factors contributing to peripheral
  • the present invention features compositions and methods for identifying and treating CNS lupus and related disease characterized by microglia mediated synapse loss.
  • the invention provides a method of treating a subject having a disease or disorder characterized by reactive microglia mediated synapse loss, the method involving administering to the subject an agent that inhibits binding to an interferon alpha/beta receptor, wherein the disease or disorder is not CNS lupus.
  • the invention provides a method of treating a subject having CNS lupus, the method involving administering to the subject an anti-interferon alpha/beta receptor antibody or anti-interferon alpha antibody, wherein the subject is selected as having reactive microglia mediated synapse loss.
  • the invention provides a method of selecting therapy for a subject having CNS lupus, the method involving detecting increased type I interferon in a
  • IFNAR anti-interferon alpha eta receptor
  • the invention provides a method of identifying a subject as having CNS lupus, the method involving detecting reactive microglia mediated synapse loss or increased type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein said detection identifies the subject as having CNS lupus.
  • the invention provides a method of monitoring CNS lupus therapy in a subject, the method involving detecting type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein the reference level is the level of interferon alpha present in the cerebrospinal fluid of the subject prior to treatment with an anti- IFNAR antibody treatment.
  • the invention provides a method of reducing the level of activated microglia present in a subject in need thereof, the method involving administering an anti- interferon alpha/beta receptor antibody to the subject.
  • the invention provides a kit containing an anti-IFNAR antibody and instructions for the treatment of CNS lupus.
  • the kit further contains a capture molecule that specifically binds interferon.
  • the invention provides a method of depleting activated microglia in a subject in need thereof, the method involving administering to the subject an effective amount of an anti-IFNAR antibody to the subject.
  • the subject has a disease or disorder characterized by neurological or neuropsychiatric symptoms.
  • the agent is an anti-interferon alpha/beta receptor antibody or an anti- interferon alpha antibody.
  • the subject has increased levels of peripheral interferon.
  • the subject has an autoimmune disease, a neurodegenerative disease, or a chronic viral infection.
  • the subject has Sjogren's syndrome, Alzheimer's disease, or Human Immunodeficiency Virus Infection.
  • the subject presents with neuropsychiatric or neurological symptoms (e.g., anxiety phenotype, depression, cognitive impairment, and social interaction defects).
  • the anti-IFNAR antibody is a human, humanized or chimeric antibody.
  • the anti-IFNAR antibody contains a VH domain containing the amino acid sequence of SEQ ID NO: 1 or a VK domain containing the amino acid sequence of SEQ ID NO: 2.
  • the disease state of the subject is characterized using brain imaging studies, functional or conventional magnetic resonance imaging, Pre-pulse Inhibition, measuring gray matter volume, or using a Positron Emission Topography studies.
  • compositions and methods for identifying and treating CNS lupus and related disease characterized by microglia mediated synapse loss Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.
  • CNS lupus-related disease or disorder any disease characterized by reactive microglia mediated synapse loss.
  • diseases include an autoimmune disease or disorder, such as Sjogren's syndrome, a neurodegenerative disease, such as Alzheimer's disease, or a chronic viral infection, such as Human Immunodeficiency Virus Infection.
  • the presence or absence of reactive microglia mediated synapse loss is characterized as described herein below.
  • type I interferon polypeptide is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. AAI12303.1 and having a biological activity or function of a type I interferon polypeptide.
  • the interferon type I class includes: interferon (IFN)-a (alpha), IFN- ⁇ (beta), IFN- ⁇ (kappa), IFN- ⁇
  • IFN- ⁇ epsilon
  • IFN- ⁇ tau
  • IFN-co omega
  • IFN- ⁇ zeta
  • Biological activities or functions of a type I interferon polypeptide include, without limitation, binding of the IFN-alpha/beta receptor (IFNAR) and regulation of immune system response.
  • IFNAR IFN-alpha/beta receptor
  • the sequence of IFN-alpha at NCBI Accession No. AAI12303.1 is shown below:
  • type I interferon polynucleotide is meant a polynucleotide encoding any type I interferon polypeptide.
  • An exemplary type I interferon polynucleotide sequence e.g., IFN-alpha polynucleotide is provided at NCBI Accession No. NM_024013.2. The sequence is provided below:
  • interferon beta (IFN-beta) polypeptide is meant a polypeptide or fragment thereof, having at least about 85% amino acid identity to NCBI Accession No.
  • AAC41702.1 and having a biological activity or function of an IFN-beta polypeptide.
  • IFN-beta polypeptide Biological activities or functions of an IFN-beta polypeptide include, without limitation, binding of the IFN-alpha/beta receptor (IFNAR) and regulation of immune system
  • IFNAR IFN-alpha/beta receptor
  • interferon beta (IFN-beta) polynucleotide is meant a polynucleotide encoding an IFN-beta polypeptide.
  • An exemplary IFN-beta polynucleotide sequence is provided at NCBI Accession No. NM_002176.3. The sequence is provided below:
  • B-cell receptor polypeptide is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. NP_001762.2 and having a biological activity or function of a B-cell receptor.
  • Biological activities or functions of a B-cell receptor include, without limitation, antigen binding and signaling transduction.
  • the B-cell receptor is a transgenic B-cell receptor specific for the well- known lupus antigen, SSB/La, described by Berland et al. ⁇ Immunity 25, 429-440, 2006) and Chatterjee et al.
  • the B-cell receptor is a human B-cell receptor.
  • the sequence at NCBI Accession No. NP_001762.2 is shown below:
  • B-cell receptor polynucleotide is meant a polynucleotide encoding a B cell receptor polypeptide.
  • An exemplary B-cell receptor polynucleotide sequence is provided at NCBI Accession No. NM_001771.3. The sequence is provided below:
  • gagtcccagg aagtcactct gacctgcttg ctgaatttct cctgctatgg gtatccgatc
  • CNS lupus is meant the presence of neurological changes and/or behavioral clinical syndromes in a patient that has systemic lupus erythematosus.
  • CNS lupus Symptoms of CNS lupus include, but are not limited to, cognitive dysfunction (not thinking clearly, memory deficits), headaches, seizure, altered mental alertness (e.g. stupor or coma), aseptic meningitis (inflammation of the covering of the brain), stroke (disturbance of the blood supply to different parts of the brain), peripheral neuropathy (e.g. numbness, tingling, burning of the hands and feet), movement disorders, myelitis (disruption) of the spinal cord, visual alternations, autonomic neuropathy (e.g., flushing reaction or mottled skin), personality changes, and changes in sociability.
  • CNS lupus is characterized by changes in frontal cortex and/or hippocampus.
  • interferon (IFN)-alpha/beta receptor (IFNAR) polypeptide is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. NP_000620.2 and having a biological activity or function of an IFNAR.
  • Biological activities or functions of an IFNAR include, without limitation, binding type I interferons including interferon-a and interferon - ⁇ , and/or signaling via pathways downstream of IFNAR (e.g., activation of the JAK-STAT signaling pathway).
  • binding type I interferons including interferon-a and interferon - ⁇
  • signaling via pathways downstream of IFNAR e.g., activation of the JAK-STAT signaling pathway.
  • IFN-alpha/beta receptor (IFNAR) polynucleotide is meant a polynucleotide encoding an IFNAR polypeptide.
  • An exemplary IFNAR polynucleotide sequence is provided at NCBI Accession No. NM_000629.2. The sequence is provided below:
  • anti-interferon alpha/beta receptor (IFNAR) antibody is meant an antibody or fragment thereof that specifically binds an interferon receptor.
  • the anti- IFNAR antibody is "MEDI-546,” also termed “anifrolumab,” which refers to an Fc-modified version of the anti-IFNAR 9D4 antibody described in U.S. Pat. No. 7,662,381, which is incorporated by reference in its entirety. The sequence of MEDI-546 is described in U.S. 2011-0059078.
  • MEDI-546 comprises a combination of three mutations: L234F, L235E, and P331 S, wherein the numbering is according to the EU index as set forth in Kabat, introduced into the lower hinge and CH2 domain of human IgGl, which cause a decrease in their binding to human Fc.gamma.RI (CD64), Fc.gamma.RIIA (CD32A), Fc.gamma.RIII (CD 16) and Clq. See, e.g., US 2011/0059078 and Oganesyan et al. Acta Crystallographica D 64:700-704 (2008), which are hereby incorporated by reference in their entireties.
  • anti-interferon alpha antibody is meant or fragment thereof that specifically binds interferon alpha. In one embodiment, the antibody does not bind interferon beta.
  • Such antibodies are known in the art and include antibodies described in US Patent No. 7,087,726, Sifalimumab (Medi-545) Yao et al., Arthritis Rheum. 2009 Jun; 60(6): 1785-96.
  • agent any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.
  • ameliorate decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.
  • alteration is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein.
  • an alteration includes a 10% change in expression levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels.
  • antibody refers to an immunoglobulin molecule which specifically binds with an antigen.
  • the antigen is IFN-alpha/beta receptor (IFNAR).
  • IFNAR IFN-alpha/beta receptor
  • Tetramers may be naturally occurring or reconstructed from single chain antibodies or antibody fragments.
  • Antibodies also include dimers that may be naturally occurring or constructed from single chain antibodies or antibody fragments.
  • the antibodies in the present invention may exist in a variety of forms including, for example, polyclonal antibodies, monoclonal antibodies, Fv, Fab and F(ab') 2 , as well as single chain antibodies (scFv), humanized antibodies, and human antibodies (Harlow et al., 1999, In: Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY; Harlow et al., 1989, In: Antibodies: A Laboratory Manual, Cold Spring Harbor, New York; Houston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; Bird et al., 1988, Science 242:423-426).
  • antibody fragment refers to a portion of an intact antibody and refers to the antigenic determining variable regions of an intact antibody.
  • antibody fragments include, but are not limited to, Fab, Fab', F(ab') 2 , and Fv fragments, linear antibodies, scFv antibodies, single-domain antibodies, such as camelid antibodies
  • the antibody fragment also includes a human antibody or a humanized antibody or a portion of a human antibody or a humanized antibody.
  • Antibodies can be made by any of the methods known in the art utilizing a polypeptide or immunogenic fragments thereof, as an immunogen.
  • One method of obtaining antibodies is to immunize suitable host animals with an immunogen and to follow standard procedures for polyclonal or monoclonal antibody production.
  • the immunogen will facilitate presentation of the immunogen on the cell surface.
  • Immunization of a suitable host can be carried out in a number of ways. Nucleic acid sequences encoding a polypeptide of the invention or immunogenic fragments thereof, can be provided to the host in a delivery vehicle that is taken up by immune cells of the host. The cells will in turn express the receptor on the cell surface generating an immunogenic response in the host. Alternatively, nucleic acid sequences encoding the polypeptide, or immunogenic fragments thereof, can be expressed in cells in vitro, followed by isolation of the polypeptide and administration of the polypeptide to a suitable host in which antibodies are raised.
  • antibodies against the polypeptide may, if desired, be derived from an antibody phage display library.
  • a bacteriophage is capable of infecting and reproducing within bacteria, which can be engineered, when combined with human antibody genes, to display human antibody proteins.
  • Phage display is the process by which the phage is made to 'display' the human antibody proteins on its surface. Genes from the human antibody gene libraries are inserted into a population of phage. Each phage carries the genes for a different antibody and thus displays a different antibody on its surface.
  • Antibodies made by any method known in the art can then be purified from the host.
  • Antibody purification methods may include salt precipitation (for example, with ammonium sulfate), ion exchange chromatography (for example, on a cationic or anionic exchange column preferably run at neutral pH and eluted with step gradients of increasing ionic strength), gel filtration chromatography (including gel filtration HPLC), and chromatography on affinity resins such as protein A, protein G, hydroxyapatite, and anti-immunoglobulin.
  • Antibodies can be conveniently produced from hybridoma cells engineered to express the antibody. Methods of making hybridomas are well known in the art.
  • the hybridoma cells can be cultured in a suitable medium, and spent medium can be used as an antibody source. Polynucleotides encoding the antibody of interest can in turn be obtained from the hybridoma that produces the antibody, and then the antibody may be produced synthetically or recombinantly from these DNA sequences. For the production of large amounts of antibody, it is generally more convenient to obtain an ascites fluid.
  • the method of raising ascites generally comprises injecting hybridoma cells into an immunologically naive histocompatible or immunotolerant mammal, especially a mouse. The mammal may be primed for ascites production by prior administration of a suitable composition (e.g., Pristane).
  • a suitable composition e.g., Pristane
  • capture reagent is meant a reagent that specifically binds a nucleic acid molecule or polypeptide to select or isolate the nucleic acid molecule or polypeptide.
  • a capture reagent of the invention binds Interferon alpha.
  • Detect refers to identifying the presence, absence or amount of the analyte to be detected.
  • disease is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Examples of diseases include diseases
  • microglia mediated synapse loss such as CNS lupus, Sjogren's syndrome, HIV, Alzheimer's disease, and chronic viral infections.
  • an effective amount is meant the amount of a required 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 a disease 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 invention provides a number of targets that are useful for the development of highly specific drugs to treat or a disorder characterized by the methods delineated herein.
  • the methods of the invention provide a facile means to identify therapies that are safe for use in subjects.
  • the methods of the invention provide a route for analyzing virtually any number of compounds for effects on a disease described herein with high-volume throughput, high sensitivity, and low complexity.
  • fragment is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide.
  • a fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.
  • Hybridization means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
  • adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds.
  • isolated refers to material that is free to varying degrees from components which normally accompany it as found in its native state.
  • Isolate denotes a degree of separation from original source or surroundings.
  • Purify denotes a degree of separation that is higher than isolation.
  • a “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized.
  • Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography.
  • the term "purified" can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel.
  • modifications for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.
  • isolated polynucleotide is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene.
  • the term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences.
  • the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.
  • an “isolated polypeptide” is meant a polypeptide of the invention that has been separated from components that naturally accompany it.
  • the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated.
  • the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, a polypeptide of the invention.
  • An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
  • a marker of the invention is the level of a cytokine, such as a type I interferon (e.g., IFN alpha or beta) in a bodily fluid (e.g., cerebrospinal fluid, blood, serum, plasma).
  • a cytokine such as a type I interferon (e.g., IFN alpha or beta) in a bodily fluid (e.g., cerebrospinal fluid, blood, serum, plasma).
  • microglia is meant an immune cell of myeloid lineage resident in the central nervous system.
  • obtaining as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.
  • reference is meant a standard or control condition.
  • telomere binding By “specifically binds” is meant a compound or antibody that recognizes and binds a polypeptide of the invention, but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample, which naturally includes a polypeptide of the invention.
  • Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having "substantial identity" to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity.
  • Polynucleotides having "substantial identity" to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule.
  • hybridize is meant pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency.
  • complementary polynucleotide sequences e.g., a gene described herein
  • stringent salt concentration will ordinarily be less than about 750 mM
  • NaCl and 75 mM trisodium citrate preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and more preferably less than about 250 mM NaCl and 25 mM trisodium citrate.
  • Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide.
  • Stringent temperature conditions will ordinarily include temperatures of at least about 30° C, more preferably of at least about 37° C, and most preferably of at least about 42° C.
  • Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those of ordinary skill in the art.
  • Various levels of stringency are accomplished by combining these various conditions as needed.
  • hybridization will occur at 30° C in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS.
  • hybridization will occur at 37° C in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 .mu.g/ml denatured salmon sperm DNA (ssDNA).
  • hybridization will occur at 42° C in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 ⁇ g/ml ssDNA. Useful variations on these conditions will be readily apparent to those of ordinary skill in the art.
  • wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature.
  • stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.
  • Stringent temperature conditions for the wash steps will ordinarily include a temperature of at least about 25° C, more preferably of at least about 42° C, and even more preferably of at least about 68° C.
  • wash steps will occur at 25° C in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 42 C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 68° C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS.
  • Hybridization techniques are well known to those of ordinary skill in the art and are described, for example, in Benton and Davis (Science 196: 180, 1977); Grunstein and
  • substantially identical is meant a polypeptide 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).
  • a reference amino acid sequence for example, any one of the amino acid sequences described herein
  • 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 more 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). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine;
  • BLAST program may be used, with a probability score between e "3 and e "100 indicating a closely related sequence.
  • subject is meant a mammal, including, but not limited to, a human or non- human mammal, such as a bovine, equine, canine, ovine, or feline.
  • Ranges provided herein are understood to be shorthand for all of the values within the range.
  • a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
  • treat refers to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
  • the term "about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.
  • the recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups.
  • the recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
  • compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.
  • FIGS. 1 A-1L show behavioral phenotyping of 564Igi mice.
  • FIG. IB is a graph showing that 564I
  • FIG. 1G is a graph showing increased prepulse inhibition in 564Igi mice.
  • FIG. II is a graph showing that rotarod performance of 564Igi mice
  • FIGS. 1 A-1L data are mean ⁇ s.e.m.
  • FIG. 2A is a graph showing behavior in wild-type and 564Igi mice in the elevated plus maze. Elevated plus maze evaluates anxiety-like phenotypes. 564, 564Igi mice; WT, wild-type mice. Isotype, isotype-control antibody; anti-IFNAR, anti-IFNAR antibody. Two-way ANOVA with Tukey's test.
  • FIG. 2B is a graph showing cognitive function in wild-type and 564Igi mice in the novelty Y maze. Novelty Y maze evaluates cognitive function.
  • FIG. 1A-1L data are mean ⁇ s.e.m.
  • FIGS. 2A-2J depict behavioral phenotypes and reactive microglia in 564Igi mice.
  • FIG. 2A is a graph showing behavior
  • FIG. 2C is a graph showing sociability in wild-type and 564Igi mice in the three-chamber test. Three- chamber test evaluates sociability.
  • FIG. 2D is a graph showing sensorimotor function in wild-type and 564Igi mice in the prepulse-inhibition test. Prepulse-inhibition test evaluates sensorimotor gating at three different tone intensities.
  • FIG. 2E depict microglial activation state analysis in wild-type, 564Igi, and NZB/NZW mice. Arrows indicate reactive microglia.
  • FIG. 2F is a graph showing percentage reactive microglia out of total microglia in the hippocampus, cortex, and cerebellum.
  • FIG. 2G depicts qPCR analysis of Ifiia in the spleen of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls.
  • FIG. 2H depicts qPCR analysis oiMxl in the spleen of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls.
  • FIG. 2G depicts qPCR analysis of Ifiia in the spleen of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls.
  • FIG. 21 depicts qPCR analysis of Ifiia in the hippocampus of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls.
  • FIG. 2J depicts qPCR analysis of Mxl in the hippocampus of
  • NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls.
  • FIGS. 2G-2J Two-way ANOVA with Tukey's test. Data are mean ⁇ s.e.m. *P ⁇ 0.05, **P ⁇ 0.01, ***P ⁇ 0.001, ****P ⁇ 0.0001 using a two-way ANOVA with Sidak's test, unless indicated otherwise.
  • n 10 mice per group
  • n 3 mice per group.
  • FIGS. 3 A-3F depict no significant cellular infiltration or microglia proliferation in
  • FIG. 3 A depicts representative images of haematoxylin and eosin staining. No evidence of cellular infiltration or gross anatomical abnormalities was observed in 564Igi mice. Scale bar, 100 ⁇ .
  • FIG. 3B depicts
  • FIG. 3C depicts
  • FIG. 3D depicts representative images of Ibal and CD68 staining, and the common microglia activation state scores observed in adult mouse tissue. Microglia, which fell into the category of 3 or higher, were pooled to form the reactive microglia population. Scale bar, 20 ⁇ .
  • FIG. 3E shows similar microglia density for cortex, hippocampus and cerebellum in wild-type, 564Igi and NZB/NZW mice.
  • 3F are images and a graph showing that MRL-lpr mice exhibited increased reactive microglia at 8 weeks, similar to NZB/NZW mice.
  • data are mean ⁇ s.e.m.
  • FIGS. 4A-4J showing that Ifiib was not expressed and anti-IFNAR treatment was effective in both 564Igi and NZB/NZW mice.
  • FIG. 4A is a graph showing
  • 4C is a graph showing a significant increase in expression of Ifi44 in the spleen in 564Igi and NZB/ NZW mice compared to wild-type mice, as measured by qPCR.
  • the increase of Ifi44 expression in the spleen was reduced with anti-IFNAR treatment.
  • FIG. 4D is a graph showing a significant increase in expression of Oasl in the spleen in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR.
  • FIG. 4E is a graph showing a significant increase in expression of Ifi44 in the hippocampus in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR.
  • FIG. 4F a graph showing a significant increase in expression of Oasl in the hippocampus in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR.
  • FIG. 4G is a graph showing expression of Ifiia in the spleen in 564Igi and NZB/NZW mice ⁇ anti-IFNAR treatment, as measured by qPCR.
  • n 3 mice per group, **P ⁇ 0.01, two-way ANOVA with Tukey's test.
  • FIG. 4G is a graph showing expression of Ifiia in the spleen in 564Igi and NZB/NZW mice ⁇ anti-IFNAR treatment, as measured by qPCR.
  • n 3 mice per group, **P ⁇ 0.01, two-way ANOVA with Tukey's test.
  • FIG. 4H is a graph showing autoreactive B cell
  • FIG. 41 is a graph showing expression of Ifiia in the hippocampus in 564Igi and NZB/NZW mice ⁇ anti-IFNAR treatment, as measured by qPCR.
  • n 3 mice per group, P > 0.05, two-way ANOVA with Tukey's test.
  • FIG. 4J is a representative image from a Mxl-Cre Tdtomato reporter mouse immunostained against the neuronal marker NeuN (dark gray), showing clusters of neurons and that are positive for Mxl (pseudocoloured light gray). Scale bar, 50 ⁇ .
  • data are mean ⁇ s.e.m.
  • FIGS. 5A-5J show that IFNAR signalling regulated microglia activation state.
  • FIG. 5 A is a graph depicting Mxl mRNA expression in spleen.
  • FIG. 5B is a graph depicting Mxl mRNA expression in hippocampus.
  • FIG. 5C are images depicting microglial activation state analysis. Arrows indicate reactive microglia.
  • FIG. 5D is a graph of percent reactive microglia from FIG. 5C.
  • FIG. 5E are images depicting activation state analysis in 12-week-old 564Igi Mxl-Cre Tdtomato mice. Arrows indicate Mxl + microglia.
  • FIG. 5F is a graph of percent reactive microglia from FIG. 5E.
  • FIG. 5H is a graph depicting expression of Mxl in microglia from bone marrow chimeras, as measured by qPCR.
  • FIG. 51 is a graph depicting activation state analysis in 564Igi bone marrow chimeras.
  • FIG. 5 J are images showing RNAscope in situ hybridization on control and SLE cases for YY and AIF1 (marking microglia). Circles indicate microglia;
  • FIGS. 6A-6D show a direct role of IFNAR signalling in the brain in bone marrow chimera mice.
  • FIG. 6A is a schematic showing that bone marrow extracted from wild-type (CD45.1) or 564Igi mice was administered to wild-type or IfiiarF 1' mice after lethal irradiation. Head shielding was added to protect the CNS during lethal irradiation. Mice were analyzed six weeks after bone marrow transplant.
  • FIG. 6A is a schematic showing that bone marrow extracted from wild-type (CD45.1) or 564Igi mice was administered to wild-type or IfiiarF 1' mice after lethal irradiation. Head shielding was added
  • FIG. 6C is a graph showing that expression of Ifiia in purified microglia revealed similar expression levels in wild-type and IfiiarF 1' recipients of wild-type or 564Igi bone marrow, as measured by qPCR.
  • n 3 mice per group, P > 0.05, two-way ANOVA with Sidak's test.
  • FIG. 6D is a graph showing that expression of Ifiib in purified microglia revealed significant upregulation in wild-type recipients of 564Igi bone marrow relative to IfiiarF 1' recipients, as measured by qPCR.
  • data are mean ⁇ s.e.m.
  • FIGS. 7A-7D depict increased MXA signal in hippocampal brain sections from patients with SLE.
  • FIG. 7A is a table showing clinical data for the patient brain sections analyzed by immunohistochemistry for MXA. Highlighted cases showed higher MXA levels than controls.
  • FIG. 7B depicts representative images of hippocampal brain sections for the cases that showed increased MXA signal. Scale bars, 100 ⁇ m.
  • FIG. 7C depicts antibody specificity validation: staining with an isotype control antibody (top) or only the secondary antibody (bottom) showed no signal.
  • FIGS. 8A-8D depict sorting of microglia for RNA-seq analysis.
  • FIG. 8 A shows that macrophages were sorted on the basis of CD45 Mgl1 expression.
  • FIG. 8B shows that similar macrophage frequencies were observed in wild-type and 564Igi brain suspensions.
  • n 4 mice per group, P > 0.05 (not significant), unpaired t-test.
  • FIG. 8C are plots showing post-sort flow cytometry to validate microglia purity revealed surface expression of two additional microglial markers, CD39 and CX3CR1, in > 99% of sorted cells.
  • FIG. 8A-8D depict sorting of microglia for RNA-seq analysis.
  • FIG. 8 A shows that macrophages were sorted on the basis of CD45 Mgl1 expression.
  • FIG. 8B shows that similar macrophage frequencies were observed in wild-type and 564Igi brain suspensions.
  • n 4 mice per group, P > 0.05 (not significant), unpaired
  • FIGS. 8A-8D is a graph showing elevated expression of 20 out of 25 microglia-specific genes by RNA-seq analysis in sorted microglia relative to sorted meningeal macrophages.
  • data are mean ⁇ s.e.m.
  • FIGS. 9A-9E depict RNA-seq and Gene Ontology analysis.
  • FIG 9A depicts a multidimensional scaling analysis showing clustering of samples by treatment group. Dim, dimension; FC, fold change.
  • FIG. 9B is a smear plot showing significant changes in gene expression (gray) in 564Igi versus wild-type mice. CPM, counts per million reads.
  • FIG. 9C depicts Gene Ontology analysis using GOseq identified enriched pathways in microglia derived from 564Igi relative to wild-type mice, q ⁇ 0.05 for all pathways, size of the square is relative to q value.
  • FIG. 9D depicts distribution of genes classified as IFNAR-dependent or - independent.
  • FIG. 9E depicts microglia sensome genes that are significantly upregulated in 564Igi versus wild-type mice.
  • Wild type versus 564Igi all genes, q ⁇ 0.05; * 564Igi versus 564Igi + anti-IFNAR: q ⁇ 0.05, GLM likelihood ratio test. Data are mean ⁇ s.e.m.
  • FIGS. 10A-10K show that genetic and functional changes in microglia were IFNAR- dependent.
  • FIG. 1 OA is a graph showing that interferon- response genes were significantly upregulated in 564Igi compared to wild-type microglia (Benjamini-Hochberg false discovery rate of q ⁇ 0.05 for all genes, generalized linear model (GLM) likelihood ratio test).
  • FIG. 1 OA is a graph showing that interferon- response genes were significantly upregulated in 564Igi compared to wild-type microglia (Benjamini-Hochberg false discovery rate of q ⁇ 0.05 for all
  • FIG. 1 OB is a GOseq Gene Ontology analysis of the IFNAR-dependent and IFNAR-independent gene sets.
  • FIG. IOC are plots depicting flow cytometry gating of microglia (left) and tau- GFP + microglia (right).
  • FIG. 10D is a graph depicting quantification of the percentage tau- GFP + microglia out of total microglia.
  • C cerebellum
  • F frontal cortex
  • H hippocampus.
  • ***P ⁇ 0.0009 two-way ANOVA with Sidak's test.
  • FIG. 10E is a graph depicting flow cytometry engulfment analysis of cells from anti-IFNAR-treated 564Igi mice or isotype- treated controls.
  • FIG. 10F depicts quantification of confocal images of tau-GFP internalization in the frontal cortex.
  • FIG. 10G is a graph depicting quantification of confocal images for tau-GFP
  • FIG. 101 depicts images showing that biotinylated IFNa could be detected within the brain (gray). Active IFNAR signalling was also observed (light gray).
  • FIG. lOJ is a graph depicting flow cytometry analysis of tau-GFP mice injected with IFNa.
  • FIG. 1 OK is a graph depicting flow cytometry analysis of tau- GFP mice injected with IFNp. * P ⁇ 0.05, **P ⁇ 0.01, unpaired t-test.
  • FIGS. 11 A-l 1G show that interferon can enter via an intact blood-brain barrier and is sufficient to trigger engulfment of neuronal material by microglia.
  • FIG. 11 A are a series of plots depicting gating for tau-GFP + microglia for engulfment analysis based on tau-GFP " control mice (gate set to ⁇ 0.5% in tau-GFP- mice).
  • FIG. 1 IB is a graph depicting that tau- GFP mean fluorescence intensity (MFI) for microglia was significantly higher in the frontal cortex of 564Igi relative to wild-type mice.
  • n 3 mice per group, ****P ⁇ 0.0001, two-way ANOVA with Sidak's test.
  • FIG. 11 A are a series of plots depicting gating for tau-GFP + microglia for engulfment analysis based on tau-GFP " control mice (gate set to ⁇ 0.5% in tau-GFP- mice).
  • FIG. 1 IB is
  • FIG. 11C are images showing that revealed no leakage of 10 kDa FITC-dextran tracer (intravenous injection) from blood vessels (CD31 + ) in 564Igi mice up to 24 weeks of age.
  • FIG. 1 ID are images showing no increase in IgG deposition within the CNS in 564Igi mice compared to C57BL/6 controls, when staining for IgG. In contrast, MRL-lpr did show a notable increase.
  • FIG. 1 IE is a graph showing that similar
  • FIG. 11G is a plot showing that flow cytometry analysis of tau-GFP mice injected with IFNa demonstrated significant increases in tau-GFP+ frequencies compared to vehicle.
  • n 3 mice per group, *P ⁇ 0.05, **P ⁇ 0.01, unpaired t-test.
  • FIG. 11H is a plot showing that flow cytometry analysis of tau-GFP mice injected with IFNP demonstrated significant increases in tau-GFP + frequencies compared to vehicle.
  • n 3 mice per group, *P ⁇ 0.05, **P ⁇ 0.01, unpaired t-test.
  • data are mean ⁇ s.e.m.
  • FIGS. 12A-12D show validation of microglia engulfment data.
  • FIG. 12A are images showing staining of Ibal . Left, staining of Ibal revealed inclusions within microglia cytoplasm (white arrows and inset) and lysosomes (white asterisk). Right, some inclusions contained structures consistent with synaptic vesicles (white arrows, right inset).
  • FIG. 12B are plots comparing staining with mouse IgGl and synaptic material (SV2). Permeabilized microglia were stained in parallel with similar concentrations of Alexa-633 labelled mouse IgGl . Fluorescence was several logs lower than observed with SV2 staining.
  • FIG. 12A are images showing staining of Ibal . Left, staining of Ibal revealed inclusions within microglia cytoplasm (white arrows and inset) and lysosomes (white asterisk). Right, some inclusions contained structures consistent with synaptic vesicles (
  • FIG. 12C is a plot showing staining of SV2 in nonpermeabilized microglia. To verify internalization of SV2, staining was also done on nonpermeabilized microglia. Very few (0.78%) microglia showed signal over the isotype control. No microglia could be detected in the 8 ⁇ 2 ⁇ ⁇ gate used for analysis in FIGS. 13A-13E.
  • FIG. 12D are images showing internalization of SV2. To further validate internalization of SV2, permeabilized microglia were slide-mounted by cytospin and imaged at 63 ⁇ by confocal. SV2 signal appeared colocalized with CD68 in many, but not all, microglia.
  • FIGS. 13A-13E depict IFNAR-dependent synapse loss in 564Igi mice.
  • FIG. 13 A is a TEM image of microglia (MG; light gray in the inset) surrounding synaptic elements (white arrow; dark gray in the inset). Presynaptic terminals are indicated by asterisks.
  • FIG. 13B depicts flow cytometry analysis of synaptic material (SV2) uptake by microglia in 564Igi or controls.
  • FIG. 13C is a graph of the flow cytometry analysis shown in FIG. 13B. *P ⁇ 0.05, two-way ANOVA with Sidak's test. *P ⁇ 0.05, two-way ANOVA with Sidak's test.
  • FIG. 13 A is a TEM image of microglia (MG; light gray in the inset) surrounding synaptic elements (white arrow; dark gray in the inset). Presynaptic terminals are indicated by asterisks.
  • FIG. 13B depicts flow cyto
  • FIG. 13D is a graph depicting analysis of confocal images of the synapse density in the frontal cortex. *P ⁇ 0.05, t-test.
  • data are mean ⁇ s.e.m.
  • FIGS. 14A-14F shows that synapse loss, but not neuron or axon loss, was observed in the frontal cortex of 564Igi mice.
  • FIG. 14A depicts representative images showing staining for presynaptic (synaptophysin, dark gray) and postsynaptic (homer, gray) markers revealed structural synapses (colocalized markers, light gray) in wild-type (left) and 564Igi (right) mice . Scale bar, 25 ⁇ .
  • FIG. 14B is a graph showing significant decreases in synaptophysin puncta in 564Igi (right) mice compared to wild-type mice (left).
  • FIG. 14C is a graph showing significant decreases in homer puncta in 564Igi (right) mice compared to wild-type mice (left).
  • n 3 mice per group, *P ⁇ 0.05, **P ⁇ 0.01, unpaired t-test.
  • FIG. 14D is a graph showing that reduced synapse density was observed in 8-week-old MRL-lpr mice by immunohistochemistry.
  • n 3 mice per group, *P ⁇ 0.05, unpaired t-test.
  • data are mean ⁇ s.e.m. DETAILED DESCRIPTION OF THE INVENTION
  • the invention features compositions and methods that are useful for identifying and treating patients with CNS lupus and related diseases characterized by microglia mediated synapse loss.
  • the invention is based, at least in part, on the discoveries of a direct role for interferon alpha receptor (IFNAR) signaling in regulating microglia activation state in a murine model of lupus; and the finding that IFNAR blocking antibodies could reduce physical and behavioral changes in these mice relative to wild-type control mice. Behavioral phenotypes and synapse loss in lupus-prone mice were prevented by blocking type I interferon (JFK) signalling. Furthermore, type I IFN stimulated microglia to become reactive and engulf neuronal and synaptic material in lupus-prone mice.
  • IFNAR interferon alpha receptor
  • Peripheral type I interferon enters the brain and stimulates microglial engulfment of synaptic material resulting in synapse loss.
  • Type I IFN IFNAR signaling was found to be necessary and sufficient to stimulate microglia engulfment of neuronal material.
  • blocking IFNAR signaling was effective, not only in preventing structural connectivity defects in the brain, but also in blocking changes in behavior.
  • the invention provides therapeutic methods for treating CNS lupus and related diseases characterized by microglia mediated synapse loss in a subject, as well as diagnostic methods for characterizing CNS lupus and related diseases characterized by microglia mediated synapse loss in a subject, and selecting subjects for treatment or of monitoring the treatment of such subjects.
  • antibodies that specifically bind to and block the activation of the interferon alpha/beta receptor are useful for the treatment of CNS lupus and related diseases characterized by microglia mediated synapse loss or to inhibit the progression of CNS lupus and other diseases characterized by an increase in reactive microglia and/or synapse loss.
  • Such antibodies may be directed against the INFNAR or against IFN-alpha.
  • Methods of preparing antibodies are well known to those of ordinary skill in the science of immunology.
  • the term “antibody” means not only intact antibody molecules, but also fragments of antibody molecules that retain immunogen-binding ability. Such fragments are also well known in the art and are regularly employed both in vitro and in vivo. Accordingly, as used herein, the term “antibody” means not only intact
  • immunoglobulin molecules but also the well-known active fragments F(ab') 2 , and Fab.
  • the antibodies of the invention comprise whole native antibodies, bispecific antibodies; chimeric antibodies; Fab, Fab', single chain V region fragments (scFv), fusion polypeptides, and unconventional antibodies.
  • Unconventional antibodies include, but are not limited to, nanobodies, linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062,1995), single domain antibodies, single chain antibodies, and antibodies having multiple valencies ⁇ e.g., diabodies, tribodies, tetrabodies, and pentabodies).
  • Nanobodies are the smallest fragments of naturally occurring heavy-chain antibodies that have evolved to be fully functional in the absence of a light chain. Nanobodies have the affinity and specificity of conventional antibodies although they are only half of the size of a single chain Fv fragment. The consequence of this unique structure, combined with their extreme stability and a high degree of homology with human antibody frameworks, is that nanobodies can bind therapeutic targets not accessible to conventional antibodies.
  • Recombinant antibody fragments with multiple valencies provide high binding avidity and unique targeting specificity to cancer cells.
  • These multimeric scFvs ⁇ e.g., diabodies, tetrabodies
  • offer an improvement over the parent antibody since small molecules of ⁇ 60-100kDa in size provide faster blood clearance and rapid tissue uptake See Power et al., (Generation of recombinant multimeric antibody fragments for tumor diagnosis and therapy. Methods Mol Biol, 207, 335-50, 2003); and Wu et al. (Anti-carcinoembryonic antigen (CEA) diabody for rapid tumor targeting and imaging. Tumor Targeting, 4, 47-58, 1999).
  • CEA Anti-carcinoembryonic antigen
  • Bispecific antibodies produced using leucine zippers are described by Kostelny et al. (J. Immunol. 148(5): 1547-1553, 1992). Diabody technology is described by Hollinger et al. (Proc. Natl. Acad. Sci. USA 90:6444-6448, 1993). Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) diners is described by Gruber et al. (J. Immunol. 152:5368, 1994). Trispecific antibodies are described by Tutt et al. (J. Immunol. 147:60, 1991).
  • Single chain Fv polypeptide antibodies include a covalently linked VH: :VL heterodimer which can be expressed from a nucleic acid including V H - and V L -encoding sequences either joined directly or joined by a peptide-encoding linker as described by Huston, et al. (Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Patent Nos. 5,091,513, 5, 132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754.
  • an antibody is monoclonal.
  • the antibody is a polyclonal antibody.
  • the preparation and use of polyclonal antibodies are also known the skilled artisan.
  • the 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.
  • Antibodies can be made by any of the methods known in the art utilizing soluble polypeptides, or immunogenic fragments thereof, as an immunogen.
  • One method of obtaining antibodies is to immunize suitable host animals with an immunogen and to follow standard procedures for polyclonal or monoclonal antibody production.
  • the immunogen will facilitate presentation of the immunogen on the cell surface.
  • Immunization of a suitable host can be carried out in a number of ways. Nucleic acid sequences encoding polypeptides or immunogenic fragments thereof, can be provided to the host in a delivery vehicle that is taken up by immune cells of the host. The cells will in turn express the polypeptide thereby generating an immunogenic response in the host.
  • nucleic acid sequences encoding human polypeptides or immunogenic fragments thereof can be expressed in cells in vitro, followed by isolation of the polypeptide and administration of the polypeptide to a suitable host in which antibodies are raised.
  • antibodies may, if desired, be derived from an antibody phage display library.
  • a bacteriophage is capable of infecting and reproducing within bacteria, which can be engineered, when combined with human antibody genes, to display human antibody proteins.
  • Phage display is the process by which the phage is made to 'display' the human antibody proteins on its surface. Genes from the human antibody gene libraries are inserted into a population of phage. Each phage carries the genes for a different antibody and thus displays a different antibody on its surface.
  • Antibodies made by any method known in the art can then be purified from the host.
  • Antibody purification methods may include salt precipitation (for example, with ammonium sulfate), ion exchange chromatography (for example, on a cationic or anionic exchange column preferably run at neutral pH and eluted with step gradients of increasing ionic strength), gel filtration chromatography (including gel filtration HPLC), and chromatography on affinity resins such as protein A, protein G, hydroxyapatite, and anti-immunoglobulin.
  • Antibodies can be conveniently produced from hybridoma cells engineered to express the antibody. Methods of making hybridomas are well known in the art.
  • the hybridoma cells can be cultured in a suitable medium, and spent medium can be used as an antibody source. Polynucleotides encoding the antibody of interest can in turn be obtained from the hybridoma that produces the antibody, and then the antibody may be produced synthetically or recombinantly from these DNA sequences. For the production of large amounts of antibody, it is generally more convenient to obtain an ascites fluid.
  • the method of raising ascites generally comprises injecting hybridoma cells into an immunologically naive histocompatible or immunotolerant mammal, especially a mouse. The mammal may be primed for ascites production by prior administration of a suitable composition ⁇ e.g., Pristane).
  • Monoclonal antibodies (Mabs) produced by methods of the invention can be any monoclonal antibodies (Mabs) produced by methods of the invention.
  • Humanized antibodies by methods known in the art. “Humanized” antibodies are antibodies in which at least part of the sequence has been altered from its initial form to render it more like human immunoglobulins. Techniques to humanize antibodies are particularly useful when non- human animal (e.g., murine) antibodies are generated. Examples of methods for humanizing a murine antibody are provided in U. S. patents 4,816,567, 5,530, 101, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.
  • the present invention provides methods of treating disease and/or disorders or symptoms thereof which comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an anti-IFNAR antibody described herein to a subject (e.g., a mammal such as a human).
  • a subject e.g., a mammal such as a human.
  • one embodiment is a method of treating a subject suffering from or susceptible to Systemic lupus erythematosus (SLE) and central nervous system (CNS) lupus or a symptom thereof.
  • the method includes the step of administering to the mammal a therapeutic amount of an amount of an agent herein sufficient to treat the disease or disorder or symptom thereof, under conditions such that the disease or disorder is treated.
  • the methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of a compound described herein, or a composition described herein to produce such effect. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method).
  • the terms "treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
  • the terms "prevent,” “preventing,” “prevention,” “prophylactic treatment” and the like refer to reducing the probability of developing a disorder or condition in a subject, who does not have, but is at risk of or susceptible to developing a disorder or condition.
  • the therapeutic methods of the invention in general comprise administration of a therapeutically effective amount of the compounds herein, such as a compound of the formulae herein to a subject (e.g., animal, human) in need thereof, including a mammal, particularly a human.
  • a subject e.g., animal, human
  • Such treatment will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Determination of those subjects "at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, Marker (as defined herein), family history, and the like).
  • the compounds herein may be also used in the treatment of any other disorders in which microglial activation by interferon may be implicated.
  • the invention provides a method of monitoring treatment progress.
  • the method includes the step of determining a level of diagnostic marker, such as the level of peripheral interferon or activated microglia (Marker) or other diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to CNS lupus or related diseases characterized by microglia mediated synapse loss or symptoms thereof (e.g., neuropsychiatric symptoms), in which the subject has been administered a therapeutic amount of a compound herein sufficient to treat the CNS lupus and related diseases characterized by microglia mediated synapse loss, or symptoms thereof.
  • a level of diagnostic marker such as the level of peripheral interferon or activated microglia (Marker) or other diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to CNS lupus or related diseases characterized by microglia mediated synapse loss or symptoms thereof (e.g., neuropsychiatric symptoms)
  • the level of Marker determined in the method can be compared to known levels of Marker in either healthy normal controls or in other afflicted patients, such as patients suffering from lupus that do not have CNS lupus or a related disease characterized by microglia mediated synapse loss, to establish the subject's disease status.
  • a second level of Marker in the subject is determined at a time point later than the determination of the first level, and the two levels are compared to monitor the course of disease or the efficacy of the therapy.
  • a pre-treatment level of Marker in the subject is determined prior to beginning treatment according to this invention; this pre-treatment level of Marker can then be compared to the level of Marker in the subject after the treatment commences, to determine the efficacy of the treatment.
  • type I interferon e.g., interferon alpha
  • CSF cerebrospinal fluid
  • PBMC peripheral blood mononuclear cells
  • type I interferon level is measured in a peripheral blood monocyte isolated from blood.
  • the level of peripheral interferon in a biological fluid sample e.g., cerebrospinal fluid (CSF), blood, plasma, serum
  • CSF cerebrospinal fluid
  • plasma blood
  • serum serum
  • expression of a marker of the invention is increased by at least about 2, 3, 4, 5 or 10-fold in a patient having CNS lupus or a related disease relative to the level in a reference sample (i.e., a patient that does not have CNS lupus or a related disease characterized by microglia mediated synapse loss).
  • a reference sample i.e., a patient that does not have CNS lupus or a related disease characterized by microglia mediated synapse loss.
  • PBMCs are assayed for an interferon signature (e.g., increases in mxl, ifit3, oas2, and stat2 or any other gene defined in Figure 9 ⁇ ).
  • IFN polypeptide or polynucleotide fold change values are determined using any method known in the art, including but not limited to quantitative PCR, RT-PCR, Northern blotting, Western blotting, flow cytometry, immunocytochemistry, binding to magnetic and/or antibody-coated beads, in situ hybridization, fluorescence in situ hybridization (FISH), flow chamber adhesion assay, ELISA, microarray analysis,
  • colorimetric assays ⁇ e.g., laser desorption/ionization mass spectrometry
  • fluorescence ⁇ e.g. sandwich immunoassay
  • surface plasmon resonance ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ .g., laser desorption/ionization mass spectrometry
  • fluorescence ⁇ e.g. sandwich immunoassay
  • surface plasmon resonance e.g., ellipsometry
  • atomic force microscopy atomic force microscopy
  • CNS lupus (or another disease characterized by reactive microglia) is characterized in a subject using brain imaging studies.
  • functional magnetic resonance imaging (fMRI) is used to measure alterations in brain connectivity.
  • Pre-pulse Inhibition (PPI) is used to characterize the startle reflex in a subject. PPI has been used to characterize deficits in PPI of the startle reflex in schizophrenia and autism spectrum disorders.
  • sensory motor defects are characterized in a subject with CNS lupus or a related disease.
  • CNS lupus is characterized by measuring gray matter volume using conventional MRI.
  • a Positron Emission Topography (PET) studies are used to identify activated microglia or to detect changes in synaptic density in iving human brain.
  • an SV2A PET ligand is:
  • CNS lupus or a related disease is characterized by detecting changes in activated microglia/exomes present in CSF.
  • CNS lupus or a related disease is characterized in a neurological exam, or by characterizing an anxiety phenotype, depression, cognitive impairment, or social interaction defects.
  • Antibodies of the invention can be administered in a pharmaceutically acceptable excipient, such as water, saline, aqueous dextrose, glycerol, or ethanol.
  • a pharmaceutical composition of the invention is administered to a subject identified as having CNS lupus or a related disease characterized by microglia mediated synapse loss.
  • the characterization of CNS lupus or a related disease characterized by microglia mediated synapse loss in a subject involves, for example, identifying the presence of increased levels of peripheral interferon in a biological sample of the subject, such as CSF.
  • the compositions can also contain other medicinal agents, pharmaceutical agents, adjuvants, carriers, and auxiliary substances such as wetting or emulsifying agents, and pH buffering agents.
  • a "therapeutically effective amount” is an amount sufficient to effect a beneficial or desired clinical result.
  • a therapeutically effective amount can be administered in one or more doses.
  • an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of CNS lupus or a related disease characterized by microglia mediated synapse loss.
  • an effective amount is an amount sufficient to reduce neuropsychiatric symptoms associated with CNS lupus or a related disease characterized by microglia mediated synapse loss.
  • therapeutically effective amount can be provided in one or a series of administrations.
  • the effective amount is generally determined by the physician on a case-by-case basis and is within the skill of one in the art.
  • the dosage for in vivo therapeutics or diagnostics will vary. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the patient, the condition being treated, the severity of the condition and the form of the antibody being administered.
  • the dosage of the antibody compositions can vary from about 0.01 mg/m 2 to about
  • the dosages of the antibody compositions can vary from about 0.01 mg/kg per day to about 1000 mg/kg per day. It is expected that doses ranging from about 50 to about 2000 mg/kg will be suitable.
  • a dosage ranging from about 0.5 to about 100 mg/kg of body weight is useful; or any dosage range in which the low end of the range is any amount between 0.1 mg/kg/day and 90 mg/kg/day and the upper end of the range is any amount between 1 mg/kg/day and 100 mg/kg/day (e.g., 0.5 mg/kg/day and 5 mg/kg/day, 25 mg/kg/day and 75 mg/kg/day). In one embodiment, 12.5 mg/kg of antibody is administered every 4 days.
  • Administrations can be conducted infrequently, or on a regular weekly basis until a desired, measurable parameter is detected, such as diminution of disease symptoms.
  • Administration can then be diminished, such as to a biweekly or monthly basis, as appropriate.
  • administration is weekly.
  • compositions of the present invention comprising anti-IFNAR antibodies are administered by a mode appropriate for the form of composition.
  • Available routes of administration include subcutaneous, intramuscular, intraperitoneal, intradermal, oral, intranasal, intrapulmonary (i.e., by aerosol), intravenously, intramuscularly, subcutaneously, intracavity, intrathecally or transdermally.
  • Compositions for oral, intranasal, or topical administration can be supplied in solid, semi-solid or liquid forms, including tablets, capsules, powders, liquids, and suspensions.
  • Compositions for injection can be supplied as liquid solutions or suspensions, as emulsions, or as solid forms suitable for dissolution or suspension in liquid prior to injection.
  • compositions are preferably supplied in unit dosage form suitable for administration of a precise amount. Also contemplated by this invention are slow release or sustained release forms, whereby a relatively consistent level of the active compound are provided over an extended period.
  • compositions of the invention that includes an interferon antibody can be monitored using any of the methods defined herein for characterizing a patient with CNS lupus or a related disease.
  • a subject is monitored by assessing neurological symptoms, neuropsychiatric symptoms, cognitive function, grey matter changes, or the level of peripheral interferon or reactive microglia present in the patient.
  • Compositions that produce a reduction in the severity of any one or more of the preceding symptoms are considered useful in the methods of the invention.
  • Neurological diagnostic tools for monitoring a patient having CNS lupus or a related disease include, for example, X-rays, Brain scans (magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET), and computed tomography (CT), Electroencephalograms (to capture the electrical pattern of brain activity), sensorimotor gating assessment using auditory prepulse inhibition assays, or spinal tap (to examine fluid in the spinal column).
  • MRI magnetic resonance imaging
  • fMRI functional MRI
  • PET positron emission tomography
  • CT computed tomography
  • Electroencephalograms to capture the electrical pattern of brain activity
  • sensorimotor gating assessment using auditory prepulse inhibition assays or spinal tap (to examine fluid in the spinal column).
  • CNS lupus or a related disease characterized by microglia mediated synapse loss may be monitored by characterizing an increase or decrease in one or more of the following: headaches, confusion, fatigue, depression, seizures, stroke, vision problems, mood swings, difficulty concentrating, memory loss, and difficulty expressing thoughts.
  • an increase or decrease in numbness, burning, or tingling is monitored. Kits
  • kits for the treatment of CNS lupus or a related disease characterized by microglia mediated synapse loss includes a composition containing an anti-interferon alpha/beta receptor (IFNAR) antibody.
  • IFNAR anti-interferon alpha/beta receptor
  • the kit comprises a sterile container which contains a therapeutic or prophylactic cellular composition; such containers can be boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
  • an agent of the invention is provided together with instructions for administering the agent to a subject having or at risk of developing a neurological disease or disorder of the central nervous system.
  • the instructions will generally include information about the use of the composition for the treatment or prevention of the disease or disorder.
  • the instructions include at least one of the following: description of the therapeutic agent; dosage schedule and administration for treatment or prevention of a neurological disease or symptoms thereof; precautions; warnings; indications; counter- indications; overdosage information; adverse reactions; animal pharmacology; clinical studies; and/or references.
  • the instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
  • Example 1 Development of an animal model for use in CNS lupus study.
  • the 564Igi lupus-prone mouse strain is a B-cell-receptor insertion model with known autoantibody specificity, mild peripheral inflammation and interferon-a receptor 1 (IFNAR)-dependent autoimmunity (Berland et al. Immunity 25, 429-440, 2006; Das et al. Immunity 46, 106-119, 2017).
  • IFNAR interferon-a receptor 1
  • Lupus-like disease progresses slowly in 564Igi mice compared to other mouse models of lupus, therefore CNS development is unaffected by disease complications such as lupus nephritis (onset at 12 months) (Berland et al.
  • 564Igi mice and wild-type littermates were treated with IFNARblocking antibody or isotype-control to determine whether the behavioral phenotypes were IFNAR-dependent.
  • 564Igi mice treated with the anti-IFNAR antibody behaved similarly to wild-type mice. Without being bound by theory, this indicates the involvement of IFNAR signalling or peripheral autoimmunity in general (FIGS. 2A-2D). Notably, the 564Igi strain showed no inflammation or cellular infiltration in the brain (FIGS. 3 A-3C). Without being bound by theory, treatment with the anti-IFNAR antibody probably affects CNS-resident cells rather than infiltrates immune cells.
  • Microglia resident macrophages of the brain, respond to local inflammation or CNS damage by becoming reactive and increasing phagocytic activity and inflammatory cytokine production (Lynch, Mol. Neurobiol. 40, 139-156, 2009). Reactive microglia have been detected in some lupus-prone mouse models (Crupi et al. Biol. Psychiatry 67, 558-566, 2010; Mondal et al. Brain Behav. Immun. 22, 949-959, 2008). However, whether these cells promote CNS disease in lupus or arise in response to CNS disease in lupus is unclear. To determine whether and when reactive microglia develop in 564Igi and NZB/NZW lupus- prone strains, both of which have IFNAR-dependent lupus pathology (Berland et al.
  • Microglia are sensitive to type I IFN and become reactive in response to constitutive
  • IFNAR activity Goldmann et al. EMBO J. 34, 1612-1629, 2015. Elevated type I IFN levels due to mutations in TREX1 or USP18 can result in the severe neurodevelopmental disorders of Aicardi-Goutieres syndrome or pseudo-TORCH syndrome (Crow et al. Nat. Genet. 38, 917-920, 2006; Meu Giveaway et al. J. Exp. Med. 213, 1163-1174, 2016) and have been implicated in cognitive decline in ageing and Alzheimer's disease (Taylor et al. Neurobiol. Aging 35, 1012-1023, 2014; Baruch et al. Science 346, 89-93, 2014).
  • Elevated type I IFN in the periphery is a hallmark of SLE21 and it is one of several cytokines detected in the serum and cerebrospinal fluid (Trysberg et al. Lupus 9, 498-503, 2000; Santer et al. J. Immunol. 182, 1192-1201, 2009) of patients with SLE. Without being bound by theory, increased type I IFN could therefore affect microglia. However, whether IFNAR signalling is increased in the lupus brain and is linked to CNS lupus symptoms remains unknown.
  • qPCR Quantitative PCR
  • mice were crossed with Mxl-Cre Tdtomato reporter mice in which IFNAR signaling (Mxl expression) stimulates Tdtomato expression.
  • Mxl expression IFNAR signaling
  • microglia were the most prevalent Mxl + cell type (10-30% of microglia were Mxl + ), with small clusters of neurons and other glia appearing in some regions (FIG. 4J). More Mxl + microglia were reactive than Mxl " microglia, consistent with IFNAR signalling promoting reactive microglia in lupus (FIGS. 5E and 5F).
  • Example 3 Identification of IFNAR signaling as a therapeutic target in CNS lupus.
  • IFNAR signalling is important for the regulation of peripheral autoimmunity (Das et al. Immunity 46, 106-119, 2017; Baccala et al. J. Immunol 189, 5976-5984, 2012), bone marrow chimeras were used to separate direct effects of type I IFN on the brain from indirect effects associated with peripheral inflammation. Head-shielded wild-type and IfiiarF 1' mice were lethally irradiated and reconstituted with wild-type- or 564Igi-derived bone marrow. As expected, wild-type and IfiiarF 1' recipients showed comparable chimerism, percentages of idiotype-positive B cells (FIGS.
  • IfiiarF 1' recipients of 564Igi-derived bone marrow were protected. Without being bound by theory, this supports a direct role for IFNAR in regulating microglial activation in lupus-prone mice.
  • Elevated IFNAR signalling was also found in brains from patients with lupus.
  • MXA encoded by ⁇ 7
  • immunohistochemistry on hippocampal brain sections revealed immunoreactivity in four out of six patients with SLE in grey and white matter and negligible signal in four patients without SLE, with isotype- and secondary-only controls showing no signal (FIGS. 7A-7C).
  • MX1 + microglia were detected in brains from patient with SLE relative to controls by RNAscope with probes specific for MX1 and AIF1 (a microglia marker) (FIG. 5 J).
  • Probes for the neuron-specific gene, EN02 were analyzed in parallel to verify comparable RNA integrity (FIG. 7D).
  • IFNAR signaling stimulates genes associated with phagocytosis, lysosome organization, and endosomal trafficking.
  • RNA- sequencing was performed on microglia and perivascular/meningeal macrophages sorted from the cortex and hippocampus of 564Igi and wild-type mice following treatment with anti-IFNAR or isotype-control antibodies. Macrophage frequencies (identified as ⁇ >45 ⁇ ? 3 ⁇ 4 ⁇ 1 ⁇ + cells) were similar in both strains. Without being bound by theory, this suggests no significant infiltration of blood-derived myeloid cells in 564Igi mice (FIGS. 8A and 8B).
  • Microglia purity was verified after sorting using two additional cell surface microglia markers (CX3CR1 and CD39) and expression of 25 established microgliaspecific genes (Hickman et al. Nat. Neurosci. 16, 1896-1905, 2013) (FIGS. 8C and 8D).
  • Multidimensional scaling analysis revealed clustering by genotype and treatment group (FIG. 9A). Differences in expression (q ⁇ 0.05) were found for 1,946 genes between 564Igi and wild-type microglia using EdgeR, 20% of which were IFNAR-dependent (FIGS. 9B and 9D); 21 known IFN-stimulated genes, including Mxl, Ifit3, Oas2 and Stat2, were upregulated, forming a microglial IFN signature comparable to that of peripheral immune cells from patients with SLE (Kirou et al. Arthritis Rheum. 50, 3958-3967, 2004; Baechler et al. Proc. Natl Acad. Sci. £7X4100, 2610-2615, 2003).
  • IFNAR-independent genes were associated with cellular metabolism, purinergic signalling, production of type I interferon, phagocytosis, lysosome organization, endosomal trafficking and the microglia sensome, which has receptors for endogenous ligands and microbes (Hickman et al. Nat. Neurosci. 16, 1896-1905, 2013) (FIG. 10B).
  • sensome genes were upregulated in 564Igi mice (q ⁇ 0.05), and six of these genes were downregulated by anti-IFNAR treatment (FIG. 9E).
  • type I IFN signalling as a major regulator of microglia gene expression in lupus promoting sensitivity and phagocytic activity in 564Igi microglia.
  • Example 5 IFNAR signaling is necessary and sufficient to stimulate microglia engulfment of neuronal material
  • IFN and Mxl signal were detected in the brain within three hours, due to some permeability of the blood-brain barrier for type I IFN28 (FIG. 101), despite intact blood-brain-barrier integrity in 564Igi mice up to 24 weeks (FIGS. 1 lC-1 IF).
  • tau- GFP + microglia increased 24 hr after injection of IFNa /IFNp (FIGS. 10J, 10K, 11G, and 11H).
  • Microglia were identified on the basis of their characteristic nuclear morphology, a single-profile endoplasmic reticulum and an electron-dark shading of the cytoplasm with confirmation by immuno-electron microscopy (FIG. 12 A). Microglial processes often contacted neuronal structures and, in several cases, microglial cytoplasm surrounded neuronal structures, consistent with internalization. Synaptic structures specifically (most commonly membrane-bound compartments containing synaptic vesicles) were visible within 564Igi microglia and rarely observed in wild-type controls (FIG. 13 A).
  • permeabilized 564Igi and control microglia were stained for a synaptic vesicle protein (SV2) and analyzed by flow cytometry.
  • SV2 synaptic vesicle protein
  • Significantly more SY2 Ugh microglia were detected in the frontal cortex and hippocampus (but not cerebellum) in 564Igi mice compared to controls (FIGS. 13B and 13C).
  • Isotype-control antibodies and non- permeabilized microglia showed no signal.
  • confocal imaging of sorted microglia verified SV2 colocalization with CD68, a marker of lysosomes (FIGS. 12B-12D). Without being bound by theory, these data indicate that microglia engulf synaptic material in the 564Igi model.
  • Example 6 Anti-IFNAR antibody treatment prevents neuronal structural connectivity defects and blocks changes in behavior.
  • synapse density was measured using high-resolution confocal imaging. Despite similar neuronal and axonal density, 564Igi mice and MRL/lpr mice had reduced synapse density in the frontal cortex relative to wild-type mice (FIGS. 13D and 14A-14F). Frontal cortex synapse loss was verified by TEM, and found to be significantly reduced in 564Igi mice treated with anti -IFNAR antibody (FIG. 13E).
  • peripheral type I peripheral type I
  • IFN enters the brain and stimulates microglial engulfment of synaptic material, resulting in synapse loss.
  • Linking type I IFN and CNS lupus helps to account for the high incidence and high variability of CNS lupus symptoms, as 50-80% of patients with SLE display a type I IFN signature (Kirou et al. Arthritis Rheum. 50, 3958-3967, 2004; Baechler et al. Proc. Natl Acad. Sci. USA IOO, 2610-2615, 2003) and many microglia genes and pathways are IFNAR- dependent. Why and how IFNAR-stimulated microglia target synapses remain unclear.
  • Neuronal damage occurs in lupus-prone mice and patients with SLE in response to anti- double-stranded DNA antibodies cross-reacting with NMDA receptors at the synapse (DeGiorgio et al. Nat. Med. 7, 1189-1193, 2001). Wihtout being bound by theory, this antibody binding could initiate microglial engulfment, although substantial antibody deposition in the CNS was not detected in the 564Igi mice. Another mechanism promoting engulfment may be activation of the classical complement cascade, which is important for early synapse loss in Alzheimer's disease models (Hong et al. Science 352, 712-716, 2016; Stevens et al. Cell 131, 1164-1178, 2007).
  • CD68 staining was analyzed and scored as 0 (no/scarce expression), 1 (punctate expression), 2 (aggregated expression or punctate expression all over the cell). These two scores were summed to give a final score of microglial activation state (0-5).
  • Microglia with an activation state of 3 or higher were then categorized as reactive and the percentage of reactive microglia was compared between lupus and control mice. All analyses were performed blind to genotype and treatment group.
  • Microglia were first sorted from brain region homogenates using the FACSAria. For each mouse, 1000 microglia were sorted from the suspension into 20 ⁇ 1 guanidine thiocyanate buffer (Qiagen) supplemented with 1% ⁇ -mercaptoethanol. RNA was isolated using
  • RNAClean XP beads (Agencourt A63987). Template switching, cDNA synthesis, and cDNA amplification were adapted from previous studies (Islam et al., Nat. Methods 11, 163-166, 2014). Libraries were prepared using the Nextera kit (Illumina). Libraries were sequenced on an Illumina HiSeq 2000. For RNA-seq analysis, 40-bp single-end reads were aligned to the mouse reference genome (mm 10) using Star Aligner. Gene read count was performed using HTseq-count with Refseq mm 10 annotation. Differential gene expression analysis was performed using EdgeR and gene ontology analysis was performed using GOseq (Young et al., Genome Biol. 11, R14, 2010). Treemap was created using Revigo (http://revigo.irb.hr/).
  • mice 564Igi Ig heavy and light chain knock-in (564Igi) mice have been described (Berland et al., Immunity 25, 429-440, 2006; Chatterjee et al., Eur. J. Immunol. 43, 2441- 2450, 2013). All 564Igi mice were genotyped for the presence of the transgenic heavy and light chains by specific PCR analysis of tail DNA. Peripheral blood B cells (PBMCs) were analyzed by FACS for the presence of both the 564Igi heavy and light chains, which were identified with a specific anti-idiotype antibody (Chatterjee et al., Eur. J. Immunol. 43, 2441- 2450, 2013).
  • PBMCs Peripheral blood B cells
  • mice used for the experiments were selected to be heterozygous for the transgenic (IgMa) and endogenous (IgMb ) IgH alleles. For each of the experiments performed, mice of both sexes were analyzed at 12 weeks of age unless otherwise indicated. Additionally, 564Igi mice with similar idiotype-positive B cell frequencies in blood were used within an experiment. C57BL/6, NZB/NZW ( 7 hybrids of the NZB and NZW strains), Mxl-Cre, Ifnarl '1' , and tau-GFP mice (Tucker et al., Nat. Neurosci. 4, 29-37, 2001) were purchased from Jackson Laboratories.
  • Tissue from MRL- lpr and MRL-mpj strains was generously provided by G. C. Tsokos (Boston, MA). Experiments were approved by the Boston Children's Hospital and Harvard Medical School institutional animal use and care committee in accordance with NIH guidelines for the humane treatment of animals.
  • mice were injected with 25C ⁇ g of anti-IFNAR, intraperitoneally every 4 days for 1 month (Das et al., Immunity 46, 106-119, 2017). Treatment for NZB/NZW mice was from 4 to 8 weeks. 564Igi mice were treated from 8 to 12 weeks. After one month, mice were euthanized and cells were isolated for analysis of frequency of idiotype-positive B cells or microglia analysis.
  • Recipient mice were lethally irradiated with a dose of 10 Gy by a 137Cs irradiator. Subsequently, 1 x 10 7 donor-derived bone marrow cells were intravenously injected into the recipients the following day. Recipient mice were fed with sulfamethoxazole/trimethoprim- containing water for two weeks following reconstitution and analyzed 6-8 weeks after reconstitution. Microglia isolation
  • brain regions were microdissected and the tissue was digested in 330 U papain in DPBS at 35°C for 30 minutes. Papain was neutralized in an ovomucoid solution and cells were dissociated by gentle trituration and filtered through a 70- ⁇ nylon mesh to remove clumps. Microglia were then purified by magnetic purification using anti-CD45 microbeads (Miltenyi).
  • Blood-brain-barrier leakage was assayed using established protocols (Armulik et al., Nature 468, 557-561, 2010; Ben-Zvi et al., Nature 507-511, 2014).
  • Mice were injected intravenously with 10 kDa FITC-dextran (2 mg per 20 g mouse). After 4 hr of circulation, mice were euthanized and brains were fixed in 4% PFA. Sagittal brain sections (40 ⁇ ) were stained with anti-CD31 (1 :200, Biolegend) to mark blood vessels and imaged by confocal microscopy. Three fields of view from two brain sections per animal were quantified using Image J. Leakage was measured as a decrease in colocalization of FITC-dextran with CD31.
  • FFPE FFPE autopsy-derived brain tissue from the hippocampus using a DAKO autostainer.
  • the antibody M143, which is suitable for FFPE tissue was kindly provided by G. Kochs
  • In situ hybridization was done on human FFPE autopsy-derived brain tissue from the hippocampus using the RNAscope 2.5 HD Duplex Chromogenic Assay kit (Advanced Cell Diagnostics, Inc.). In situ hybridization protocol was performed as recommended in the RNAscope 2.5 HD Duplex Chromogenic Assay user manual following specifications for brain tissue. Probes against human MX1 (403831), AIFI (433121-C2) and EN02 (421401) were commercially available from Advanced Cell Diagnostics, Inc.
  • Microglial engulfrnent analysis was performed similar to previously described methods (Schafer et al., Neuron 74, 691-705 (2012); Schafer et al., J. Vis. Exp. 88, e51482, 2014).
  • 564Igi Tau-gfp mice were sacrificed at 12 wks, perfused with cold PBS, and brains were fixed in 4% paraformaldehyde (PFA) for 4 hr (4°C). After cryoprotection in 30% sucrose, tissue was sectioned coronally in 40 ⁇ thick slices on a cryostat, and collected in PBS.
  • PFA paraformaldehyde
  • the sections were blocked and permeabilized in 5% BSA with 0.2% Triton X-100 for 30 min-1 hr at room temperature, then incubated overnight at room temperature with a primary antibody against Iba-1 (Wako, 019-19741, 1 :500) in block solution. The next day, the sections were incubated 1.5-2 hr at room temperature with an Alexa-488 conjugated secondary antibody and mounted on slides in Vectashield with DAPI (Vector Laboratories). For each animal, two sections of the frontal cortex were chosen for microglia engulfment analysis.
  • Imaris software (Bitplane) was used to create 3D volume surface renderings of each z stack. Surface rendered images were used to determine the volume of the microglia and of all tau-GFP. To visualize and measure the volume of engulfed inputs, any fluorescence that was not within the microglia volume was subtracted from the image using the mask function. The remaining engulfed/internal fluorescence was surface rendered using parameters previously determined for all tau-GFP and total volume of engulfed/internal tau-GFP was calculated. To determine percentage of engulfment, the following calculation was used: volume of internalized tau-GFP ( ⁇ 3 )/ volume microglial cell ( ⁇ 3 ). All analyses were performed blind to animal genotype.
  • mice were perfused with a 2% paraformaldehyde/ 2.5% glutaraldehyde solution in 0.1M phosphate buffer and drop fixed overnight in the same solution.
  • Sagittal sections 150 ⁇ ) including frontal cortex were cut by vibratome. Sections were either processed for immunoEM or prepared for synapse quantification.
  • immunoEM were performed similar to previously described methods (Tremblay et al., PLoSBiol. 8, el000527, 2010; Bisht et al., Glia 64, 826-839, 2016). In brief, sections were treated with 0.1% sodium borohydride for 30 minutes followed by 1 hr incubation in blocking solution (3% BSA and 0.01% Triton X- 100).
  • a synapse was defined as an electron-dense post-synaptic density area juxtaposed to a presynaptic terminal filled with synaptic vesicles.
  • Microglia were identified on the basis of their characteristic nuclear morphology, a single-profile endoplasmic reticulum and an electron-dark shading of the cytoplasm (Bisht et al., Glia 64, 826-839, 2016; Mori and Leblond J. Comp. Neurol. 135, 57- 79, 1969).
  • the mouse open field chambers (Med Associates) are made of Plexiglas and consist of a square base (27 cm ⁇ 27 cm) with walls that are 20 cm high. All walls are clear but opaque barriers are added between arenas so that subjects do not see one another during testing. For each testing session, the mouse is allowed free exploration in the environment for 1 hr.
  • a computer-assisted infrared tracking system and software (Activity Monitor, Med Associates) are used to record the number of beam breaks and time and entries into center and peripheral zones. The total distance travelled (cm) is used as a measurement of general locomotor activity.
  • the elevated plus maze consists of two open and two closed arms that extend out from a central platform. Each arm of the maze is 30 cm long and 5 cm wide. The maze surface is 85 cm above the floor and test is carried out in dim ambient lighting. Mice are placed in the center platform of the maze, facing an open arm, and allowed to explore the apparatus for 5 min.
  • a computer-assisted video-tracking system (TopScan software, CleverSys Inc.) is used to record the number of open and closed arm entries (all four paws in an arm) as well as the total time spent in open, closed and center compartments. A decrease in the per cent time spent in the open arms or a decrease in the per cent entries into the open arms is used as a surrogate measure of anxiolytic-like behavior.
  • the number of closed arm entries is used as a measure of general locomotor activity.
  • the three-chamber sociability test included two consecutive 10-min sessions and was performed in a rectangular arena of clear Plexiglas with dimensions 63 cm length x 40 cm width x 22 cm height.
  • the test arena contained three equally sized chambers (40 cm length ⁇ 20 cm width ⁇ 22 cm height), and the outer left and right chambers each contained an inverted wire cup.
  • test mice were initially placed into the center chamber and allowed to freely explore the three-chambered arena.
  • test mice were returned to the center chamber, an unfamiliar target mouse was placed under one of the two wire cups, an object under the second cup and test mice were again allowed to move freely among the three chambers.
  • the position of the first target mouse was alternated and equally distributed between the left and right cups for both mutant and control groups. The position was not changed between the social interaction and social recognition sessions.
  • the test operator was blinded to test mouse genotype and remained outside of the test room during all sessions.
  • Test subject performance was recorded automatically using TopScan software (CleverSys, Inc.), and the following behaviors were scored: amount of time spent in close proximity (3 cm radius) of the wire cups, amount of time spent in each chamber of the three-chamber arena and latency to approach each wire cup. Water T maze.
  • the testing apparatus is a plus maze (each arm 14.1 long and 4.6 cm wide) made of clear Plexiglas with each arm designated as north (N), south (S), east (E) or west (W).
  • N north
  • S south
  • E east
  • W west
  • dividers are placed to block off the either the N or S arm. Mice are placed in the N or S arms, in a semi-random order, at the start of each trial.
  • the maze is filled with 25-26 °C water and made opaque by adding nontoxic white paint so the mouse cannot see the submerged escape platform.
  • the hidden escape platform is placed in the E arm. Mice are carried to the starting point and the experimenter scores a correct or incorrect response for each trial based on whether the arm with the escape platform is chosen. Regardless of the response, mice are allowed to remain on the platform for 10 s at the end. Mice are given 10 trials per day and the percentage correct responses is calculated by averaging correct responses across the 10 trials for each day. Acquisition criterion is achieved when a mouse scores 80% or more correct responses over two consecutive days. After all mice reach acquisition criterion, the reversal trial begins: the platform is moved to the opposite side (W) and the same procedure is repeated until all mice learn the platform's new location.
  • W opposite side
  • testing was conducted in a clear acrylic Y maze that has three arms (one start arm and two test arms, all— 31 cm in length).
  • the testing room has distinct visual cues and the maze has a removable partition to block the appropriate arm.
  • the blocked arm is randomized and balanced for each test group.
  • the test consists of a forced choice trial followed by a free- choice trial.
  • For the forced choice trial the start arm and one test arm is open with access to the second test arm blocked by the partition.
  • Individual subjects are placed in the start arm and allowed to explore the open test arm for 3 min, after which they are removed from the maze, and placed in a holding cage as the maze is cleaned.
  • mice are then immediately placed back into the Y maze for the free choice trial and allowed to explore both the open and test arms for 3 min.
  • the delay between the forced choice and free choice trials is approximately 2 min.
  • Animal behavior is video recorded during both trials and the time spent in the previously accessible arm (that is, familiar arm; tf) and the previously blocked arm (that is, novel arm; t n ) is determined during the free choice trial using Cleversys software.
  • the purpose of the rotarod test is to assess the sensorimotor coordination and/or fatigue resistance of the mouse.
  • the test is sensitive to damage of the basal ganglia and cerebellum, and to drugs that affect motor functions.
  • the rotarod apparatus consists of a gritted or textured plastic roller (Ugo Basile) flanked by large round plates on each end to prevent the animal from escaping.
  • the plastic rod sits at a height of approximately 20 cm above individual electronic sensing platforms.
  • the sensing platforms are not cushioned, but mice do not appear to experience any discomfort from falling from that height.
  • mice Prior to actual testing, mice are habituated to the rotarod apparatus by placing them onto the rod as it revolves at a very low rotation speed (4 r.p.m.
  • mice are tested in the accelerated rotarod (4-40 r.p.m. in 3 min). The latency until the mouse falls from the rod onto the sensing platform below is recorded automatically. This test is repeated after a 15-min break.
  • mice are suspended by the tail (taped onto a suspension hook so that the animal hangs with its tail in a straight line) above a flat surface covered with soft padding material.
  • the duration of immobility is scored automatically (Med Associates) or by an experimenter. Forced swim test.
  • mice This procedure is used to induce a despair-like state and to test the effects of antidepressants in mice. Antidepressants will reduce the amount time the mouse spends immobile in this test.
  • Mice are placed for 6 min in a glass cylinder (height, 35 cm; diameter, 17 cm) filled with water (25 ⁇ 2° C) to a depth of 25 cm. The water depth is adjusted so that the animals must swim or float without their hind limbs or tail touching the bottom.
  • the duration of immobility (the time during which the subject makes only the small movements necessary to keep their heads above water) is scored. The experimenter monitors each mouse continuously during the entire session. The mouse is immediately taken out of the cylinder and excluded from the study if it fails to swim or keep its head above water. After completion of the trial, the subject is dried using a paper towel and placed back in its home cage. After every trial, the water is changed and the cylinder rinsed with clean water. Social dominance tube test.
  • mice from different litters that are sex-matched and weight-matched are placed inside opposite ends of a white PVC pipe that is 30.5 cm in length, 2.5 cm internal diameter. Mice are released simultaneously at both ends of tube. Start sides are alternated between trials.
  • the latency of each trial is recorded as the percentage of trials won by each mouse. Mice are considered socially dominant if they win more than 50% of the trials.
  • the pipe is cleaned with 70% ethanol between each trial.
  • the novelty suppressed feeding (NSF) paradigm is a conflict test that elicits competing motivations between the drive to eat and the fear of venturing into the center of a brightly lit arena.
  • NSF measures the latency of a mouse in approaching and eating a familiar food in a novel environment following an extended period (up to 24 hr) of food deprivation. Increased latency to begin eating is used as an index of anxiety-like behavior.
  • This test can also be used as a pharmacological model of anxiolytic and antidepressant activity because acute anxiolytics and chronic antidepressant drugs decrease latency to feed in the novel environment. Approximately 18-24 h before testing, mice are placed in a clean cage without food (singly housed).
  • the apparatus is either a NOR chamber covered with white laminated paper or a mouse shipping crate.
  • the floor is covered with 2 cm of bedding.
  • a small pre-weighed food chow pellet (normal chow) is placed in the centre of the arena on a piece of white circular filter paper. The lights in the room are increased to the brightest level.
  • mice are transferred to a holding room for a ⁇ 1-hr habituation period.
  • each mouse is placed in a random corner of the testing arena and the time to the first feeding event is recorded during 10 min. The time for the mouse to grab the pellet and start eating is recorded.
  • the mouse is removed immediately and then placed alone in its home cage for 5 min with the pre-weighed piece of chow. At the end of the 5-min period, the amount of food consumed is also measured.

Abstract

As described below, the invention provides compositions and methods for identifying and treating diseases characterized by reactive microglia and synapse loss (e.g., central nervous system (CNS) lupus, Alzheimer's disease).

Description

COMPOSITIONS AND METHODS FOR TREATING DISEASES
CHARACTERIZED BY REACTIVE MICROGLIA MEDIATED SYNAPSE LOSS
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to and the benefit of U.S. Provisional Application No. 62/448,840, filed January 20, 2017, the disclosure of which is incorporated herein by reference in its entirety.
STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY
SPONSORED RESEARCH
This invention was made with Government support under Grant Nos. AI74549-6A1 and AI039246 awarded by the National Institutes of Health. The Government has certain rights in the invention.
BACKGROUND OF THE INVENTION
Systemic lupus erythematosus (SLE) is an incurable autoimmune disease
characterized by autoantibody deposition in tissues, such as kidney, skin, and lungs. Notably, up to 75% of patients with SLE experience neuropsychiatric symptoms that range from anxiety, depression and cognitive impairment to seizures and, in rare cases, psychosis— collectively this is referred to as "central nervous system (CNS) lupus." In some cases, certain autoantibodies, such as anti-N-Methyl D-Aspartate Receptor (NMDAR) or anti- phospholipid antibodies promote CNS lupus. However, in most patients, the mechanisms that underlie these symptoms are unknown.
CNS lupus typically presents at lupus diagnosis or within the first year. Without being bound by theory, this suggests that early factors contributing to peripheral
autoimmunity may promote CNS lupus symptoms. Current methods for detecting and treating CNS lupus and neurological disorders with similar symptoms are inadequate.
Accordingly, improved compositions and methods for identifying and treating CNS lupus and related diseases are required. SUMMARY OF THE INVENTION
As described below, the present invention features compositions and methods for identifying and treating CNS lupus and related disease characterized by microglia mediated synapse loss.
In one aspect, the invention provides a method of treating a subject having a disease or disorder characterized by reactive microglia mediated synapse loss, the method involving administering to the subject an agent that inhibits binding to an interferon alpha/beta receptor, wherein the disease or disorder is not CNS lupus.
In another aspect, the invention provides a method of treating a subject having CNS lupus, the method involving administering to the subject an anti-interferon alpha/beta receptor antibody or anti-interferon alpha antibody, wherein the subject is selected as having reactive microglia mediated synapse loss.
In another aspect, the invention provides a method of selecting therapy for a subject having CNS lupus, the method involving detecting increased type I interferon in a
cerebrospinal fluid of the subject relative to a reference level, wherein detection of said increase selects the subject for anti-interferon alpha eta receptor (IFNAR) antibody therapy.
In another aspect, the invention provides a method of identifying a subject as having CNS lupus, the method involving detecting reactive microglia mediated synapse loss or increased type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein said detection identifies the subject as having CNS lupus.
In another aspect, the invention provides a method of monitoring CNS lupus therapy in a subject, the method involving detecting type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein the reference level is the level of interferon alpha present in the cerebrospinal fluid of the subject prior to treatment with an anti- IFNAR antibody treatment.
In another aspect, the invention provides a method of reducing the level of activated microglia present in a subject in need thereof, the method involving administering an anti- interferon alpha/beta receptor antibody to the subject.
In another aspect, the invention provides a kit containing an anti-IFNAR antibody and instructions for the treatment of CNS lupus. In one embodiment, the kit further contains a capture molecule that specifically binds interferon. In another aspect, the invention provides a method of depleting activated microglia in a subject in need thereof, the method involving administering to the subject an effective amount of an anti-IFNAR antibody to the subject.
In various embodiments of the above aspects, the subject has a disease or disorder characterized by neurological or neuropsychiatric symptoms. In other embodiments of the above aspects, the agent is an anti-interferon alpha/beta receptor antibody or an anti- interferon alpha antibody. In other embodiments of the above aspects, the subject has increased levels of peripheral interferon. In other embodiments of the above aspects, the subject has an autoimmune disease, a neurodegenerative disease, or a chronic viral infection. In other embodiments of the above aspects, the subject has Sjogren's syndrome, Alzheimer's disease, or Human Immunodeficiency Virus Infection. In other embodiments of the above aspects, the subject presents with neuropsychiatric or neurological symptoms (e.g., anxiety phenotype, depression, cognitive impairment, and social interaction defects). In other embodiments of the above aspects, the anti-IFNAR antibody is a human, humanized or chimeric antibody. In other embodiments of the above aspects, the anti-IFNAR antibody contains a VH domain containing the amino acid sequence of SEQ ID NO: 1 or a VK domain containing the amino acid sequence of SEQ ID NO: 2. In other embodiments of the above aspects, the disease state of the subject is characterized using brain imaging studies, functional or conventional magnetic resonance imaging, Pre-pulse Inhibition, measuring gray matter volume, or using a Positron Emission Topography studies.
The invention provides compositions and methods for identifying and treating CNS lupus and related disease characterized by microglia mediated synapse loss. Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.
Definitions
Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person of ordinary skill in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.
By "CNS lupus-related disease or disorder" is meant any disease characterized by reactive microglia mediated synapse loss. Such diseases include an autoimmune disease or disorder, such as Sjogren's syndrome, a neurodegenerative disease, such as Alzheimer's disease, or a chronic viral infection, such as Human Immunodeficiency Virus Infection. The presence or absence of reactive microglia mediated synapse loss is characterized as described herein below.
By "type I interferon polypeptide" is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. AAI12303.1 and having a biological activity or function of a type I interferon polypeptide. The interferon type I class includes: interferon (IFN)-a (alpha), IFN-β (beta), IFN-κ (kappa), IFN-δ
(delta), IFN-ε (epsilon), IFN-τ (tau), IFN-co (omega), and IFN-ζ (zeta). Biological activities or functions of a type I interferon polypeptide include, without limitation, binding of the IFN-alpha/beta receptor (IFNAR) and regulation of immune system response. The sequence of IFN-alpha at NCBI Accession No. AAI12303.1 is shown below:
1 maspfallmv lvvlsckssc slgcdlpeth sldnrrtlml laqmsrisps sclmdrhdfg 61 fpqeefdgnq fqkapaisvl heliqqifnl fttkdssaaw dedlldkfct elyqqlndle 121 acvmqeervg etplmnadsi lavkkyfrri tlyltekkys pcawevvrae imrslslstn
181 lqerlrrke
By "type I interferon polynucleotide" is meant a polynucleotide encoding any type I interferon polypeptide. An exemplary type I interferon polynucleotide sequence (e.g., IFN-alpha polynucleotide) is provided at NCBI Accession No. NM_024013.2. The sequence is provided below:
1 caaggttcag agtcacccat ctcagcaagc ccagaagtat ctgcaatatc tacgatggcc 61 tcgccctttg ctttactgat ggtcctggtg gtgctcagct gcaagtcaag ctgctctctg 121 ggctgtgatc tccctgagac ccacagcctg gataacagga ggaccttgat gctcctggca
181 caaatgagca gaatctctcc ttcctcctgt ctgatggaca gacatgactt tggatttccc 241 caggaggagt ttgatggcaa ccagttccag aaggctccag ccatctctgt cctccatgag 301 ctgatccagc agatcttcaa cctctttacc acaaaagatt catctgctgc ttgggatgag 361 gacctcctag acaaattctg caccgaactc taccagcagc tgaatgactt ggaagcctgt 421 gtgatgcagg aggagagggt gggagaaact cccctgatga atgcggactc catcttggct
481 gtgaagaaat acttccgaag aatcactctc tatctgacag agaagaaata cagcccttgt 541 gcctgggagg ttgtcagagc agaaatcatg agatccctct ctttatcaac aaacttgcaa 601 gaaagattaa ggaggaagga ataacatctg gtccaacatg aaaacaattc ttattgactc 661 atacaccagg tcacgctttc atgaattctg tcatttcaaa gactctcacc cctgctataa 721 ctatgaccat gctgataaac tgatttatct atttaaatat ttatttaact attcataaga 781 tttaaattat ttttgttcat ataacgtcat gtgcaccttt acactgtggt tagtgtaata 841 aaacatgttc cttatattta etc
By "interferon beta (IFN-beta) polypeptide" is meant a polypeptide or fragment thereof, having at least about 85% amino acid identity to NCBI Accession No.
AAC41702.1 and having a biological activity or function of an IFN-beta polypeptide.
Biological activities or functions of an IFN-beta polypeptide include, without limitation, binding of the IFN-alpha/beta receptor (IFNAR) and regulation of immune system
response. The sequence of IFN-beta at NCBI Accession No. AAC41702.1 is shown below: 1 mtnkcllqia lllcfsttal smsynllgfl qrssncqcqk llwqlngrle yclkdrrnfd
61 ipeeikqlqq fqkedaavti yemlqnifai frqdssstgw netivenlla nvyhqrnhlk 121 tvleekleke dftrgkrmss lhlkryygri lhylkakeds hcawtivrve ilrnfyvinr 181 ltgylrn By "interferon beta (IFN-beta) polynucleotide" is meant a polynucleotide encoding an IFN-beta polypeptide. An exemplary IFN-beta polynucleotide sequence is provided at NCBI Accession No. NM_002176.3. The sequence is provided below:
1 ccatacccat ggagaaagga cattctaact gcaacctttc gaagcctttg ctctggcaca
61 acaggtagta ggcgacactg ttcgtgttgt caacatgacc aacaagtgtc tcctccaaat
121 tgctctcctg ttgtgcttct ccactacagc tctttccatg agctacaact tgcttggatt
181 cctacaaaga agcagcaatt ttcagtgtca gaagctcctg tggcaattga atgggaggct
241 tgaatactgc ctcaaggaca ggatgaactt tgacatccct gaggagatta ageagctgea
301 gcagttccag aaggaggacg ccgcattgac catctatgag atgetccaga acatctttgc
361 tattttcaga caagattcat ctagcactgg ctggaatgag actattgttg agaacctcct
421 ggctaatgtc tatcatcaga taaaccatct gaagacagtc ctggaagaaa aactggagaa
481 agaagatttc accaggggaa aactcatgag cagtctgcac ctgaaaagat attatgggag
541 gattctgeat tacctgaagg ccaaggagta cagtcactgt gcctggacca tagtcagagt
601 ggaaatccta aggaactttt acttcattaa cagacttaca ggttacctcc gaaactgaag
661 atctcctagc ctgtgcctct gggactggac aattgettea agcattcttc aaccagcaga
721 tgctgtttaa gtgactgatg gctaatgtac tgcatatgaa aggacactag aagattttga
781 aatttttatt aaattatgag ttatttttat ttatttaaat tttattttgg aaaataaatt
841 atttttggtg caaaagtca By "B-cell receptor polypeptide" is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. NP_001762.2 and having a biological activity or function of a B-cell receptor. Biological activities or functions of a B-cell receptor include, without limitation, antigen binding and signaling transduction. In one embodiment, the B-cell receptor is a transgenic B-cell receptor specific for the well- known lupus antigen, SSB/La, described by Berland et al. {Immunity 25, 429-440, 2006) and Chatterjee et al. {European Journal of Immunology 43, 2441-2450, 2013), which are incorporated herein by reference in their entirety. In particular embodiments, the B-cell receptor is a human B-cell receptor. The sequence at NCBI Accession No. NP_001762.2 is shown below:
1 mhllgpwlll lvleylafsd sskwvfehpe tlyawegacv wipctyrald gdlesfilfh 61 npeynkntsk fdgtrlyest kdgkvpseqk rvqflgdknk nctlsihpvh lndsgqlglr 121 mesktekwme rihlnvserp fpphiqlppe iqesqevtlt cllnfscygy piqlqwlleg 181 vpmrqaavts tsltiksvft rselkfspqw shhgkivtcq lqdadgkfls ndtvqlnvkh
241 tpkleikvtp sdaivregds vtmtcevsss npeyttvswl kdgtslkkqn tftlnlrevt 301 kdqsgkyccq vsndvgpgrs eevflqvqya pepstvqilh spavegsqve flcmslanpl 361 ptnytwyhng kemqgrteek vhipkilpwh agtyscvaen ilgtgqrgpg aeldvqyppk 421 kvttviqnpm piregdtvtl scnynssnps vtryewkphg aweepslgvl kiqnvgwdnt 481 tiacaacnsw cswaspvaln vqyaprdvrv rkikplseih sgnsvslqcd fssshpkevq
541 ffwekngrll gkesqlnfds ispedagsys cwvnnsigqt askawtlevl yaprrlrvsm 601 spgdqvmegk satltcesda nppvshytwf dwnnqslpyh sqklrlepvk vqhsgaywcq 661 gtnsvgkgrs plstltvyys petigrrvav glgsclaili laicglklqr rwkrtqsqqg 721 lqenssgqsf fvrnkkvrra plsegphslg cynpmmedgi syttlrfpem niprtgdaes 781 semqrpppdc ddtvtysalh krqvgdyenv ipdfpedegi hyseliqfgv gerpqaqenv
841 dyvilkh
By "B-cell receptor polynucleotide" is meant a polynucleotide encoding a B cell receptor polypeptide. An exemplary B-cell receptor polynucleotide sequence is provided at NCBI Accession No. NM_001771.3. The sequence is provided below:
1 acttctcctt ttgctctcag atgctgccag ggtccctgaa gagggaagac acgcggaaac 61 aggcttgcac ccagacacga caccatgcat ctcctcggcc cctggctcct gctcctggtt 121 ctagaatact tggctttctc tgactcaagt aaatgggttt ttgagcaccc tgaaaccctc 181 tacgcctggg agggggcctg cgtctggatc ccctgcacct acagagccct agatggtgac
241 ctggaaagct tcatcctgtt ccacaatcct gagtataaca agaacacctc gaagtttgat 301 gggacaagac tctatgaaag cacaaaggat gggaaggttc cttctgagca gaaaagggtg 361 caattcctgg gagacaagaa taagaactgc acactgagta tccacccggt gcacctcaat 421 gacagtggtc agctggggct gaggatggag tccaagactg agaaatggat ggaacgaata
481 cacctcaatg tctctgaaag gccttttcca cctcatatcc agctccctcc agaaattcaa
541 gagtcccagg aagtcactct gacctgcttg ctgaatttct cctgctatgg gtatccgatc
601 caattgcagt ggctcctaga gggggttcca atgaggcagg ctgctgtcac ctcgacctcc
661 ttgaccatca agtctgtctt cacccggagc gagctcaagt tctccccaca gtggagtcac
721 catgggaaga ttgtgacctg ccagcttcag gatgcagatg ggaagttcct ctccaatgac
781 acggtgcagc tgaacgtgaa gcacaccccg aagttggaga tcaaggtcac tcccagtgat
841 gccatagtga gggaggggga ctctgtgacc atgacctgcg aggtcagcag cagcaacccg
901 gagtacacga cggtatcctg gctcaaggat gggacctcgc tgaagaagca gaatacattc
961 acgctaaacc tgcgcgaagt gaccaaggac cagagtggga agtactgctg tcaggtctcc
1021 aatgacgtgg gcccgggaag gtcggaagaa gtgttcctgc aagtgcagta tgccccggaa
1081 ccttccacgg ttcagatcct ccactcaccg gctgtggagg gaagtcaagt cgagtttctt
1141 tgcatgtcac tggccaatcc tcttccaaca aattacacgt ggtaccacaa tgggaaagaa
1201 atgcagggaa ggacagagga gaaagtccac atcccaaaga tcctcccctg gcacgctggg
1261 acttattcct gtgtggcaga aaacattctt ggtactggac agaggggccc gggagctgag
1321 ctggatgtcc agtatcctcc caagaaggtg accacagtga ttcaaaaccc catgccgatt
1381 cgagaaggag acacagtgac cctttcctgt aactacaatt ccagtaaccc cagtgttacc
1441 cggtatgaat ggaaacccca tggcgcctgg gaggagccat cgcttggggt gctgaagatc
1501 caaaacgttg gctgggacaa cacaaccatc gcctgcgcag cttgtaatag ttggtgctcg
1561 tgggcctccc ctgtcgccct gaatgtccag tatgcccccc gagacgtgag ggtccggaaa
1621 atcaagcccc tttccgagat tcactctgga aactcggtca gcctccaatg tgacttctca
1681 agcagccacc ccaaagaagt ccagttcttc tgggagaaaa atggcaggct tctggggaaa
1741 gaaagccagc tgaattttga ctccatctcc ccagaagatg ctgggagtta cagctgctgg
1801 gtgaacaact ccataggaca gacagcgtcc aaggcctgga cacttgaagt gctgtatgca
1861 cccaggaggc tgcgtgtgtc catgagcccg ggggaccaag tgatggaggg gaagagtgca
1921 accctgacct gtgagagcga cgccaaccct cccgtctccc actacacctg gtttgactgg
1981 aataaccaaa gcctccccta ccacagccag aagctgagat tggagccggt gaaggtccag
2041 cactcgggtg cctactggtg ccaggggacc aacagtgtgg gcaagggccg ttcgcctctc
2101 agcaccctca ccgtctacta tagcccggag accatcggca ggcgagtggc tgtgggactc
2161 gggtcctgcc tcgccatcct catcctggca atctgtgggc tcaagctcca gcgacgttgg
2221 aagaggacac agagccagca ggggcttcag gagaattcca gcggccagag cttctttgtg
2281 aggaataaaa aggttagaag ggcccccctc tctgaaggcc cccactccct gggatgctac
2341 aatccaatga tggaagatgg cattagctac accaccctgc gctttcccga gatgaacata
2401 ccacgaactg gagatgcaga gtcctcagag atgcagagac ctcccccgga ctgcgatgac
2461 acggtcactt attcagcatt gcacaagcgc caagtgggcg actatgagaa cgtcattcca
2521 gattttccag aagatgaggg gattcattac tcagagctga tccagtttgg ggtcggggag
2581 cggcctcagg cacaagaaaa tgtggactat gtgatcctca aacattgaca ctggatgggc
2641 tgcagcagag gcactggggg cagcgggggc cagggaagtc cccgagtttc cccagacacc
2701 gccacatggc ttcctcctgc gcgcatgtgc gcacacacac acacacacgc acacacacac
2761 acacacactc actgcggaga accttgtgcc tggctcagag ccagtctttt tggtgagggt 2821 aaccccaaac ctccaaaact cctgcccctg ttctcttcca ctctccttgc tacccagaaa 2881 tccatctaaa tacctgccct gacatgcaca cctccccctg cccccaccac ggccactggc 2941 catctccacc cccagctgct tgtgtccctc ctgggatctg ctcgtcatca tttttccttc 3001 ccttctccat ctctctggcc ctctacccct gatctgacat ccccactcac gaatattatg 3061 cccagtttct gcctctgagg gaaagcccag aaaaggacag aaacgaagta gaaaggggcc
3121 cagtcctggc ctggcttctc ctttggaagt gaggcattgc acggggagac gtacgtatca 3181 gcggcccctt gactctgggg actccgggtt tgagatggac acactggtgt ggattaacct 3241 gccagggaga cagagctcac aataaaaatg gctcagatgc cacttcaaag aaaaaaaaaa By "CNS lupus" is meant the presence of neurological changes and/or behavioral clinical syndromes in a patient that has systemic lupus erythematosus. Symptoms of CNS lupus include, but are not limited to, cognitive dysfunction (not thinking clearly, memory deficits), headaches, seizure, altered mental alertness (e.g. stupor or coma), aseptic meningitis (inflammation of the covering of the brain), stroke (disturbance of the blood supply to different parts of the brain), peripheral neuropathy (e.g. numbness, tingling, burning of the hands and feet), movement disorders, myelitis (disruption) of the spinal cord, visual alternations, autonomic neuropathy (e.g., flushing reaction or mottled skin), personality changes, and changes in sociability. In one embodiment, CNS lupus is characterized by changes in frontal cortex and/or hippocampus.
By "interferon (IFN)-alpha/beta receptor (IFNAR) polypeptide" is meant a polypeptide or fragment thereof having at least about 85% amino acid identity to NCBI Accession No. NP_000620.2 and having a biological activity or function of an IFNAR.
Biological activities or functions of an IFNAR include, without limitation, binding type I interferons including interferon-a and interferon -β, and/or signaling via pathways downstream of IFNAR (e.g., activation of the JAK-STAT signaling pathway). The sequence at NCBI Accession No. NP_000620.2 is shown below:
1 mmvvllgatt lvlvavapwv lsaaaggknl kspqkvevdi iddnfilrwn rsdesvgnvt 61 fsfdyqktgm dnwiklsgcq nitstkcnfs slklnvyeei klriraeken tsswyevdsf 121 tpfrkaqigp pevhleaedk aivihispgt kdsvmwaldg lsftyslviw knssgveeri
181 eniysrhkiy klspettycl kvkaalltsw kigvyspvhc ikttvenelp ppenievsvq 241 nqnyvlkwdy tyanmtfqvq wlhaflkrnp gnhlykwkqi pdcenvkttq cvfpqnvfqk 301 giyllrvqas dgnntsfwse eikfdteiqa fllppvfnir slsdsfhiyi gapkqsgntp 361 viqdypliye iifwentsna erkiiekktd vtvpnlkplt vycvkaraht mdeklnkssv 421 fsdavcektk pgntskiwli vgicialfal pfviyaakvf lrcinyvffp slkpssside
481 yfseqplknl llstseeqie kcfiienist iatveetnqt dedhkkyssq tsqdsgnysn 541 edesesktse elqqdfv By "IFN-alpha/beta receptor (IFNAR) polynucleotide" is meant a polynucleotide encoding an IFNAR polypeptide. An exemplary IFNAR polynucleotide sequence is provided at NCBI Accession No. NM_000629.2. The sequence is provided below:
1 aggcggcgcg tgcgtagagg ggcggtgaga gctaagaggg gcagcgcgtg tgcagagggg
61 cggtgtgact taggacgggg cgatggcggc tgagaggagc tgcgcgtgcg cgaacatgta
121 actggtggga tctgcggcgg ctcccagatg atggtcgtcc tcctgggcgc gacgacccta
181 gtgctcgtcg ccgtggcgcc atgggtgttg tccgcagccg caggtggaaa aaatctaaaa
241 tctcctcaaa aagtagaggt cgacatcata gatgacaact ttatcctgag gtggaacagg
301 agcgatgagt ctgtcgggaa tgtgactttt tcattcgatt atcaaaaaac tgggatggat
361 aattggataa aattgtctgg gtgtcagaat attactagta ccaaatgcaa cttttcttca
421 ctcaagctga atgtttatga agaaattaaa ttgcgtataa gagcagaaaa agaaaacact
481 tcttcatggt atgaggttga ctcatttaca ccatttcgca aagctcagat tggtcctcca
541 gaagtacatt tagaagctga agataaggca atagtgatac acatctctcc tggaacaaaa
601 gatagtgtta tgtgggcttt ggatggttta agctttacat atagcttagt tatctggaaa
661 aactcttcag gtgtagaaga aaggattgaa aatatttatt ccagacataa aatttataaa
721 ctctcaccag agactactta ttgtctaaaa gttaaagcag cactacttac gtcatggaaa
781 attggtgtct atagtccagt acattgtata aagaccacag ttgaaaatga actacctcca
841 ccagaaaata tagaagtcag tgtccaaaat cagaactatg ttcttaaatg ggattataca
901 tatgcaaaca tgacctttca agttcagtgg ctccacgcct ttttaaaaag gaatcctgga
961 aaccatttgt ataaatggaa acaaatacct gactgtgaaa atgtcaaaac tacccagtgt
1021 gtctttcctc aaaacgtttt ccaaaaagga atttaccttc tccgcgtaca agcatctgat
1081 ggaaataaca catctttttg gtctgaagag ataaagtttg atactgaaat acaagctttc
1141 ctacttcctc cagtctttaa cattagatcc cttagtgatt cattccatat ctatatcggt
1201 gctccaaaac agtctggaaa cacgcctgtg atccaggatt atccactgat ttatgaaatt
1261 attttttggg aaaacacttc aaatgctgag agaaaaatta tcgagaaaaa aactgatgtt
1321 acagttccta atttgaaacc actgactgta tattgtgtga aagccagagc acacaccatg
1381 gatgaaaagc tgaataaaag cagtgttttt agtgacgctg tatgtgagaa aacaaaacca
1441 ggaaatacct ctaaaatttg gcttatagtt ggaatttgta ttgcattatt tgctctcccg
1501 tttgtcattt atgctgcgaa agtcttcttg agatgcatca attatgtctt ctttccatca
1561 cttaaacctt cttccagtat agatgagtat ttctctgaac agccattgaa gaatcttctg
1621 ctttcaactt ctgaggaaca aatcgaaaaa tgtttcataa ttgaaaatat aagcacaatt
1681 gctacagtag aagaaactaa tcaaactgat gaagatcata aaaaatacag ttcccaaact
1741 agccaagatt caggaaatta ttctaatgaa gatgaaagcg aaagtaaaac aagtgaagaa
1801 ctacagcagg actttgtatg accagaaatg aactgtgtca agtataaggt ttttcagcag
1861 gagttacact gggagcctga ggtcctcacc ttcctctcag taactacaga gaggacgttt
1921 ccctgtttag ggaaagaaaa aacatcttca gatcataggt cctaaaaata cgggcaagct
1981 cttaactatt taaaaatgaa attacaggcc cgggcacggt ggctcacacc tgtaatccca
2041 gcactttggg aggctgaggc aggcagatca tgaggtcaag agatcgagac cagcctggcc 2101 aacgtggtga aaccccatct ctactaaaaa tacaaaaatt agccgggtgt ggtggcgcgc
2161 gcctgttgtc ttagctactc aggaggctga ggcaggagaa tcgcttgaaa acaggaggtg
2221 gaggttgcag tgagccgaga tcacgccact gcactccagc ctggtgacag cgtgagactc
2281 tttaaaaaaa gaaattaaaa gagttgagac aaacgtttcc tacattcttt tccatgtgta
2341 aaatcatgaa aaagcctgtc accggacttg cattggatga gatgagtcag accaaaacag
2401 tggccacccg tcttcctcct gtgagcctaa gtgcagccgt gctagctgcg caccgtggct
2461 aaggatgacg tctgtgttcc tgtccatcac tgatgctgct ggctactgca tgtgccacac
2521 ctgtctgttc gccattccta acattctgtt tcattcttcc tcgggagata tttcaaacat
2581 ttggtctttt cttttaacac tgagggtagg cccttaggaa atttatttag gaaagtctga
2641 acacgttatc acttggtttt ctggaaagta gcttacccta gaaaacagct gcaaatgcca
2701 gaaagatgat ccctaaaaat gttgagggac ttctgttcat tcatcccgag aacattggct
2761 tccacatcac agtatctacc cttacatggt ttaggattaa agccaggcaa tcttttacta
2821 tgcattaaga cctctgattc aaaacttatt agaacagtag cttctgctgg aatttgcaat
2881 cactgaagtc atagaaaata ggtaactatc taattagaga aataattgtt gtattttaag
2941 atctgagagt gtgtacaagt tttagtatac atgccatgcc agaagatagt gtatgcaaga
3001 agtcttggga ccagaaaatg gcaatgatag gagactgaca tagaagaaga atgcttccct
3061 aggaaaaagg tcgctggctt tggtgcaaga ggaagaagaa tgttccactg gaagcctgag
3121 cacctaatca gctctcagtg atcaacccac tcttgttatg ggtggtctct gtcactttga
3181 atgccaggct ggcttctcgt ctagcagtat tcagataccc cttctgctca gcctgcttgg
3241 cgttaaaata caaatcattg aactgagggg gaaaaatgta actaggaaga aaaacccaat
3301 ttaagaaatt acataatgct ttccaaaggc acctacaact tagttttaaa ttacttgcta
3361 ctggggatta cccatggata tccttaatag gcaggaagtc tgggaattct ggtggcctct
3421 agggcagtgt tctcacagca ccgttccgac agggaccagt gaaagaaaag agacaaagtt
3481 agaacgtgct ggggagcggc catttctaag gccagtctgg tttaagtagt catttctgct
3541 gaaaaaacag atgatcctgg tggaagaaaa ggttgaaggc agctgccctc gggagggctg
3601 tgatgctcgg cacatcctgc ctggcacata cacgtgtctg caggccacac cgtgcatgtc
3661 cccagacctg ccgcctggct tctggagtgc ttcaagcaga gcatggtggg tcattgagga
3721 gacccaggaa tctcatctga gaacccactc tctgccggag aaccccatgg tgacacattt
3781 tcatctttct gaccagaggc tgtttttttt tttttttgag acagtctcat tctgttgccc
3841 aggctggagt gcagtggctt gatctcggct cactgcaacc tcgcctcccg ggttcaagca
3901 attctctgcc gcagcctcca gagtagctgg gataacaggt gcccaccacc acaccccact
3961 aatttttgta tttgtatttt tagtagagat ggggtttcac catgttggtc aggctggtct
4021 tggactcctg acctcatgct ccacccgctt cggcctccca aagttctggg attacaggtg
4081 tgagccaccg tgcacggccg gcctgacctt tggaaaagcc ttgtcacttt ggacgtttgc
4141 gtctttgaag aggcgatggg agcatatcat gactgcctgc caccattgct tttcagacta
4201 ccacaactca atcatgctgt ccaggacttc tggccctgtg ttcaccactg ggaaaacgta
4261 cttcagactg gatagcctaa aaaggagcaa tgcccttgta ggatgtggag aagggaaaat
4321 acggacatta acattaaaag acaccagtga aattgttagg tctctaggaa gttggagcac
4381 aaggcttcac gctttaagac catctgtggt tttcagtgaa caagcgctga gcaccagcag
4441 cagaaaacaa caacaaaaaa acacctcgtt tttaccttgt cttctagaca tgaaaaggca 4501 gttgcattcc actctgcatt atgttctaca tgttgcttta tcagtatatg cttagctgta 4561 agtgacaagt attttttctg aacagaagtt tacttagaaa taccatgcac ttgggggtac 4621 caattaaccg cctgaaaatt agcatattga tagttcttag agagaccaga tataatctaa 4681 gaatttatat gaaagatttg tatcattaga gccagaaata attttatatt aatatataat 4741 acagattaac attatatata atatgtacct gtgtcacttc tgacatgagc ctgtaaacat 4801 atattcatat atgtacctgc acatgtaccc acctgatgta ggtcttattc ctttagtatg 4861 gacttaaagt acttattcat ataccttgta actaaaaatt agaacagctc cctagaattg 4921 tgaactttta agagtctgac tagaaatttg caacttataa aaaagttact tttaaaaata 4981 taagttaggg ctaggcacag tggctcatgc ctataatctc agcacttttg ggaggccaag 5041 acaggaggat cacttcaggc caggagttca agatcaacca acctgggtaa catggccaga 5101 ccccatctct atttatatat atatatataa aacttagagt ttttatcttc ccctaaaaga 5161 ggccgtgata tttgcagcag cctcaaattg ctcttaaggg gtttaggtgt gcagaagctt 5221 tcctttccct acccagtaac catgtgacta ctaacgtggt atattgattt attttgtttg 5281 ctgtctgtct cccctgcccc actgctggaa cagaggctcc aagaaaacag ggaccttatt 5341 attcattact gcatccccag taatgaaagt acttagaaaa taattattga atgaatgaaa 5401 tctaaactgt gaacctgagg gtgtttgtgg cagtgtttgt tttactgaat tgtagaagga 5461 cataaccgtg ttttcagtgt ttctatggaa caaacttgta cattttattt cacttgtgtt 5521 ttgtcttaaa ccctactgct ggaaacaatt ttatgtaata agcaatgggc ccaaaagtct 5581 aggagttttt ttgtacttag tgaatttgta tgcaacagag atgctgcagc tgatgccttt 5641 aaaaggtatt catcatggaa gagctgaggc ctgtgcttgg tgttccagag cccagggttg 5701 agcatcctga aggagccact gcagccgtca ctgtccccag agcctgtgga gatagagcct 5761 gtttgctgct ttttcttccc gctcttaaga catggctgga gctcagtctt cattgaatga 5821 agtttgctgt ggtattgcat agccttgctt tcttgaacta aactgtttgc ccttcacaag 5881 tagttcttct ttcaggatta gttcgttcca aggaggctct tcagtctcac agataagtag 5941 atctctcctg ctgtctggac acatttcact cggaaattga atacaatttg tattcaggct 6001 gggaacctga acacacactt gtgtttttaa gcttcccttt tttacagtgg acaaggacac 6061 aaataataaa taaatcatcc ctaatgccca aagaaaaaaa
By "anti-interferon alpha/beta receptor (IFNAR) antibody" is meant an antibody or fragment thereof that specifically binds an interferon receptor. In one embodiment, the anti- IFNAR antibody is "MEDI-546," also termed "anifrolumab," which refers to an Fc-modified version of the anti-IFNAR 9D4 antibody described in U.S. Pat. No. 7,662,381, which is incorporated by reference in its entirety. The sequence of MEDI-546 is described in U.S. 2011-0059078. MEDI-546 comprises a combination of three mutations: L234F, L235E, and P331 S, wherein the numbering is according to the EU index as set forth in Kabat, introduced into the lower hinge and CH2 domain of human IgGl, which cause a decrease in their binding to human Fc.gamma.RI (CD64), Fc.gamma.RIIA (CD32A), Fc.gamma.RIII (CD 16) and Clq. See, e.g., US 2011/0059078 and Oganesyan et al. Acta Crystallographica D 64:700-704 (2008), which are hereby incorporated by reference in their entireties.
TABLE 1
MEDI-546 VH EVQLVQSGAEVKKPGESLKISCKGSGYIFTNYWIAWVRQMPGKCLESMGI
(SEQ ID NO: 1) IYPGDSDIRYSPSFQGQVTISADKSI TTAYLQWSSLKASDTA YYCARHD
IEGFDYWGRGTLVTVSS
MEDI-546 VK EIVLTQSPGTLSLSPGERATLSCRASQSVSSSFFAWYQQ PGQAPRLLIY
(SEQ ID NO: 2) GASSRATGIPDRLSGSGSGTDFTLTI TRLEPEDFAVYYCQQYDSSAITFG
QGTRLEIK By "anti-interferon alpha" antibody is meant or fragment thereof that specifically binds interferon alpha. In one embodiment, the antibody does not bind interferon beta. Such antibodies are known in the art and include antibodies described in US Patent No. 7,087,726, Sifalimumab (Medi-545) Yao et al., Arthritis Rheum. 2009 Jun; 60(6): 1785-96.
By "agent" is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.
By "ameliorate" is meant decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.
By "alteration" is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 10% change in expression levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels.
The term "antibody," as used herein, refers to an immunoglobulin molecule which specifically binds with an antigen. In one embodiment, the antigen is IFN-alpha/beta receptor (IFNAR). Methods of preparing antibodies are well known to those of ordinary skill in the science of immunology. Antibodies can be intact immunoglobulins derived from natural sources or from recombinant sources and can be immunoreactive portions of intact immunoglobulins. Antibodies are typically tetramers of immunoglobulin molecules.
Tetramers may be naturally occurring or reconstructed from single chain antibodies or antibody fragments. Antibodies also include dimers that may be naturally occurring or constructed from single chain antibodies or antibody fragments. The antibodies in the present invention may exist in a variety of forms including, for example, polyclonal antibodies, monoclonal antibodies, Fv, Fab and F(ab') 2 , as well as single chain antibodies (scFv), humanized antibodies, and human antibodies (Harlow et al., 1999, In: Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY; Harlow et al., 1989, In: Antibodies: A Laboratory Manual, Cold Spring Harbor, New York; Houston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; Bird et al., 1988, Science 242:423-426).
The term "antibody fragment" refers to a portion of an intact antibody and refers to the antigenic determining variable regions of an intact antibody. Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab') 2 , and Fv fragments, linear antibodies, scFv antibodies, single-domain antibodies, such as camelid antibodies
(Riechmann, 1999, Journal of Immunological Methods 231 :25-38), composed of either a VL or a VH domain which exhibit sufficient affinity for the target, and multispecific antibodies formed from antibody fragments. The antibody fragment also includes a human antibody or a humanized antibody or a portion of a human antibody or a humanized antibody.
Antibodies can be made by any of the methods known in the art utilizing a polypeptide or immunogenic fragments thereof, as an immunogen. One method of obtaining antibodies is to immunize suitable host animals with an immunogen and to follow standard procedures for polyclonal or monoclonal antibody production. The immunogen will facilitate presentation of the immunogen on the cell surface. Immunization of a suitable host can be carried out in a number of ways. Nucleic acid sequences encoding a polypeptide of the invention or immunogenic fragments thereof, can be provided to the host in a delivery vehicle that is taken up by immune cells of the host. The cells will in turn express the receptor on the cell surface generating an immunogenic response in the host. Alternatively, nucleic acid sequences encoding the polypeptide, or immunogenic fragments thereof, can be expressed in cells in vitro, followed by isolation of the polypeptide and administration of the polypeptide to a suitable host in which antibodies are raised.
Alternatively, antibodies against the polypeptide may, if desired, be derived from an antibody phage display library. A bacteriophage is capable of infecting and reproducing within bacteria, which can be engineered, when combined with human antibody genes, to display human antibody proteins. Phage display is the process by which the phage is made to 'display' the human antibody proteins on its surface. Genes from the human antibody gene libraries are inserted into a population of phage. Each phage carries the genes for a different antibody and thus displays a different antibody on its surface.
Antibodies made by any method known in the art can then be purified from the host. Antibody purification methods may include salt precipitation (for example, with ammonium sulfate), ion exchange chromatography (for example, on a cationic or anionic exchange column preferably run at neutral pH and eluted with step gradients of increasing ionic strength), gel filtration chromatography (including gel filtration HPLC), and chromatography on affinity resins such as protein A, protein G, hydroxyapatite, and anti-immunoglobulin.
Antibodies can be conveniently produced from hybridoma cells engineered to express the antibody. Methods of making hybridomas are well known in the art. The hybridoma cells can be cultured in a suitable medium, and spent medium can be used as an antibody source. Polynucleotides encoding the antibody of interest can in turn be obtained from the hybridoma that produces the antibody, and then the antibody may be produced synthetically or recombinantly from these DNA sequences. For the production of large amounts of antibody, it is generally more convenient to obtain an ascites fluid. The method of raising ascites generally comprises injecting hybridoma cells into an immunologically naive histocompatible or immunotolerant mammal, especially a mouse. The mammal may be primed for ascites production by prior administration of a suitable composition (e.g., Pristane).
By "capture reagent" is meant a reagent that specifically binds a nucleic acid molecule or polypeptide to select or isolate the nucleic acid molecule or polypeptide. In one embodiment, a capture reagent of the invention binds Interferon alpha.
In this disclosure, "comprises," "comprising," "containing" and "having" and the like can have the meaning ascribed to them in U.S. Patent law and can mean " includes,"
"including," and the like; "consisting essentially of or "consists essentially" likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
In this disclosure, "comprises," "comprising," "containing" and "having" and the like can have the meaning ascribed to them in U.S. Patent law and can mean " includes,"
"including," and the like; "consisting essentially of or "consists essentially" likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
"Detect" refers to identifying the presence, absence or amount of the analyte to be detected. By "disease" is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Examples of diseases include diseases
characterized by microglia mediated synapse loss, such as CNS lupus, Sjogren's syndrome, HIV, Alzheimer's disease, and chronic viral infections.
By "effective amount" is meant the amount of a required 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 a disease 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 invention provides a number of targets that are useful for the development of highly specific drugs to treat or a disorder characterized by the methods delineated herein. In addition, the methods of the invention provide a facile means to identify therapies that are safe for use in subjects. In addition, the methods of the invention provide a route for analyzing virtually any number of compounds for effects on a disease described herein with high-volume throughput, high sensitivity, and low complexity.
By "fragment" is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.
"Hybridization" means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds.
The terms "isolated," "purified," or "biologically pure" refer to material that is free to varying degrees from components which normally accompany it as found in its native state. "Isolate" denotes a degree of separation from original source or surroundings. "Purify" denotes a degree of separation that is higher than isolation. A "purified" or "biologically pure" protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography. The term "purified" can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.
By "isolated polynucleotide" is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.
By an "isolated polypeptide" is meant a polypeptide of the invention that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, a polypeptide of the invention. An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
By "marker" is meant any clinical indicator, protein, metabolite, or polynucleotide having an alteration associated with a disease, disorder, or condition. In one embodiment, a marker of the invention is the level of a cytokine, such as a type I interferon (e.g., IFN alpha or beta) in a bodily fluid (e.g., cerebrospinal fluid, blood, serum, plasma).
By "microglia" is meant an immune cell of myeloid lineage resident in the central nervous system. As used herein, "obtaining" as in "obtaining an agent" includes synthesizing, purchasing, or otherwise acquiring the agent.
By "increases" or "reduces" is meant a positive or negative alteration, respectively, of at least 10%, 25%, 50%, 75%, or 100%.
By "reference" is meant a standard or control condition.
By "specifically binds" is meant a compound or antibody that recognizes and binds a polypeptide of the invention, but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample, which naturally includes a polypeptide of the invention.
Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having "substantial identity" to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having "substantial identity" to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By "hybridize" is meant pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).
For example, stringent salt concentration will ordinarily be less than about 750 mM
NaCl and 75 mM trisodium citrate, preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and more preferably less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C, more preferably of at least about 37° C, and most preferably of at least about 42° C. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those of ordinary skill in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In a preferred: embodiment, hybridization will occur at 30° C in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more preferred embodiment, hybridization will occur at 37° C in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 .mu.g/ml denatured salmon sperm DNA (ssDNA). In a most preferred embodiment, hybridization will occur at 42° C in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variations on these conditions will be readily apparent to those of ordinary skill in the art.
For most applications, washing steps that follow hybridization will also vary in stringency. Wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature. For example, stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperature conditions for the wash steps will ordinarily include a temperature of at least about 25° C, more preferably of at least about 42° C, and even more preferably of at least about 68° C. In a preferred embodiment, wash steps will occur at 25° C in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 42 C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 68° C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS.
Additional variations on these conditions will be readily apparent to those of ordinary skill in the art. Hybridization techniques are well known to those of ordinary skill in the art and are described, for example, in Benton and Davis (Science 196: 180, 1977); Grunstein and
Hogness (Proc. Natl. Acad. Sci., USA 72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, New York, 2001); Berger and Kimmel (Guide to Molecular Cloning Techniques, 1987, Academic Press, New York); and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York.
By "substantially identical" is meant a polypeptide 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). Preferably, such a sequence is at least 60%, more preferably 80% or 85%, and more 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). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. 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. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e"3 and e"100 indicating a closely related sequence.
By "subject" is meant a mammal, including, but not limited to, a human or non- human mammal, such as a bovine, equine, canine, ovine, or feline.
Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
As used herein, the terms "treat," treating," "treatment," and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
Unless specifically stated or obvious from context, as used herein, the term "or" is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms "a", "an", and "the" are understood to be singular or plural.
Unless specifically stated or obvious from context, as used herein, the term "about" is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about. The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.
BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1 A-1L show behavioral phenotyping of 564Igi mice. FIG. 1 A is a graph showing that 564Igi mice exhibited anxiety-like behavior in an elevated plus maze assay, n = 10 mice per group, *P < 0.05, unpaired t-test. FIG. IB is a graph showing that 564Igi mice exhibited anxiety-like behavior in a novelty suppressed feeding assay, n = 10 mice per group, *P < 0.05, unpaired t-test. FIG. 1C is a graph showing impaired cognitive performance of 564Igi mice, n = 10 mice per group, **P = 0.007, two-way ANOVA with Sidak's test. FIG. ID is a graph showing that 564Igi mice exhibited impaired spatial learning in a water T maze, n = 10 mice per group, P = 0.0001, comparison of nonlinear fits test. FIG. IE is a graph showing that increased social dominance/aggression was observed in 564Igi mice, n = 10 mice per group, *P = 0.04, paired t-test. FIG. IF is a graph showing Impaired social interaction in 564Igi mice, n = 10 mice per group, **** P < 0.0001, two-way ANOVA with Sidak's test. FIG. 1G is a graph showing increased prepulse inhibition in 564Igi mice. n = 10 mice per group, *P = 0.03, ****p < 0.0001, two-way ANOVA with Sidak's test. FIG. 1H is a graph showing that 564Igi mice had normal levels of activity and motor function in the open field test, n = 10 mice per group; P > 0.05 (not significant), one-way ANOVA with Tukey's test. FIG. II is a graph showing that rotarod performance of 564Igi mice
demonstrated normal motor coordination, n = 10 mice per group; P > 0.05 (not significant), two-way ANOVA with Sidak's test. FIG. 1 J is a graph showing that marble-burying behavior was normal in 564Igi mice, n = 10 mice per group; P > 0.05 (not significant), unpaired t-test. FIG. IK is a graph showing that 564Igi mice did not exhibit depression-like phenotypes in a forced swim test, n = 10 mice P > 0.05 (not significant), unpaired t-test. FIG. 1L is a graph showing that 564Igi mice did not exhibit depression-like phenotypes in a tail suspension test, n = 10 mice P > 0.05 (not significant), unpaired t-test. In FIGS. 1 A-1L, data are mean ± s.e.m. FIGS. 2A-2J depict behavioral phenotypes and reactive microglia in 564Igi mice. FIG. 2A is a graph showing behavior in wild-type and 564Igi mice in the elevated plus maze. Elevated plus maze evaluates anxiety-like phenotypes. 564, 564Igi mice; WT, wild-type mice. Isotype, isotype-control antibody; anti-IFNAR, anti-IFNAR antibody. Two-way ANOVA with Tukey's test. FIG. 2B is a graph showing cognitive function in wild-type and 564Igi mice in the novelty Y maze. Novelty Y maze evaluates cognitive function. FIG. 2C is a graph showing sociability in wild-type and 564Igi mice in the three-chamber test. Three- chamber test evaluates sociability. FIG. 2D is a graph showing sensorimotor function in wild-type and 564Igi mice in the prepulse-inhibition test. Prepulse-inhibition test evaluates sensorimotor gating at three different tone intensities. FIG. 2E depict microglial activation state analysis in wild-type, 564Igi, and NZB/NZW mice. Arrows indicate reactive microglia. FIG. 2F is a graph showing percentage reactive microglia out of total microglia in the hippocampus, cortex, and cerebellum. n = 4 mice per group, two-way ANOVA with Tukey's test. FIG. 2G depicts qPCR analysis of Ifiia in the spleen of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls. FIG. 2H depicts qPCR analysis oiMxl in the spleen of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls. FIG. 21 depicts qPCR analysis of Ifiia in the hippocampus of NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls. FIG. 2J depicts qPCR analysis of Mxl in the hippocampus of
NZB/NZW (6- and 16-week-old) and 564Igi (16-week old) mice compared to wild-type controls. In FIGS. 2G-2J, Two-way ANOVA with Tukey's test. Data are mean ± s.e.m. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 using a two-way ANOVA with Sidak's test, unless indicated otherwise. In FIGS. 2A-2D, n = 10 mice per group, in FIGS. 2G-2J n = 3 mice per group.
FIGS. 3 A-3F depict no significant cellular infiltration or microglia proliferation in
564Igi mice and comparison with MRL-lpr mice. FIG. 3 A depicts representative images of haematoxylin and eosin staining. No evidence of cellular infiltration or gross anatomical abnormalities was observed in 564Igi mice. Scale bar, 100 μπι. FIG. 3B depicts
immunohistochemistry analysis, showing that no infiltration of B cells or T cells in the frontal cortex (top) or hippocampus (bottom). Scale bar, 20 μπι. FIG. 3C depicts
representative staining in spleen for T cells (CD3), B cells (B220) and all bone-marrow- derived cells (CD45), showing antibody specificity despite lack of signal in the brain. Scale bar, 20 μπι. FIG. 3D depicts representative images of Ibal and CD68 staining, and the common microglia activation state scores observed in adult mouse tissue. Microglia, which fell into the category of 3 or higher, were pooled to form the reactive microglia population. Scale bar, 20 μιη. FIG. 3E shows similar microglia density for cortex, hippocampus and cerebellum in wild-type, 564Igi and NZB/NZW mice. FIG. 3F are images and a graph showing that MRL-lpr mice exhibited increased reactive microglia at 8 weeks, similar to NZB/NZW mice. n = 3 mice per group ***P = 0.0002, unpaired t-test. Scale bar, 20 μιη. In FIGS. 3A-3F, data are mean ± s.e.m.
FIGS. 4A-4J showing that Ifiib was not expressed and anti-IFNAR treatment was effective in both 564Igi and NZB/NZW mice. FIG. 4A is a graph showing similar expression levels of Ifiib in the spleen in wild-type, 564Igi and NZB/NZW mice as measured by qPCR. n = 3 mice per group, P > 0.05, ANOVA. FIG. 4B is a graph showing similar expression levels of Ifiib in the hippocampus in wild-type, 564Igi and NZB/NZW mice as measured by qPCR. n = 3 mice per group, P > 0.05, ANOVA. FIG. 4C is a graph showing a significant increase in expression of Ifi44 in the spleen in 564Igi and NZB/ NZW mice compared to wild-type mice, as measured by qPCR. The increase of Ifi44 expression in the spleen was reduced with anti-IFNAR treatment. n = 3 mice per group, *P < 0.049, **P = 0.002, two-way
ANOVA with Sidak's test. FIG. 4D is a graph showing a significant increase in expression of Oasl in the spleen in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR. The increase of Oasl expression in the spleen in 564Igi and NZB/W mice was reduced with anti-IFNAR treatment. n = 3 mice per group, *P = 0.03, ****P < 0.0001, two- way ANOVA with Tukey's test. FIG. 4E is a graph showing a significant increase in expression of Ifi44 in the hippocampus in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR. The increase of Ifi44 expression in the hippocampus in 564Igi and NZB/W mice was reduced with anti-IFNAR treatment. n = 3 mice per group, *P < 0.04, **P = 0.001, two-way ANOVA with Tukey's test. FIG. 4F a graph showing a significant increase in expression of Oasl in the hippocampus in 564Igi and NZB/W mice compared to wild-type mice, as measured by qPCR. The increase of Oasl expression in the hippocampus in 564Igi and NZB/W mice was reduced with anti-IFNAR treatment. n = 3 mice per group, *P = 0.04, **P = 0.001, two-way ANOVA with Tukey's test. FIG. 4G is a graph showing expression of Ifiia in the spleen in 564Igi and NZB/NZW mice ± anti-IFNAR treatment, as measured by qPCR. n = 3 mice per group, **P < 0.01, two-way ANOVA with Tukey's test. FIG. 4H is a graph showing autoreactive B cell frequencies (percentage of B220+ cells) showed significant decreases after anti-IFNAR treatment, as analyzed by flow cytometry, n = 4 mice per group, **P < 0.01, two-way ANOVA with Tukey's test. FIG. 41 is a graph showing expression of Ifiia in the hippocampus in 564Igi and NZB/NZW mice ± anti-IFNAR treatment, as measured by qPCR. n = 3 mice per group, P > 0.05, two-way ANOVA with Tukey's test. FIG. 4J is a representative image from a Mxl-CreTdtomato reporter mouse immunostained against the neuronal marker NeuN (dark gray), showing clusters of neurons and that are positive for Mxl (pseudocoloured light gray). Scale bar, 50 μιτι. In FIGS. 4A- 4F, data are mean ± s.e.m.
FIGS. 5A-5J show that IFNAR signalling regulated microglia activation state. FIG.
5 A is a graph depicting Mxl mRNA expression in spleen. FIG. 5B is a graph depicting Mxl mRNA expression in hippocampus. FIG. 5C are images depicting microglial activation state analysis. Arrows indicate reactive microglia. FIG. 5D is a graph of percent reactive microglia from FIG. 5C. FIG. 5E are images depicting activation state analysis in 12-week-old 564Igi Mxl-CreTdtomato mice. Arrows indicate Mxl+ microglia. FIG. 5F is a graph of percent reactive microglia from FIG. 5E. FIG. 5G is a graph depicting percentages of idiotype- positive (Id+; autoreactive) B cells in bone marrow (BM) chimeras. P = 0.5 (not significant). FIG. 5H is a graph depicting expression of Mxl in microglia from bone marrow chimeras, as measured by qPCR. FIG. 51 is a graph depicting activation state analysis in 564Igi bone marrow chimeras. FIG. 5 J are images showing RNAscope in situ hybridization on control and SLE cases for YY and AIF1 (marking microglia). Circles indicate microglia;
arrowheads indicate MX1+ signal. Data are mean ± s.e.m. In FIGS. 5A-5I, n = 3 mice per group. *P < 0.05, **P < 0.01. In FIG. 5J, n = 3 cases per condition. *P < 0.05, **P < 0.01. In FIGS. 5A-5F and 5H, two-way ANOVA with Tukey's test. In FIG. 5G, 51, and 5 J, unpaired t-test.
FIGS. 6A-6D show a direct role of IFNAR signalling in the brain in bone marrow chimera mice. FIG. 6A is a schematic showing that bone marrow extracted from wild-type (CD45.1) or 564Igi mice was administered to wild-type or IfiiarF1' mice after lethal irradiation. Head shielding was added to protect the CNS during lethal irradiation. Mice were analyzed six weeks after bone marrow transplant. FIG. 6B is a plot (left) and a graph (right) showing a similar percentage of chimerism was achieved for both IfiiarF1' and wild- type mice. n = 4 mice per group, P = 0.9670 (not significant), unpaired t-test. FIG. 6C is a graph showing that expression of Ifiia in purified microglia revealed similar expression levels in wild-type and IfiiarF1' recipients of wild-type or 564Igi bone marrow, as measured by qPCR. n = 3 mice per group, P > 0.05, two-way ANOVA with Sidak's test. FIG. 6D is a graph showing that expression of Ifiib in purified microglia revealed significant upregulation in wild-type recipients of 564Igi bone marrow relative to IfiiarF1' recipients, as measured by qPCR. n = 3 mice per group, ***P = 0.0003, two-way ANOVA with Sidak's test. In FIGS. 6B-6D, data are mean ± s.e.m.
FIGS. 7A-7D depict increased MXA signal in hippocampal brain sections from patients with SLE. FIG. 7A is a table showing clinical data for the patient brain sections analyzed by immunohistochemistry for MXA. Highlighted cases showed higher MXA levels than controls. FIG. 7B depicts representative images of hippocampal brain sections for the cases that showed increased MXA signal. Scale bars, 100 μ m. FIG. 7C depicts antibody specificity validation: staining with an isotype control antibody (top) or only the secondary antibody (bottom) showed no signal. FIG. 7D depicts RNAscope in situ hybridization for the neuronal marker, EN02. Quantification showed no significant differences between no significant differences between control and SLE cases. Data are mean ± s.e.m. n = 3 cases per group, P > 0.05, unpaired t-test.
FIGS. 8A-8D depict sorting of microglia for RNA-seq analysis. FIG. 8 A shows that macrophages were sorted on the basis of CD45Mgl1 expression. FIG. 8B shows that similar macrophage frequencies were observed in wild-type and 564Igi brain suspensions. n = 4 mice per group, P > 0.05 (not significant), unpaired t-test. FIG. 8C are plots showing post-sort flow cytometry to validate microglia purity revealed surface expression of two additional microglial markers, CD39 and CX3CR1, in > 99% of sorted cells. FIG. 8D is a graph showing elevated expression of 20 out of 25 microglia-specific genes by RNA-seq analysis in sorted microglia relative to sorted meningeal macrophages. In FIGS. 8A-8D, data are mean ± s.e.m.
FIGS. 9A-9E depict RNA-seq and Gene Ontology analysis. FIG 9A depicts a multidimensional scaling analysis showing clustering of samples by treatment group. Dim, dimension; FC, fold change. FIG. 9B is a smear plot showing significant changes in gene expression (gray) in 564Igi versus wild-type mice. CPM, counts per million reads. FIG. 9C depicts Gene Ontology analysis using GOseq identified enriched pathways in microglia derived from 564Igi relative to wild-type mice, q < 0.05 for all pathways, size of the square is relative to q value. FIG. 9D depicts distribution of genes classified as IFNAR-dependent or - independent. FIG. 9E depicts microglia sensome genes that are significantly upregulated in 564Igi versus wild-type mice. Wild type versus 564Igi: all genes, q < 0.05; * 564Igi versus 564Igi + anti-IFNAR: q < 0.05, GLM likelihood ratio test. Data are mean ± s.e.m. FIGS. 10A-10K show that genetic and functional changes in microglia were IFNAR- dependent. FIG. 1 OA is a graph showing that interferon- response genes were significantly upregulated in 564Igi compared to wild-type microglia (Benjamini-Hochberg false discovery rate of q < 0.05 for all genes, generalized linear model (GLM) likelihood ratio test). FIG. 1 OB is a GOseq Gene Ontology analysis of the IFNAR-dependent and IFNAR-independent gene sets. FIG. IOC are plots depicting flow cytometry gating of microglia (left) and tau- GFP+ microglia (right). FIG. 10D is a graph depicting quantification of the percentage tau- GFP+ microglia out of total microglia. C, cerebellum; F, frontal cortex; H, hippocampus. ***P < 0.0009, two-way ANOVA with Sidak's test. FIG. 10E is a graph depicting flow cytometry engulfment analysis of cells from anti-IFNAR-treated 564Igi mice or isotype- treated controls. *P = 0.04, unpaired t-test. FIG. 10F depicts quantification of confocal images of tau-GFP internalization in the frontal cortex. The percentage engulfment (E) is calculated from the volume (J7) as follows: E = Ftau-GFP / ^microglia- *P = 0.03, ratio paired t- test. FIG. 10G is a graph depicting quantification of confocal images for tau-GFP
internalization in the frontal cortex of 564Igi tau-GFP Mxl-CreTdtomato mice. **P =
0.0002, unpaired t-test. FIG. 10H is a graph depicting flow cytometry engulfment analysis comparing Mxl+ and Mxl~ microglia in slices from the frontal cortex of 564Igi tau-GFP Mxl-CreTdtomato and wild-type tau- GFP Mxl-CreTdtomato. **P = 0.0011, two-way ANOVA with Sidak's test. FIG. 101 depicts images showing that biotinylated IFNa could be detected within the brain (gray). Active IFNAR signalling was also observed (light gray). FIG. lOJ is a graph depicting flow cytometry analysis of tau-GFP mice injected with IFNa. *P < 0.05, **P < 0.01, unpaired t-test. FIG. 1 OK is a graph depicting flow cytometry analysis of tau- GFP mice injected with IFNp. * P < 0.05, **P < 0.01, unpaired t-test. In FIGS. 10D-10K, data are mean ± s.e.m. n = 3 mice per group.
FIGS. 11 A-l 1G show that interferon can enter via an intact blood-brain barrier and is sufficient to trigger engulfment of neuronal material by microglia. FIG. 11 A are a series of plots depicting gating for tau-GFP+ microglia for engulfment analysis based on tau-GFP" control mice (gate set to <0.5% in tau-GFP- mice). FIG. 1 IB is a graph depicting that tau- GFP mean fluorescence intensity (MFI) for microglia was significantly higher in the frontal cortex of 564Igi relative to wild-type mice. n = 3 mice per group, ****P < 0.0001, two-way ANOVA with Sidak's test. FIG. 11C are images showing that revealed no leakage of 10 kDa FITC-dextran tracer (intravenous injection) from blood vessels (CD31+) in 564Igi mice up to 24 weeks of age. FIG. 1 ID are images showing no increase in IgG deposition within the CNS in 564Igi mice compared to C57BL/6 controls, when staining for IgG. In contrast, MRL-lpr did show a notable increase. FIG. 1 IE is a graph showing that similar
colocalization of FITC-dextran with CD31 (blood vessels) was observed in 564Igi mice and controls. Without being bound by theory, this indicates that similar amounts of dye were contained within vessels in both groups. n = 3 mice per group, P > 0.05, unpaired t-test. FIG. 1 IF is a graph showing that quantification of MFI for IgG revealed no significant changes between 564Igi and C57BL/6 controls. MRL-lpr mice showed a significant increase compared to MRL-mpj controls. n = 3 mice per group, ****P < 0.0001, one-way ANOVA with Tukey's test. FIG. 11G is a plot showing that flow cytometry analysis of tau-GFP mice injected with IFNa demonstrated significant increases in tau-GFP+ frequencies compared to vehicle. n = 3 mice per group, *P < 0.05, **P < 0.01, unpaired t-test. FIG. 11H is a plot showing that flow cytometry analysis of tau-GFP mice injected with IFNP demonstrated significant increases in tau-GFP+ frequencies compared to vehicle. n = 3 mice per group, *P < 0.05, **P < 0.01, unpaired t-test. In FIGS. 1 lE-11H, data are mean ± s.e.m.
FIGS. 12A-12D show validation of microglia engulfment data. FIG. 12A are images showing staining of Ibal . Left, staining of Ibal revealed inclusions within microglia cytoplasm (white arrows and inset) and lysosomes (white asterisk). Right, some inclusions contained structures consistent with synaptic vesicles (white arrows, right inset). FIG. 12B are plots comparing staining with mouse IgGl and synaptic material (SV2). Permeabilized microglia were stained in parallel with similar concentrations of Alexa-633 labelled mouse IgGl . Fluorescence was several logs lower than observed with SV2 staining. FIG. 12C is a plot showing staining of SV2 in nonpermeabilized microglia. To verify internalization of SV2, staining was also done on nonpermeabilized microglia. Very few (0.78%) microglia showed signal over the isotype control. No microglia could be detected in the 8ν2Μ^ gate used for analysis in FIGS. 13A-13E. FIG. 12D are images showing internalization of SV2. To further validate internalization of SV2, permeabilized microglia were slide-mounted by cytospin and imaged at 63 χ by confocal. SV2 signal appeared colocalized with CD68 in many, but not all, microglia.
FIGS. 13A-13E depict IFNAR-dependent synapse loss in 564Igi mice. FIG. 13 A is a TEM image of microglia (MG; light gray in the inset) surrounding synaptic elements (white arrow; dark gray in the inset). Presynaptic terminals are indicated by asterisks. FIG. 13B depicts flow cytometry analysis of synaptic material (SV2) uptake by microglia in 564Igi or controls. FIG. 13C is a graph of the flow cytometry analysis shown in FIG. 13B. *P < 0.05, two-way ANOVA with Sidak's test. *P < 0.05, two-way ANOVA with Sidak's test. FIG. 13D is a graph depicting analysis of confocal images of the synapse density in the frontal cortex. *P < 0.05, t-test. FIG. 13E depicts TEM images and TEM quantification of synapse (dark gray, indicated by asterisks) density in 564Igi frontal cortex and controls with anti- IFNAR treatment. *P = 0.047, **P = 0.008, two-way ANOVA with with Tukey's test. In FIGS. 13C-13E, data are mean ± s.e.m.
FIGS. 14A-14F shows that synapse loss, but not neuron or axon loss, was observed in the frontal cortex of 564Igi mice. FIG. 14A depicts representative images showing staining for presynaptic (synaptophysin, dark gray) and postsynaptic (homer, gray) markers revealed structural synapses (colocalized markers, light gray) in wild-type (left) and 564Igi (right) mice . Scale bar, 25 μπι. FIG. 14B is a graph showing significant decreases in synaptophysin puncta in 564Igi (right) mice compared to wild-type mice (left). n = 3 mice per group, *P < 0.05, **P < 0.01, unpaired t-test. FIG. 14C is a graph showing significant decreases in homer puncta in 564Igi (right) mice compared to wild-type mice (left). n = 3 mice per group, *P < 0.05, **P < 0.01, unpaired t-test. FIG. 14D is a graph showing that reduced synapse density was observed in 8-week-old MRL-lpr mice by immunohistochemistry. n = 3 mice per group, *P < 0.05, unpaired t-test. FIG. 14E depicts images of NeuN staining and a graph showing similar neuronal density in the frontal cortex of 564Igi and wild-type mice by staining for the neuronal marker NeuN. n = 3 mice per group, P = 0.85 (not significant), unpaired t-test. FIG. 14F depicts images of neurofilament-H staining and a graph showing a slight but not significant decrease in 564Igi axon density by staining for the axonal marker neurofilament- H. n = 3 mice per group, P > 0.05 (not significant), unpaired t-test. In FIGS. 14B-14F, data are mean ± s.e.m. DETAILED DESCRIPTION OF THE INVENTION
The invention features compositions and methods that are useful for identifying and treating patients with CNS lupus and related diseases characterized by microglia mediated synapse loss.
The invention is based, at least in part, on the discoveries of a direct role for interferon alpha receptor (IFNAR) signaling in regulating microglia activation state in a murine model of lupus; and the finding that IFNAR blocking antibodies could reduce physical and behavioral changes in these mice relative to wild-type control mice. Behavioral phenotypes and synapse loss in lupus-prone mice were prevented by blocking type I interferon (JFK) signalling. Furthermore, type I IFN stimulated microglia to become reactive and engulf neuronal and synaptic material in lupus-prone mice. Without being bound by theory, these findings and the observation of increased type I IFN signalling in post-mortem hippocampal brain sections from patients with SLE may instruct the evaluation of ongoing clinical trials of anifrolumab, a type I IFN-receptor antagonist. Furthermore, identification of IFN-driven microglia-dependent synapse loss, along with microglia transcriptome data, connects CNS lupus with other CNS diseases. Without being bound by theory, this provides an explanation for the neurological symptoms observed in some patients with SLE.
As reported in more detail below, a murine model of mild lupus developed behavioral phenotypes relevant to CNS lupus symptoms. Interestingly, these behavioral changes correlated with a significant reduction in frontal cortex synapse density in 564Igi mice relative to wild-type (WT) littermates. The mice displayed elevated type I interferon signaling in the periphery. It was found that reactive microglia responded to inflammatory cytokines in the brain, including type I interferon. Significant increases in reactive microglia were observed in two murine models of lupus, 564Igi and the NZB/NZW. Peripheral type I interferon enters the brain and stimulates microglial engulfment of synaptic material resulting in synapse loss. Type I IFN IFNAR signaling was found to be necessary and sufficient to stimulate microglia engulfment of neuronal material. Significantly, blocking IFNAR signaling was effective, not only in preventing structural connectivity defects in the brain, but also in blocking changes in behavior.
Accordingly, the invention provides therapeutic methods for treating CNS lupus and related diseases characterized by microglia mediated synapse loss in a subject, as well as diagnostic methods for characterizing CNS lupus and related diseases characterized by microglia mediated synapse loss in a subject, and selecting subjects for treatment or of monitoring the treatment of such subjects.
Antibodies
As reported herein, antibodies that specifically bind to and block the activation of the interferon alpha/beta receptor (IFNAR) are useful for the treatment of CNS lupus and related diseases characterized by microglia mediated synapse loss or to inhibit the progression of CNS lupus and other diseases characterized by an increase in reactive microglia and/or synapse loss. Such antibodies may be directed against the INFNAR or against IFN-alpha. Methods of preparing antibodies are well known to those of ordinary skill in the science of immunology. As used herein, the term "antibody" means not only intact antibody molecules, but also fragments of antibody molecules that retain immunogen-binding ability. Such fragments are also well known in the art and are regularly employed both in vitro and in vivo. Accordingly, as used herein, the term "antibody" means not only intact
immunoglobulin molecules but also the well-known active fragments F(ab')2, and Fab.
F(ab')2, and Fab fragments that lack the Fc fragment of an intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding than an intact antibody (Wahl et al., J. Nucl. Med. 24:316-325 (1983). The antibodies of the invention comprise whole native antibodies, bispecific antibodies; chimeric antibodies; Fab, Fab', single chain V region fragments (scFv), fusion polypeptides, and unconventional antibodies.
Unconventional antibodies include, but are not limited to, nanobodies, linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062,1995), single domain antibodies, single chain antibodies, and antibodies having multiple valencies {e.g., diabodies, tribodies, tetrabodies, and pentabodies). Nanobodies are the smallest fragments of naturally occurring heavy-chain antibodies that have evolved to be fully functional in the absence of a light chain. Nanobodies have the affinity and specificity of conventional antibodies although they are only half of the size of a single chain Fv fragment. The consequence of this unique structure, combined with their extreme stability and a high degree of homology with human antibody frameworks, is that nanobodies can bind therapeutic targets not accessible to conventional antibodies. Recombinant antibody fragments with multiple valencies provide high binding avidity and unique targeting specificity to cancer cells. These multimeric scFvs {e.g., diabodies, tetrabodies) offer an improvement over the parent antibody since small molecules of ~60-100kDa in size provide faster blood clearance and rapid tissue uptake See Power et al., (Generation of recombinant multimeric antibody fragments for tumor diagnosis and therapy. Methods Mol Biol, 207, 335-50, 2003); and Wu et al. (Anti-carcinoembryonic antigen (CEA) diabody for rapid tumor targeting and imaging. Tumor Targeting, 4, 47-58, 1999).
Various techniques for making and using unconventional antibodies have been described. Bispecific antibodies produced using leucine zippers are described by Kostelny et al. (J. Immunol. 148(5): 1547-1553, 1992). Diabody technology is described by Hollinger et al. (Proc. Natl. Acad. Sci. USA 90:6444-6448, 1993). Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) diners is described by Gruber et al. (J. Immunol. 152:5368, 1994). Trispecific antibodies are described by Tutt et al. (J. Immunol. 147:60, 1991). Single chain Fv polypeptide antibodies include a covalently linked VH: :VL heterodimer which can be expressed from a nucleic acid including VH- and VL-encoding sequences either joined directly or joined by a peptide-encoding linker as described by Huston, et al. (Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Patent Nos. 5,091,513, 5, 132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754.
In various embodiments, an antibody is monoclonal. Alternatively, the antibody is a polyclonal antibody. The preparation and use of polyclonal antibodies are also known the skilled artisan. The 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.
In general, 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. Similarly, 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.
Antibodies can be made by any of the methods known in the art utilizing soluble polypeptides, or immunogenic fragments thereof, as an immunogen. One method of obtaining antibodies is to immunize suitable host animals with an immunogen and to follow standard procedures for polyclonal or monoclonal antibody production. The immunogen will facilitate presentation of the immunogen on the cell surface. Immunization of a suitable host can be carried out in a number of ways. Nucleic acid sequences encoding polypeptides or immunogenic fragments thereof, can be provided to the host in a delivery vehicle that is taken up by immune cells of the host. The cells will in turn express the polypeptide thereby generating an immunogenic response in the host. Alternatively, nucleic acid sequences encoding human polypeptides or immunogenic fragments thereof, can be expressed in cells in vitro, followed by isolation of the polypeptide and administration of the polypeptide to a suitable host in which antibodies are raised.
Alternatively, antibodies may, if desired, be derived from an antibody phage display library. A bacteriophage is capable of infecting and reproducing within bacteria, which can be engineered, when combined with human antibody genes, to display human antibody proteins. Phage display is the process by which the phage is made to 'display' the human antibody proteins on its surface. Genes from the human antibody gene libraries are inserted into a population of phage. Each phage carries the genes for a different antibody and thus displays a different antibody on its surface.
Antibodies made by any method known in the art can then be purified from the host. Antibody purification methods may include salt precipitation (for example, with ammonium sulfate), ion exchange chromatography (for example, on a cationic or anionic exchange column preferably run at neutral pH and eluted with step gradients of increasing ionic strength), gel filtration chromatography (including gel filtration HPLC), and chromatography on affinity resins such as protein A, protein G, hydroxyapatite, and anti-immunoglobulin.
Antibodies can be conveniently produced from hybridoma cells engineered to express the antibody. Methods of making hybridomas are well known in the art. The hybridoma cells can be cultured in a suitable medium, and spent medium can be used as an antibody source. Polynucleotides encoding the antibody of interest can in turn be obtained from the hybridoma that produces the antibody, and then the antibody may be produced synthetically or recombinantly from these DNA sequences. For the production of large amounts of antibody, it is generally more convenient to obtain an ascites fluid. The method of raising ascites generally comprises injecting hybridoma cells into an immunologically naive histocompatible or immunotolerant mammal, especially a mouse. The mammal may be primed for ascites production by prior administration of a suitable composition {e.g., Pristane).
Monoclonal antibodies (Mabs) produced by methods of the invention can be
"humanized" by methods known in the art. "Humanized" antibodies are antibodies in which at least part of the sequence has been altered from its initial form to render it more like human immunoglobulins. Techniques to humanize antibodies are particularly useful when non- human animal (e.g., murine) antibodies are generated. Examples of methods for humanizing a murine antibody are provided in U. S. patents 4,816,567, 5,530, 101, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.
The present invention provides methods of treating disease and/or disorders or symptoms thereof which comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an anti-IFNAR antibody described herein to a subject (e.g., a mammal such as a human). Thus, one embodiment is a method of treating a subject suffering from or susceptible to Systemic lupus erythematosus (SLE) and central nervous system (CNS) lupus or a symptom thereof. The method includes the step of administering to the mammal a therapeutic amount of an amount of an agent herein sufficient to treat the disease or disorder or symptom thereof, under conditions such that the disease or disorder is treated.
The methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of a compound described herein, or a composition described herein to produce such effect. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method). As used herein, the terms "treat," treating," "treatment," and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated. As used herein, the terms "prevent," "preventing," "prevention," "prophylactic treatment" and the like refer to reducing the probability of developing a disorder or condition in a subject, who does not have, but is at risk of or susceptible to developing a disorder or condition.
The therapeutic methods of the invention (which include prophylactic treatment) in general comprise administration of a therapeutically effective amount of the compounds herein, such as a compound of the formulae herein to a subject (e.g., animal, human) in need thereof, including a mammal, particularly a human. Such treatment will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Determination of those subjects "at risk" can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, Marker (as defined herein), family history, and the like). The compounds herein may be also used in the treatment of any other disorders in which microglial activation by interferon may be implicated.
In one embodiment, the invention provides a method of monitoring treatment progress. The method includes the step of determining a level of diagnostic marker, such as the level of peripheral interferon or activated microglia (Marker) or other diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to CNS lupus or related diseases characterized by microglia mediated synapse loss or symptoms thereof (e.g., neuropsychiatric symptoms), in which the subject has been administered a therapeutic amount of a compound herein sufficient to treat the CNS lupus and related diseases characterized by microglia mediated synapse loss, or symptoms thereof. The level of Marker determined in the method can be compared to known levels of Marker in either healthy normal controls or in other afflicted patients, such as patients suffering from lupus that do not have CNS lupus or a related disease characterized by microglia mediated synapse loss, to establish the subject's disease status. In preferred embodiments, a second level of Marker in the subject is determined at a time point later than the determination of the first level, and the two levels are compared to monitor the course of disease or the efficacy of the therapy. In certain preferred embodiments, a pre-treatment level of Marker in the subject is determined prior to beginning treatment according to this invention; this pre-treatment level of Marker can then be compared to the level of Marker in the subject after the treatment commences, to determine the efficacy of the treatment.
Characterizing CNS Lupus or Related Diseases in a Subject
In characterizing CNS lupus or a related disease characterized by microglia mediated synapse loss in a subject, type I interferon (e.g., interferon alpha) is measured in different types of biological fluid samples (e.g., cerebrospinal fluid (CSF), blood, plasma, serum), or by the detection of known interferon response genes (such as mxl, ifitl, ifit3, stat2, oasl, oas2, etc (see Fig. 10A) in peripheral blood mononuclear cells (PBMCs). In one
embodiment, type I interferon level is measured in a peripheral blood monocyte isolated from blood. The level of peripheral interferon in a biological fluid sample (e.g., cerebrospinal fluid (CSF), blood, plasma, serum) obtained from a subject that has CNS lupus or a related disease characterized by microglia mediated synapse loss and is in need of anti-IFNAR antibody treatment is higher than the level of peripheral interferon in a subject that does not have CNS lupus or a related disease characterized by microglia mediated synapse loss. In other embodiments, expression of a marker of the invention (e.g., peripheral IFN) is increased by at least about 2, 3, 4, 5 or 10-fold in a patient having CNS lupus or a related disease relative to the level in a reference sample (i.e., a patient that does not have CNS lupus or a related disease characterized by microglia mediated synapse loss). In another embodiment, PBMCs are assayed for an interferon signature (e.g., increases in mxl, ifit3, oas2, and stat2 or any other gene defined in Figure 9Έ). IFN polypeptide or polynucleotide fold change values are determined using any method known in the art, including but not limited to quantitative PCR, RT-PCR, Northern blotting, Western blotting, flow cytometry, immunocytochemistry, binding to magnetic and/or antibody-coated beads, in situ hybridization, fluorescence in situ hybridization (FISH), flow chamber adhesion assay, ELISA, microarray analysis,
colorimetric assays, mass spectrometry {e.g., laser desorption/ionization mass spectrometry), fluorescence {e.g. sandwich immunoassay), surface plasmon resonance, ellipsometry, and atomic force microscopy.
In other embodiments, CNS lupus (or another disease characterized by reactive microglia) is characterized in a subject using brain imaging studies. In one embodiment, functional magnetic resonance imaging (fMRI) is used to measure alterations in brain connectivity. In another embodiment, Pre-pulse Inhibition (PPI) is used to characterize the startle reflex in a subject. PPI has been used to characterize deficits in PPI of the startle reflex in schizophrenia and autism spectrum disorders. In another embodiment, sensory motor defects are characterized in a subject with CNS lupus or a related disease. In yet another embodiment, CNS lupus is characterized by measuring gray matter volume using conventional MRI. In yet another embodiment, a Positron Emission Topography (PET) studies are used to identify activated microglia or to detect changes in synaptic density in iving human brain. In one embodiment, an SV2A PET ligand is:
Figure imgf000036_0001
In yet another embodiment, CNS lupus or a related disease is characterized by detecting changes in activated microglia/exomes present in CSF. In yet another embodiment, CNS lupus or a related disease is characterized in a neurological exam, or by characterizing an anxiety phenotype, depression, cognitive impairment, or social interaction defects.
Pharmaceutical Compositions
Antibodies of the invention (e.g., antibodies that specifically bind an IFN alpha/beta receptor (IFNAR) or IFN alpha) can be administered in a pharmaceutically acceptable excipient, such as water, saline, aqueous dextrose, glycerol, or ethanol. In one embodiment, a pharmaceutical composition of the invention is administered to a subject identified as having CNS lupus or a related disease characterized by microglia mediated synapse loss. The characterization of CNS lupus or a related disease characterized by microglia mediated synapse loss in a subject involves, for example, identifying the presence of increased levels of peripheral interferon in a biological sample of the subject, such as CSF. The compositions can also contain other medicinal agents, pharmaceutical agents, adjuvants, carriers, and auxiliary substances such as wetting or emulsifying agents, and pH buffering agents.
Standard texts, such as Remington: The Science and Practice of Pharmacy, 17th edition, Mack Publishing Company, incorporated herein by reference, can be consulted to prepare suitable compositions and formulations for administration, without undue experimentation. Suitable dosages can also be based upon the text and documents cited herein. A
determination of the appropriate dosages is within the skill of one in the art given the parameters herein. A "therapeutically effective amount" is an amount sufficient to effect a beneficial or desired clinical result. A therapeutically effective amount can be administered in one or more doses. In terms of treatment, an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of CNS lupus or a related disease characterized by microglia mediated synapse loss. In another embodiment, an effective amount is an amount sufficient to reduce neuropsychiatric symptoms associated with CNS lupus or a related disease characterized by microglia mediated synapse loss. A
therapeutically effective amount can be provided in one or a series of administrations. The effective amount is generally determined by the physician on a case-by-case basis and is within the skill of one in the art.
As a rule, the dosage for in vivo therapeutics or diagnostics will vary. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the patient, the condition being treated, the severity of the condition and the form of the antibody being administered.
The dosage of the antibody compositions can vary from about 0.01 mg/m2 to about
500 mg/m2, preferably about 0.1 mg/m2 to about 200 mg/m2, most preferably about 0.1 mg/m2 to about 10 mg/m2. Alternatively, the dosages of the antibody compositions can vary from about 0.01 mg/kg per day to about 1000 mg/kg per day. It is expected that doses ranging from about 50 to about 2000 mg/kg will be suitable. In various embodiments, a dosage ranging from about 0.5 to about 100 mg/kg of body weight is useful; or any dosage range in which the low end of the range is any amount between 0.1 mg/kg/day and 90 mg/kg/day and the upper end of the range is any amount between 1 mg/kg/day and 100 mg/kg/day (e.g., 0.5 mg/kg/day and 5 mg/kg/day, 25 mg/kg/day and 75 mg/kg/day). In one embodiment, 12.5 mg/kg of antibody is administered every 4 days.
Administrations can be conducted infrequently, or on a regular weekly basis until a desired, measurable parameter is detected, such as diminution of disease symptoms.
Administration can then be diminished, such as to a biweekly or monthly basis, as appropriate. In one embodiment, administration is weekly.
Compositions of the present invention comprising anti-IFNAR antibodies are administered by a mode appropriate for the form of composition. Available routes of administration include subcutaneous, intramuscular, intraperitoneal, intradermal, oral, intranasal, intrapulmonary (i.e., by aerosol), intravenously, intramuscularly, subcutaneously, intracavity, intrathecally or transdermally. Compositions for oral, intranasal, or topical administration can be supplied in solid, semi-solid or liquid forms, including tablets, capsules, powders, liquids, and suspensions. Compositions for injection can be supplied as liquid solutions or suspensions, as emulsions, or as solid forms suitable for dissolution or suspension in liquid prior to injection. For administration via the respiratory tract, a preferred composition is one that provides a solid, powder, or liquid aerosol when used with an appropriate aerosolizer device. Although not required, compositions are preferably supplied in unit dosage form suitable for administration of a precise amount. Also contemplated by this invention are slow release or sustained release forms, whereby a relatively consistent level of the active compound are provided over an extended period.
Patient Monitoring
The treatment or disease state of a patient administered a composition of the invention that includes an interferon antibody can be monitored using any of the methods defined herein for characterizing a patient with CNS lupus or a related disease. In particular embodiments, a subject is monitored by assessing neurological symptoms, neuropsychiatric symptoms, cognitive function, grey matter changes, or the level of peripheral interferon or reactive microglia present in the patient. Compositions that produce a reduction in the severity of any one or more of the preceding symptoms are considered useful in the methods of the invention.
Neurological diagnostic tools for monitoring a patient having CNS lupus or a related disease include, for example, X-rays, Brain scans (magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET), and computed tomography (CT), Electroencephalograms (to capture the electrical pattern of brain activity), sensorimotor gating assessment using auditory prepulse inhibition assays, or spinal tap (to examine fluid in the spinal column). In other embodiments, CNS lupus or a related disease characterized by microglia mediated synapse loss may be monitored by characterizing an increase or decrease in one or more of the following: headaches, confusion, fatigue, depression, seizures, stroke, vision problems, mood swings, difficulty concentrating, memory loss, and difficulty expressing thoughts. In still other embodiments, an increase or decrease in numbness, burning, or tingling is monitored. Kits
The invention provides kits for the treatment of CNS lupus or a related disease characterized by microglia mediated synapse loss. In one embodiment, the kit includes a composition containing an anti-interferon alpha/beta receptor (IFNAR) antibody.
In some embodiments, the kit comprises a sterile container which contains a therapeutic or prophylactic cellular composition; such containers can be boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
If desired an agent of the invention is provided together with instructions for administering the agent to a subject having or at risk of developing a neurological disease or disorder of the central nervous system. The instructions will generally include information about the use of the composition for the treatment or prevention of the disease or disorder. In other embodiments, the instructions include at least one of the following: description of the therapeutic agent; dosage schedule and administration for treatment or prevention of a neurological disease or symptoms thereof; precautions; warnings; indications; counter- indications; overdosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
The practice of the present invention employs, unless otherwise indicated,
conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of an artisan of ordinary skill in the art. Such techniques are explained fully in the literature, such as, "Molecular Cloning: A Laboratory Manual", second edition (Sambrook, 1989); "Oligonucleotide Synthesis" (Gait, 1984); "Animal Cell Culture" (Freshney, 1987);
"Methods in Enzymology" "Handbook of Experimental Immunology" (Weir, 1996); "Gene Transfer Vectors for Mammalian Cells" (Miller and Calos, 1987); "Current Protocols in Molecular Biology" (Ausubel, 1987); "PCR: The Polymerase Chain Reaction", (Mullis, 1994); "Current Protocols in Immunology" (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the invention, and, as such, may be considered in making and practicing the invention. Particularly useful techniques for particular embodiments will be discussed in the sections that follow. The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the assay, screening, and therapeutic methods of the invention, and are not intended to limit the scope of what the inventors regard as their invention.
EXAMPLES
Example 1: Development of an animal model for use in CNS lupus study.
To investigate early mechanisms that promote CNS lupus, the 564Igi lupus-prone mouse strain was used. The 564Igi mouse strain is a B-cell-receptor insertion model with known autoantibody specificity, mild peripheral inflammation and interferon-a receptor 1 (IFNAR)-dependent autoimmunity (Berland et al. Immunity 25, 429-440, 2006; Das et al. Immunity 46, 106-119, 2017). Lupus-like disease progresses slowly in 564Igi mice compared to other mouse models of lupus, therefore CNS development is unaffected by disease complications such as lupus nephritis (onset at 12 months) (Berland et al. Immunity 25, 429-440, 2006). Despite mild lupus-like disease, in behavioral tests of 12-week-old wild-type and 564Igi mice, the 564Igi mice had anxiety-like phenotypes in the elevated plus maze and novelty-suppressed feeding assay (FIGS. 1 A and IB), cognitive defects indicated by performance in the novelty Y maze and water T maze (FIGS. 1C and ID), increased social aggression in the test-tube dominance test, abnormal social interaction in the three-chamber social interaction assay (FIGS. IE and IF) and enhanced prepulse inhibition (FIG. 1G). No depression-like phenotypes or motor and coordination defects were found in the 564Igi mice (FIG. 1H and II). Without being bound by theory, these findings indicate that 564Igi mice develop CNS disease and are suitable for investigating how systemic autoimmunity affects the brain.
Given that autoimmunity in 564Igi mice is IFNAR-dependent 9, 564Igi mice and wild-type littermates were treated with IFNARblocking antibody or isotype-control to determine whether the behavioral phenotypes were IFNAR-dependent. 564Igi mice treated with the anti-IFNAR antibody behaved similarly to wild-type mice. Without being bound by theory, this indicates the involvement of IFNAR signalling or peripheral autoimmunity in general (FIGS. 2A-2D). Notably, the 564Igi strain showed no inflammation or cellular infiltration in the brain (FIGS. 3 A-3C). Without being bound by theory, treatment with the anti-IFNAR antibody probably affects CNS-resident cells rather than infiltrates immune cells. Example 2: Type I IFN activates microglia in an animal model of lupus.
Microglia, resident macrophages of the brain, respond to local inflammation or CNS damage by becoming reactive and increasing phagocytic activity and inflammatory cytokine production (Lynch, Mol. Neurobiol. 40, 139-156, 2009). Reactive microglia have been detected in some lupus-prone mouse models (Crupi et al. Biol. Psychiatry 67, 558-566, 2010; Mondal et al. Brain Behav. Immun. 22, 949-959, 2008). However, whether these cells promote CNS disease in lupus or arise in response to CNS disease in lupus is unclear. To determine whether and when reactive microglia develop in 564Igi and NZB/NZW lupus- prone strains, both of which have IFNAR-dependent lupus pathology (Berland et al.
Immunity 25, 429-440, 2006; Das et al. Immunity 46, 106-119, 2017; Dubois et al. J. Am. Med. Assoc. 195, 285-289, 1966; Baccala et al. J. Immunol. 189, 5976-5984, 2012), microglial activation was assessed through cell morphology and CD68 levels during early (6 weeks) and active disease (16 weeks) (FIG. 3D). At 6 weeks, NZB/NZW mice had more reactive microglia in the cortex and hippocampus than wild-type or 564Igi mice. At 16 weeks, both lupus-prone strains showed an increase in the number of reactive microglia
(FIGS. 2E and 2F), despite similar microglial density across strains (FIG. 3E). The MRL-lpr strain, which has behavioral defects and develops severe lupus pathology by 4-5 months (Sakic et al. Brain Behav. Immun. 6, 265-285, 1992), had a similar phenotype with an earlier onset than the 564Igi strain (FIG. 3F).
Microglia are sensitive to type I IFN and become reactive in response to constitutive
IFNAR activity (Goldmann et al. EMBO J. 34, 1612-1629, 2015). Elevated type I IFN levels due to mutations in TREX1 or USP18 can result in the severe neurodevelopmental disorders of Aicardi-Goutieres syndrome or pseudo-TORCH syndrome (Crow et al. Nat. Genet. 38, 917-920, 2006; Meuwissen et al. J. Exp. Med. 213, 1163-1174, 2016) and have been implicated in cognitive decline in ageing and Alzheimer's disease (Taylor et al. Neurobiol. Aging 35, 1012-1023, 2014; Baruch et al. Science 346, 89-93, 2014). Elevated type I IFN in the periphery is a hallmark of SLE21 and it is one of several cytokines detected in the serum and cerebrospinal fluid (Trysberg et al. Lupus 9, 498-503, 2000; Santer et al. J. Immunol. 182, 1192-1201, 2009) of patients with SLE. Without being bound by theory, increased type I IFN could therefore affect microglia. However, whether IFNAR signalling is increased in the lupus brain and is linked to CNS lupus symptoms remains unknown. Quantitative PCR (qPCR) analysis of 564Igi and NZB/NZW splenic tissue revealed upregulation of Ifiia (but not Ifiib (also known as Ifiibl)) and Mxl, an IFN-stimulated gene, concurrent with changes in microglial activation state (FIGS. 2G, 2H, and 4A). In the brain, both strains showed upregulation of x7, but not Ifha, suggesting that systemic type I IFN was activating IFNAR signalling in the brain (FIGS. 21, 2 J, and 4B).
To determine the role of type I IFN in promoting reactive microglia in lupus, 564Igi, NZB/NZW and wild-type mice were treated with the anti-IFNAR antibody (Das et al.
Immunity 46, 106-119, 2017; Baccala et al. J. Immunol. 189, 5976-5984, 2012). Treatment significantly reduced IFN-stimulated gene (Mxl, Ifi44 and Oaslg) expression levels in the hippocampus and significantly reduced splenic Mxl and Ifha expression and autoreactive B cell frequencies in the blood (FIGS. 5A, 5B, and 4C-4I). Notably, anti-IFNAR treatment reduced reactive microglia percentages (FIG. 5C and 5D). To identify the precise cells affected by type I IFN in the brain, 564Igi mice were crossed with Mxl-CreTdtomato reporter mice in which IFNAR signaling (Mxl expression) stimulates Tdtomato expression. In this strain, microglia were the most prevalent Mxl+ cell type (10-30% of microglia were Mxl+), with small clusters of neurons and other glia appearing in some regions (FIG. 4J). More Mxl+ microglia were reactive than Mxl" microglia, consistent with IFNAR signalling promoting reactive microglia in lupus (FIGS. 5E and 5F).
Example 3: Identification of IFNAR signaling as a therapeutic target in CNS lupus.
Because IFNAR signalling is important for the regulation of peripheral autoimmunity (Das et al. Immunity 46, 106-119, 2017; Baccala et al. J. Immunol 189, 5976-5984, 2012), bone marrow chimeras were used to separate direct effects of type I IFN on the brain from indirect effects associated with peripheral inflammation. Head-shielded wild-type and IfiiarF1' mice were lethally irradiated and reconstituted with wild-type- or 564Igi-derived bone marrow. As expected, wild-type and IfiiarF1' recipients showed comparable chimerism, percentages of idiotype-positive B cells (FIGS. 5G, 6A, and 6B) and peripheral autoimmunity (Das et al. Immunity 46, 106-119, 2017). By contrast, microglia purified from wild-type recipients with 564Igi-derived bone marrow showed upregulation of Mxl and Ifiib, whereas IfiiarF1' recipients did not (FIGS. 5H, 6C, and 6D). Moreover, IfiiarF1' recipients had fewer reactive microglia than wild-type recipients that received 564Igi-derived bone marrow (FIG. 51). Peripheral immune cells are not likely to contribute to this phenotype, as they are bone-marrow derived and are IFNAR- sufficient in both chimeras. Thus, despite similar peripheral autoimmunity, IfiiarF1' recipients of 564Igi-derived bone marrow were protected. Without being bound by theory, this supports a direct role for IFNAR in regulating microglial activation in lupus-prone mice.
Elevated IFNAR signalling was also found in brains from patients with lupus. MXA (encoded by ¥7) immunohistochemistry on hippocampal brain sections revealed immunoreactivity in four out of six patients with SLE in grey and white matter and negligible signal in four patients without SLE, with isotype- and secondary-only controls showing no signal (FIGS. 7A-7C). Furthermore, more MX1+ microglia were detected in brains from patient with SLE relative to controls by RNAscope with probes specific for MX1 and AIF1 (a microglia marker) (FIG. 5 J). Probes for the neuron-specific gene, EN02, were analyzed in parallel to verify comparable RNA integrity (FIG. 7D). These data demonstrate active IFNAR signalling in the brains and specifically in the microglia of patients with SLE.
Without being bound by theory, this pathway has the potential to serve as a therapeutic target for CNS lupus. Example 4: IFNAR signaling stimulates genes associated with phagocytosis, lysosome organization, and endosomal trafficking.
To investigate microglia gene expression changes in lupus-prone strains, RNA- sequencing (RNA-seq) was performed on microglia and perivascular/meningeal macrophages sorted from the cortex and hippocampus of 564Igi and wild-type mice following treatment with anti-IFNAR or isotype-control antibodies. Macrophage frequencies (identified as ΟΕ>45Μ?¾ϋ1 ^+ cells) were similar in both strains. Without being bound by theory, this suggests no significant infiltration of blood-derived myeloid cells in 564Igi mice (FIGS. 8A and 8B). Microglia purity was verified after sorting using two additional cell surface microglia markers (CX3CR1 and CD39) and expression of 25 established microgliaspecific genes (Hickman et al. Nat. Neurosci. 16, 1896-1905, 2013) (FIGS. 8C and 8D).
Multidimensional scaling analysis revealed clustering by genotype and treatment group (FIG. 9A). Differences in expression (q < 0.05) were found for 1,946 genes between 564Igi and wild-type microglia using EdgeR, 20% of which were IFNAR-dependent (FIGS. 9B and 9D); 21 known IFN-stimulated genes, including Mxl, Ifit3, Oas2 and Stat2, were upregulated, forming a microglial IFN signature comparable to that of peripheral immune cells from patients with SLE (Kirou et al. Arthritis Rheum. 50, 3958-3967, 2004; Baechler et al. Proc. Natl Acad. Sci. £7X4100, 2610-2615, 2003). Gene Ontology analysis using GOseq identified many pathways, including some associated with reactive microglia: purinergic signalling, peroxisome function and phagocytosis (FIG. 9C). Pathways associated with cellular response to stress, autophagy and peroxisome maturation contained mostly IFNAR-independent genes. IFNARdependent genes were associated with cellular metabolism, purinergic signalling, production of type I interferon, phagocytosis, lysosome organization, endosomal trafficking and the microglia sensome, which has receptors for endogenous ligands and microbes (Hickman et al. Nat. Neurosci. 16, 1896-1905, 2013) (FIG. 10B). Notably, 15 sensome genes were upregulated in 564Igi mice (q < 0.05), and six of these genes were downregulated by anti-IFNAR treatment (FIG. 9E). Overall, these data implicate type I IFN signalling as a major regulator of microglia gene expression in lupus promoting sensitivity and phagocytic activity in 564Igi microglia.
Example 5: IFNAR signaling is necessary and sufficient to stimulate microglia engulfment of neuronal material
Microglia phagocytose synapses and neuronal material in normal brain development during synaptic pruning (Schafer et al. Neuron 74, 691-705, 2012) and in disease (Hong et al. Science 352, 712-716, 2016). It was hypothesized whether IFNa initiated a similar process in lupus. To visualize phagocytosis of neuronal material, the 564Igi strain was crossed to the tau-GFP strain in which neurons express a GFP-fusion protein throughout the cell. Therefore, microglia that engulf neuronal material are GFP+. Flow cytometry identified twofold more tau-GFP+ microglia and higher tau-GFP mean fluorescence intensity in the frontal cortex of 564Igi compared to wild-type tau-GFP mice (FIGS. IOC, 10D, 11 A, and 1 IB). Both strains showed a comparable signal in the cerebellum and hippocampus. IFNAR signalling was involved in the increased engulfment, as anti-IFNAR treatment reduced tau-GFP uptake (FIG. 10E). Confocal imaging confirmed more tau-GFP within frontal cortex microglia in 564Igi versus control mice (FIG. 10F).
To examine whether active IFNAR signalling correlated with increased engulfment, 564Igi tau-GFP mice were crossed with the Mxl-CreTdtomato reporter. Indeed, Mxl + microglia internalized more tau-GFP, and more Mxl+ microglia were tau-GFP+ by flow cytometry compared with Mxl" microglia (FIGS. 10G and 10H). To test whether increased type I IFN levels in the blood stimulates microglial engulfment, wild-type tau-GFP and wild- type Mxl-CreTdtomato mice were injected by intravenous injection with biotinylated IFNa or IFNp (50 μg ml"1). IFN and Mxl signal were detected in the brain within three hours, due to some permeability of the blood-brain barrier for type I IFN28 (FIG. 101), despite intact blood-brain-barrier integrity in 564Igi mice up to 24 weeks (FIGS. 1 lC-1 IF). Notably, tau- GFP+ microglia increased 24 hr after injection of IFNa /IFNp (FIGS. 10J, 10K, 11G, and 11H). Without being bound by theory, these data show that IFNAR signaling is necessary and sufficient to stimulate microglial engulfment of neuronal material.
Transmission electron microscopy (TEM) was used to identify the internalized neuronal structures. Microglia were identified on the basis of their characteristic nuclear morphology, a single-profile endoplasmic reticulum and an electron-dark shading of the cytoplasm with confirmation by immuno-electron microscopy (FIG. 12 A). Microglial processes often contacted neuronal structures and, in several cases, microglial cytoplasm surrounded neuronal structures, consistent with internalization. Synaptic structures specifically (most commonly membrane-bound compartments containing synaptic vesicles) were visible within 564Igi microglia and rarely observed in wild-type controls (FIG. 13 A). To confirm internalization, permeabilized 564Igi and control microglia were stained for a synaptic vesicle protein (SV2) and analyzed by flow cytometry. Significantly more SY2Ugh microglia were detected in the frontal cortex and hippocampus (but not cerebellum) in 564Igi mice compared to controls (FIGS. 13B and 13C). Isotype-control antibodies and non- permeabilized microglia showed no signal. Furthermore, confocal imaging of sorted microglia verified SV2 colocalization with CD68, a marker of lysosomes (FIGS. 12B-12D). Without being bound by theory, these data indicate that microglia engulf synaptic material in the 564Igi model.
Example 6: Anti-IFNAR antibody treatment prevents neuronal structural connectivity defects and blocks changes in behavior.
To determine whether increased engulfment was correlated with synapse loss, synapse density was measured using high-resolution confocal imaging. Despite similar neuronal and axonal density, 564Igi mice and MRL/lpr mice had reduced synapse density in the frontal cortex relative to wild-type mice (FIGS. 13D and 14A-14F). Frontal cortex synapse loss was verified by TEM, and found to be significantly reduced in 564Igi mice treated with anti -IFNAR antibody (FIG. 13E).
Without being bound by theory, these data support a model in which peripheral type I
IFN enters the brain and stimulates microglial engulfment of synaptic material, resulting in synapse loss. Linking type I IFN and CNS lupus helps to account for the high incidence and high variability of CNS lupus symptoms, as 50-80% of patients with SLE display a type I IFN signature (Kirou et al. Arthritis Rheum. 50, 3958-3967, 2004; Baechler et al. Proc. Natl Acad. Sci. USA IOO, 2610-2615, 2003) and many microglia genes and pathways are IFNAR- dependent. Why and how IFNAR-stimulated microglia target synapses remain unclear. Neuronal damage occurs in lupus-prone mice and patients with SLE in response to anti- double-stranded DNA antibodies cross-reacting with NMDA receptors at the synapse (DeGiorgio et al. Nat. Med. 7, 1189-1193, 2001). Wihtout being bound by theory, this antibody binding could initiate microglial engulfment, although substantial antibody deposition in the CNS was not detected in the 564Igi mice. Another mechanism promoting engulfment may be activation of the classical complement cascade, which is important for early synapse loss in Alzheimer's disease models (Hong et al. Science 352, 712-716, 2016; Stevens et al. Cell 131, 1164-1178, 2007). Althought further studies are needed to identify the pathways of synapse or neuron damage interacting with type I IFN, anti-IFNAR treatment was able to prevent synapse loss and behavioral phenotypes in 564Igi mice. In phase lib clinical trials for anti-IFNAR (anifrolumab), CNS lupus symptoms were not reported and patients with active CNS lupus were excluded from the study (Furie et al. Arthritis
Rheumatol. 69, 376-386, 2017). While CNS lupus remains a heterogeneous disease with many symptoms and probably many causes, these findings indicate that select CNS lupus patients may benefit from anti-IFNAR treatment. Therefore, these findings indicate a novel mechanism for CNS lupus and provide a rationale for expanding future clinical trials to include CNS lupus patients, particularly those with detectable interferon signatures.
The results described herein above, were obtained using the following methods and materials.
Microglia activation state analysis
Activation state analysis was performed based on previously established methods
(Schafer et al., Neuron 74, 691-705, 2012). Two 40um sagittal sections containing regions of interest of the brain were immunostained for Ibal (1 :400, Wako) and CD68 (1 :300, Serotec). For each section, four 20χ fields of view were collected per mouse. Activation state analysis was performed on maximum intensity projections of the 40um section. Microglia were scored from 0 (lowest activation) to 5 (highest activation) depending on the branching of microglia (Ibal staining) and lysosomal content (CD68). For the branching analysis, microglia scored as 0 if Ibal staining revealed >15 thin processes with multiple branches, 1 (5-15 thick processes with branches), 2 (1-5 thick processes with few branches), 3 (no clear processes). For lysosomal content, CD68 staining was analyzed and scored as 0 (no/scarce expression), 1 (punctate expression), 2 (aggregated expression or punctate expression all over the cell). These two scores were summed to give a final score of microglial activation state (0-5). Microglia with an activation state of 3 or higher were then categorized as reactive and the percentage of reactive microglia was compared between lupus and control mice. All analyses were performed blind to genotype and treatment group.
RNAseq analysis
Microglia were first sorted from brain region homogenates using the FACSAria. For each mouse, 1000 microglia were sorted from the suspension into 20μ1 guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA was isolated using
RNAClean XP beads (Agencourt A63987). Template switching, cDNA synthesis, and cDNA amplification were adapted from previous studies (Islam et al., Nat. Methods 11, 163-166, 2014). Libraries were prepared using the Nextera kit (Illumina). Libraries were sequenced on an Illumina HiSeq 2000. For RNA-seq analysis, 40-bp single-end reads were aligned to the mouse reference genome (mm 10) using Star Aligner. Gene read count was performed using HTseq-count with Refseq mm 10 annotation. Differential gene expression analysis was performed using EdgeR and gene ontology analysis was performed using GOseq (Young et al., Genome Biol. 11, R14, 2010). Treemap was created using Revigo (http://revigo.irb.hr/).
Mice
Mice 564Igi Ig heavy and light chain knock-in (564Igi) mice have been described (Berland et al., Immunity 25, 429-440, 2006; Chatterjee et al., Eur. J. Immunol. 43, 2441- 2450, 2013). All 564Igi mice were genotyped for the presence of the transgenic heavy and light chains by specific PCR analysis of tail DNA. Peripheral blood B cells (PBMCs) were analyzed by FACS for the presence of both the 564Igi heavy and light chains, which were identified with a specific anti-idiotype antibody (Chatterjee et al., Eur. J. Immunol. 43, 2441- 2450, 2013). Mice used for the experiments were selected to be heterozygous for the transgenic (IgMa) and endogenous (IgMb ) IgH alleles. For each of the experiments performed, mice of both sexes were analyzed at 12 weeks of age unless otherwise indicated. Additionally, 564Igi mice with similar idiotype-positive B cell frequencies in blood were used within an experiment. C57BL/6, NZB/NZW ( 7 hybrids of the NZB and NZW strains), Mxl-Cre, Ifnarl'1' , and tau-GFP mice (Tucker et al., Nat. Neurosci. 4, 29-37, 2001) were purchased from Jackson Laboratories. Tissue from MRL- lpr and MRL-mpj strains was generously provided by G. C. Tsokos (Boston, MA). Experiments were approved by the Boston Children's Hospital and Harvard Medical School institutional animal use and care committee in accordance with NIH guidelines for the humane treatment of animals.
Antibody treatment of 564Igi mice
To block type I interferon signaling in 564Igi strain, mice were injected with 25C^g of anti-IFNAR, intraperitoneally every 4 days for 1 month (Das et al., Immunity 46, 106-119, 2017). Treatment for NZB/NZW mice was from 4 to 8 weeks. 564Igi mice were treated from 8 to 12 weeks. After one month, mice were euthanized and cells were isolated for analysis of frequency of idiotype-positive B cells or microglia analysis.
Generation of bone marrow chimeric mice
Recipient mice were lethally irradiated with a dose of 10 Gy by a 137Cs irradiator. Subsequently, 1 x 107 donor-derived bone marrow cells were intravenously injected into the recipients the following day. Recipient mice were fed with sulfamethoxazole/trimethoprim- containing water for two weeks following reconstitution and analyzed 6-8 weeks after reconstitution. Microglia isolation
To prepare single cell suspensions, brain regions were microdissected and the tissue was digested in 330 U papain in DPBS at 35°C for 30 minutes. Papain was neutralized in an ovomucoid solution and cells were dissociated by gentle trituration and filtered through a 70- μπι nylon mesh to remove clumps. Microglia were then purified by magnetic purification using anti-CD45 microbeads (Miltenyi).
Flow cytometry
Cells were treated with antibody clone 2.4G2 to block Fc receptors prior to staining and staining was performed in Phosphate buffered saline (PBS) solution containing 5% FCS and 2mM EDTA. For intracellular staining, microglia were fixed and permeabilized (fixation and permeabilization buffers from Biolegend) before antibody staining. Anti-564Igi (antiidiotype; IgGl) monoclonal antibody (clone 9D11) and anti-SV2 (DSHB/UIowa) was prepared and conjugated to fluorochromes in-house. Monoclonal antibodies against B220, CD45, CD1 lb, and CX3CR1 were purchased from BioLegend. Stained cells were acquired using a FACS Calibur or a FACS Canto (BD Biosciences) and data were analyzed using FlowJo (Tree Star, Inc.) software. qPCR
Brain or spleen tissue was homogenized in Trizol using the Qiagen TissueLyser system and RNA was isolated by phenol-chloroform extraction. cDNA was synthesized from 500ng of RNA and prepared using the Invitrogen Superscript First-Strand kit. qPCR reactions were assembled for the genes of interest (Mxl, Ifiia, Ifiib) using 4μ1 of cDNA per reaction and samples were run on the Bio-Rad qPCR machine. Expression levels were compared using the AACt method normalized to Gapdh.
Immunohistochemistry
Brains were collected from mice after transcardial perfusion with PBS followed by 4% paraformaldehyde (PFA). Tissue was then immersed in 4% PFA for 2 hr following perfusion, cryoprotected in 30% sucrose, and embedded in a 2: 1 mixture of OCT:20% sucrose in PBS and frozen. Tissue was cryosectioned (12-14 μιη), sections were dried, washed three times in PBS, and blocked with 2% BSA and 0.2% Triton X-100 in PBS for 1 hr. Primary antibodies were diluted in antibody buffer (containing 0.2% Triton X-100 and 5% BSA) as follows: anti-Ibal (1 :400, Wako), anti-CD68 (1 :300, Serotec), anti-homerl
(1 :200, Synaptic Systems), anti-synaptophysin (1 :500, Synaptic Systems), anti-NeuN (1 :200, Millipore), anti-neurofilament (1 :200, Biolegend) and incubated overnight at 4°C. Secondary Alexa-conjugated antibodies (Invitrogen) were added at 1 :200 in antibody buffer for 2 hr at room temperature. Slides were mounted in Vectashield (containing DAPI) and imaged using the Olympus Fluoview FV1000 confocal system.
Blood brain-barrier leakage assay
Blood-brain-barrier leakage was assayed using established protocols (Armulik et al., Nature 468, 557-561, 2010; Ben-Zvi et al., Nature 507-511, 2014). Mice were injected intravenously with 10 kDa FITC-dextran (2 mg per 20 g mouse). After 4 hr of circulation, mice were euthanized and brains were fixed in 4% PFA. Sagittal brain sections (40 μπι) were stained with anti-CD31 (1 :200, Biolegend) to mark blood vessels and imaged by confocal microscopy. Three fields of view from two brain sections per animal were quantified using Image J. Leakage was measured as a decrease in colocalization of FITC-dextran with CD31.
Immunohistochemistry on tissue from patients with SLE
Immunohistochemistry was done on human formalin-fixed, paraffin-embedded
(FFPE) autopsy-derived brain tissue from the hippocampus using a DAKO autostainer. The antibody M143, which is suitable for FFPE tissue was kindly provided by G. Kochs
(Freiburg, Germany). Immunoreaction was visualized using DAB as a chromogen. Pictures from three representative regions per slide were acquired using an Olympus DP50 camera connected to the microscope. These experiments were conducted in the laboratory of Dr. C. Mawrin at the University of Magdeburg and were approved by the Chairman of the Ethics Committee of the Medical Faculty at the Otto-von-Guericke-University and University Hospital Magdeburg. RNAscope in situ hybridization
In situ hybridization was done on human FFPE autopsy-derived brain tissue from the hippocampus using the RNAscope 2.5 HD Duplex Chromogenic Assay kit (Advanced Cell Diagnostics, Inc.). In situ hybridization protocol was performed as recommended in the RNAscope 2.5 HD Duplex Chromogenic Assay user manual following specifications for brain tissue. Probes against human MX1 (403831), AIFI (433121-C2) and EN02 (421401) were commercially available from Advanced Cell Diagnostics, Inc.
Microglial engulfrnent confocal analysis
Microglial engulfrnent analysis was performed similar to previously described methods (Schafer et al., Neuron 74, 691-705 (2012); Schafer et al., J. Vis. Exp. 88, e51482, 2014). 564Igi Tau-gfp mice were sacrificed at 12 wks, perfused with cold PBS, and brains were fixed in 4% paraformaldehyde (PFA) for 4 hr (4°C). After cryoprotection in 30% sucrose, tissue was sectioned coronally in 40μπι thick slices on a cryostat, and collected in PBS. The sections were blocked and permeabilized in 5% BSA with 0.2% Triton X-100 for 30 min-1 hr at room temperature, then incubated overnight at room temperature with a primary antibody against Iba-1 (Wako, 019-19741, 1 :500) in block solution. The next day, the sections were incubated 1.5-2 hr at room temperature with an Alexa-488 conjugated secondary antibody and mounted on slides in Vectashield with DAPI (Vector Laboratories). For each animal, two sections of the frontal cortex were chosen for microglia engulfment analysis. Images were acquired on an Ultraview Vox spinning disc confocal microscope equipped with diode lasers (405 nm, 445 nm, 488 nm, 514 nm, 561 nm, and 640 nm) and Volocity image acquisition software (Perkin Elmer) at 60x using 0.2 μιη z steps. For each hemisphere, 10 fields were imaged. Subsequent images were processed and quantified using ImageJ (NIH) and Imaris software (Bitplane). For acquired z stacks, ImageJ (NIH) was used to subtract background from all fluorescent channels (rolling ball radius = 10) and a mean filter of 1.5 was used for the Iba-1 channel. Subsequently, Imaris software (Bitplane) was used to create 3D volume surface renderings of each z stack. Surface rendered images were used to determine the volume of the microglia and of all tau-GFP. To visualize and measure the volume of engulfed inputs, any fluorescence that was not within the microglia volume was subtracted from the image using the mask function. The remaining engulfed/internal fluorescence was surface rendered using parameters previously determined for all tau-GFP and total volume of engulfed/internal tau-GFP was calculated. To determine percentage of engulfment, the following calculation was used: volume of internalized tau-GFP (μπι3)/ volume microglial cell (μπι3). All analyses were performed blind to animal genotype.
Tissue preparation for TEM
Mice were perfused with a 2% paraformaldehyde/ 2.5% glutaraldehyde solution in 0.1M phosphate buffer and drop fixed overnight in the same solution. Sagittal sections (150 μπι) including frontal cortex were cut by vibratome. Sections were either processed for immunoEM or prepared for synapse quantification. For immunoEM were performed similar to previously described methods (Tremblay et al., PLoSBiol. 8, el000527, 2010; Bisht et al., Glia 64, 826-839, 2016). In brief, sections were treated with 0.1% sodium borohydride for 30 minutes followed by 1 hr incubation in blocking solution (3% BSA and 0.01% Triton X- 100). Samples were then incubated overnight with anti-Ibal (1 :400 in blocking solution, Wako) and then with secondary antibody and developed with the ABC DAB kit. After immunostaining, sections were washed in 0.1 M cacodylate buffer and post-fixed with 1% osmium tetroxide (Os04)/1.5% potassium ferrocyanide (KFeCN6) for 1 hr, washed in water three times and incubated in 1% aqueous uranyl acetate for 1 hr followed by two washes in water and subsequent dehydration in grades of alcohol (10 min each; 50%, 70%, 90%, 2x 10 min 100%)). The samples were then placed in propyleneoxide for 1 hr subsequently infiltrated overnight in a 1 : 1 mixture of propyleneoxide and TAAB Epon (Marivac Canada Inc.). The following day the samples were embedded in TAAB Epon and polymerized at 60°C for 48 hr. Ultrathin sections (about 60 nm) were cut on a Reichert Ultracut-S microtome, placed onto copper grids, stained with uranyl acetate and lead citrate and examined on a JEOL 1200EX microscope. Images were recorded with an AMT 2k CCD camera. Fifteen distinct regions of the frontal cortex were imaged per animal.. Images were used to analyze the number of synapses blind to the genotype. A synapse was defined as an electron-dense post-synaptic density area juxtaposed to a presynaptic terminal filled with synaptic vesicles. Microglia were identified on the basis of their characteristic nuclear morphology, a single-profile endoplasmic reticulum and an electron-dark shading of the cytoplasm (Bisht et al., Glia 64, 826-839, 2016; Mori and Leblond J. Comp. Neurol. 135, 57- 79, 1969).
Behavioural phenotyping
All behavioural analysis was performed in the Harvard NeuroDiscovery Center's NeuroBehaviour Laboratory Core facility.
Open field.
The mouse open field chambers (Med Associates) are made of Plexiglas and consist of a square base (27 cm χ 27 cm) with walls that are 20 cm high. All walls are clear but opaque barriers are added between arenas so that subjects do not see one another during testing. For each testing session, the mouse is allowed free exploration in the environment for 1 hr. A computer-assisted infrared tracking system and software (Activity Monitor, Med Associates) are used to record the number of beam breaks and time and entries into center and peripheral zones. The total distance travelled (cm) is used as a measurement of general locomotor activity.
Elevated plus maze.
The elevated plus maze consists of two open and two closed arms that extend out from a central platform. Each arm of the maze is 30 cm long and 5 cm wide. The maze surface is 85 cm above the floor and test is carried out in dim ambient lighting. Mice are placed in the center platform of the maze, facing an open arm, and allowed to explore the apparatus for 5 min. A computer-assisted video-tracking system (TopScan software, CleverSys Inc.) is used to record the number of open and closed arm entries (all four paws in an arm) as well as the total time spent in open, closed and center compartments. A decrease in the per cent time spent in the open arms or a decrease in the per cent entries into the open arms is used as a surrogate measure of anxiolytic-like behavior. The number of closed arm entries is used as a measure of general locomotor activity.
Three-chamber social interaction.
The three-chamber sociability test included two consecutive 10-min sessions and was performed in a rectangular arena of clear Plexiglas with dimensions 63 cm length x 40 cm width x 22 cm height. The test arena contained three equally sized chambers (40 cm length χ 20 cm width χ 22 cm height), and the outer left and right chambers each contained an inverted wire cup. During the habituation session, test mice were initially placed into the center chamber and allowed to freely explore the three-chambered arena. For the social interaction session, test mice were returned to the center chamber, an unfamiliar target mouse was placed under one of the two wire cups, an object under the second cup and test mice were again allowed to move freely among the three chambers. The position of the first target mouse was alternated and equally distributed between the left and right cups for both mutant and control groups. The position was not changed between the social interaction and social recognition sessions. The test operator was blinded to test mouse genotype and remained outside of the test room during all sessions. Test subject performance was recorded automatically using TopScan software (CleverSys, Inc.), and the following behaviors were scored: amount of time spent in close proximity (3 cm radius) of the wire cups, amount of time spent in each chamber of the three-chamber arena and latency to approach each wire cup. Water T maze.
This behavioral paradigm, encompassing similar principles to the Morris water maze, is used to assess spatial learning and memory in which a mouse uses spatial cues to navigate to find an escape platform submerged just below the water's surface. In addition, the test measures cognitive flexibility through a reversal trial requiring the mice to learn a new platform location. The testing apparatus is a plus maze (each arm 14.1 long and 4.6 cm wide) made of clear Plexiglas with each arm designated as north (N), south (S), east (E) or west (W). For the mice to choose only the E or W arm for escape, dividers are placed to block off the either the N or S arm. Mice are placed in the N or S arms, in a semi-random order, at the start of each trial. The maze is filled with 25-26 °C water and made opaque by adding nontoxic white paint so the mouse cannot see the submerged escape platform. Initially for the acquisition trial, the hidden escape platform is placed in the E arm. Mice are carried to the starting point and the experimenter scores a correct or incorrect response for each trial based on whether the arm with the escape platform is chosen. Regardless of the response, mice are allowed to remain on the platform for 10 s at the end. Mice are given 10 trials per day and the percentage correct responses is calculated by averaging correct responses across the 10 trials for each day. Acquisition criterion is achieved when a mouse scores 80% or more correct responses over two consecutive days. After all mice reach acquisition criterion, the reversal trial begins: the platform is moved to the opposite side (W) and the same procedure is repeated until all mice learn the platform's new location.
Prepulse inhibition (PPI).
PPI is monitored in Med Associates chambers (Med Associates). Mice were acclimated to the PPI apparatus for 5 min in the presence of a ~ 63 dB white-noise background. After this acclimation period the test session is automatically started. The session begins with a habituation block of 6 presentations of the startle stimulus alone, followed by 10 PPI blocks of 6 different types of trials. Trial types are: null (no stimuli), startle (120 dB), startle plus prepulse (variable dB over background noise that is, 65, 75 or 85 dB) and prepulse alone. Each trial begins with a 50 ms null period during which baseline movements are recorded. There is a subsequent 20 ms period during which prepulse stimuli are presented and responses to the prepulse measured. After further 100 ms the startle stimuli are presented for 40 ms and responses recorded for 100 ms from startle onset. Responses are sampled every ms. The inter-trial interval is variable with an average of 15 sec (range from 10 to 20 sec). Percentage PPI = (1 - (prepulse trials/startle-only trials)) χ 100.
Novelty Y maze.
Testing was conducted in a clear acrylic Y maze that has three arms (one start arm and two test arms, all— 31 cm in length). The testing room has distinct visual cues and the maze has a removable partition to block the appropriate arm. The blocked arm is randomized and balanced for each test group. The test consists of a forced choice trial followed by a free- choice trial. For the forced choice trial the start arm and one test arm is open with access to the second test arm blocked by the partition. Individual subjects are placed in the start arm and allowed to explore the open test arm for 3 min, after which they are removed from the maze, and placed in a holding cage as the maze is cleaned. The partition is removed and the mice are then immediately placed back into the Y maze for the free choice trial and allowed to explore both the open and test arms for 3 min. The delay between the forced choice and free choice trials is approximately 2 min. Animal behavior is video recorded during both trials and the time spent in the previously accessible arm (that is, familiar arm; tf) and the previously blocked arm (that is, novel arm; tn) is determined during the free choice trial using Cleversys software. For each subject the percentage time exploring the novel arm during the free choice trial is calculated using the formula: percentage of tn = tn I (tn + tf) χ 100.
Rotarod test.
The purpose of the rotarod test is to assess the sensorimotor coordination and/or fatigue resistance of the mouse. The test is sensitive to damage of the basal ganglia and cerebellum, and to drugs that affect motor functions. The rotarod apparatus consists of a gritted or textured plastic roller (Ugo Basile) flanked by large round plates on each end to prevent the animal from escaping. The plastic rod sits at a height of approximately 20 cm above individual electronic sensing platforms. The sensing platforms are not cushioned, but mice do not appear to experience any discomfort from falling from that height. Prior to actual testing, mice are habituated to the rotarod apparatus by placing them onto the rod as it revolves at a very low rotation speed (4 r.p.m. for 5 min) (the number of times a mouse falls is recorded and the mouse is placed back on the rotarod if it falls). Following the habituation session, mice are tested in the accelerated rotarod (4-40 r.p.m. in 3 min). The latency until the mouse falls from the rod onto the sensing platform below is recorded automatically. This test is repeated after a 15-min break.
Tail-suspension test.
This procedure is an alternative to the forced swim test and is used to induce a despair-like state and test the effects of antidepressants in mice. Antidepressants will reduce the amount of time the mouse spends immobile in this test. At the beginning of a trial, mice are suspended by the tail (taped onto a suspension hook so that the animal hangs with its tail in a straight line) above a flat surface covered with soft padding material. During testing (10- min trial), the duration of immobility is scored automatically (Med Associates) or by an experimenter. Forced swim test.
This procedure is used to induce a despair-like state and to test the effects of antidepressants in mice. Antidepressants will reduce the amount time the mouse spends immobile in this test. Mice are placed for 6 min in a glass cylinder (height, 35 cm; diameter, 17 cm) filled with water (25 ± 2° C) to a depth of 25 cm. The water depth is adjusted so that the animals must swim or float without their hind limbs or tail touching the bottom. During testing the duration of immobility (the time during which the subject makes only the small movements necessary to keep their heads above water) is scored. The experimenter monitors each mouse continuously during the entire session. The mouse is immediately taken out of the cylinder and excluded from the study if it fails to swim or keep its head above water. After completion of the trial, the subject is dried using a paper towel and placed back in its home cage. After every trial, the water is changed and the cylinder rinsed with clean water. Social dominance tube test.
Mice from different litters that are sex-matched and weight-matched are placed inside opposite ends of a white PVC pipe that is 30.5 cm in length, 2.5 cm internal diameter. Mice are released simultaneously at both ends of tube. Start sides are alternated between trials.
Five consecutive trials are performed for each pair with a maximum time of 2 min per trial. The trial ends when one mouse backs out of the tube so that all four limbs are outside of tube.
Matches lasting more than two minutes were excluded from analysis and scored as a draw.
The latency of each trial is recorded as the percentage of trials won by each mouse. Mice are considered socially dominant if they win more than 50% of the trials. The pipe is cleaned with 70% ethanol between each trial.
Novelty suppressed feeding.
The novelty suppressed feeding (NSF) paradigm is a conflict test that elicits competing motivations between the drive to eat and the fear of venturing into the center of a brightly lit arena. NSF measures the latency of a mouse in approaching and eating a familiar food in a novel environment following an extended period (up to 24 hr) of food deprivation. Increased latency to begin eating is used as an index of anxiety-like behavior. This test can also be used as a pharmacological model of anxiolytic and antidepressant activity because acute anxiolytics and chronic antidepressant drugs decrease latency to feed in the novel environment. Approximately 18-24 h before testing, mice are placed in a clean cage without food (singly housed). Cages with no food must be requested from the facility. The apparatus is either a NOR chamber covered with white laminated paper or a mouse shipping crate. The floor is covered with 2 cm of bedding. A small pre-weighed food chow pellet (normal chow) is placed in the centre of the arena on a piece of white circular filter paper. The lights in the room are increased to the brightest level. The day of testing, mice are transferred to a holding room for a ~ 1-hr habituation period. At the start of the experiment, each mouse is placed in a random corner of the testing arena and the time to the first feeding event is recorded during 10 min. The time for the mouse to grab the pellet and start eating is recorded. The mouse is removed immediately and then placed alone in its home cage for 5 min with the pre-weighed piece of chow. At the end of the 5-min period, the amount of food consumed is also measured.
Statistical Analysis
For all statistical analyses, R and GraphPad Prism 6 and 7 software (La Jolla, CA) were used. All replicate numbers (number of mice analyzed, unless otherwise indicated), P values, and statistical tests are indicated in the figure legends. Mice of both sexes were included in all analyses. Sample sizes were selected to achieve at least 80% power at an alpha level of 0.05. When possible, all analysis was done blind to genotype and/or treatment group. Error bars represent s.e.m. in all figures. Statistical tests were selected on the basis of F statistics to analyze differences in variances and normality tests where appropriate
Other Embodiments
From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.
The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.

Claims

What is claimed is:
1. A method of treating a subject having a disease or disorder characterized by reactive microglia mediated synapse loss, the method comprising administering to the subject an agent that inhibits binding to an interferon alpha/beta receptor, wherein the disease or disorder is not CNS lupus.
2. The method of claim 1, wherein the agent is an anti-interferon alpha/beta receptor antibody or an anti-interferon alpha antibody.
3. The method of claim 1, wherein the subject has increased levels of peripheral interferon.
4. The method of claim 1, wherein the subject has an autoimmune disease, a
neurodegenerative disease, or a chronic viral infection.
5. The method of claim 1, wherein the subject has Sjogren's syndrome, Alzheimer's disease, or Human Immunodeficiency Virus Infection.
6. A method of treating a subject having CNS lupus, the method comprising
administering to the subject an anti-interferon alpha/beta receptor antibody or anti-interferon alpha antibody, wherein the subject is selected as having reactive microglia mediated synapse loss.
7. A method of selecting therapy for a subject having CNS lupus, the method comprising detecting increased type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein detection of said increase selects the subject for anti-interferon alpha eta receptor (IFNAR) antibody therapy.
8. A method of identifying a subject as having CNS lupus, the method comprising detecting reactive microglia mediated synapse loss or increased type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein said detection identifies the subject as having CNS lupus.
9. The method of claim 8, wherein the subject presents with neuropsychiatric or neurological symptoms.
10. The method of claim 9, wherein the neuropsychiatric symptoms are selected from the group consisting an anxiety phenotype, depression, cognitive impairment, and social interaction defects.
11. A method of monitoring CNS lupus therapy in a subject, the method comprising detecting type I interferon in a cerebrospinal fluid of the subject relative to a reference level, wherein the reference level is the level of interferon alpha present in the cerebrospinal fluid of the subject prior to treatment with an anti- IFNAR antibody treatment.
12. A method of reducing the level of activated microglia present in a subject in need thereof, the method comprising administering an anti-interferon alpha/beta receptor antibody to the subject.
13. The method of any one of claims 1-12, wherein the anti-IFNAR antibody is a human, humanized or chimeric antibody.
14. The method of any one of claims 1-13, wherein the anti-IFNAR antibody comprises a VH domain comprising the amino acid sequence of SEQ ID NO: 1 or a VK domain comprising the amino acid sequence of SEQ ID NO: 2.
15. A kit comprising an anti-IFNAR antibody and instructions for the treatment of CNS lupus.
16. The kit of claim 15, further comprising a capture molecule that specifically binds interferon.
17. A method of depleting activated microglia in a subject in need thereof, the method comprising administering to the subject an effective amount of an anti-IFNAR antibody to the subject.
18. The method of claim 1, wherein the subject has a disease or disorder characterized by neurological or neuropsychiatric symptoms.
19. The method of any one of claims 1-14, wherein the disease state of the subject is characterized using brain imaging studies, functional or conventional magnetic resonance imaging, Pre-pulse Inhibition, measuring gray matter volume, or using a Positron Emission Topography studies.
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